FreeSurfer: recon-all-clinical#
This notebook was prepared for an audience of clinicians at the 2025 PACTALS conference (Pan-Asian consortium of Treatment and Research in ALS) in Melbourne.
Author: Thomas Shaw Date: 1 Sept 2025
thomshaw92
0000-0003-2490-0532License:
Note: If this notebook uses neuroimaging tools from Neurocontainers, those tools retain their original licenses. Please see Neurodesk citation guidelines for details.
Citations and Resources:#
Tools included in this workflow#
recon-all-clinical:
Karthik Gopinath, Douglas N. Greve, Colin Magdamo, Steve Arnold, Sudeshna Das, Oula Puonti, Juan Eugenio Iglesias, “Recon-all-clinical”: Cortical surface reconstruction and analysis of heterogeneous clinical brain MRI, Medical Image Analysis, Volume 103, 2025, 103608, ISSN 1361-8415, https://doi.org/10.1016/j.media.2025.103608.
Dataset:#
T1 weighted MP2RAGE at 7T (healthy control)
Shaw TB, York A, Barth M, Bollmann S. Towards Optimising MRI Characterisation of Tissue (TOMCAT) Dataset including all Longitudinal Automatic Segmentation of Hippocampal Subfields (LASHiS) data. Data Brief. 2020 Jul 20;32:106043. doi: https://doi.org/10.1016/j.dib.2020.106043 PMID: 32793772; PMCID: PMC7415822.
General Instructions:#
📘 How to Use This Notebook
This notebook is an interactive document. It mixes short explanations (like this box) with computer code that runs automatically.
- 👆 Click on a cell (the boxes with text or code)
- ▶️ Run it by pressing
Command + Enter(Mac) orControl + Enter(Windows/Linux) - ⏭️ Or use the play button in the toolbar above
- ⬇️ Move to the next cell and repeat
🧩 What happens when you run a cell?
The computer will either:
- ✏️ Show you some text or figures
- 🖥️ Run an analysis step in the background
- 📂 Save results into a folder
💡 Tip: Always read the explanation above each code cell first – it tells you in plain words what the computer will do.
There are a few dataformats that are used in this tutorial:
Files that end in ‘.mgz’ and ‘nii.gz’ are volumetric images (either showing the brain or a specific region of the brain).
Files that end in ‘.stat’ are statistics files.
Files that end in .txt are just text-files.
Files that end in ‘.csv’ are datasheets.
Files that end in ‘.pial, .surf etc’ are surface files.
Load the module for this workbook#
📦 What is a "Module"?
A module is just a way of telling the computer: “Please make this special software ready to use.”
- 🎛️ We only load the ones we need, when we need them
- 🔑 Loading a module is like unlocking the tool so we can use it
🚀 In this notebook
We will load FreeSurfer 8 – the software that analyses our scans. Once loaded, the commands will be available for us to run.
module load freesurfer/8.0.0
➡️ Just like before: click the cell, then press Command + Enter (Mac) or Control + Enter (Windows/Linux) to load it.
# we can use module to load freesurfer in a specific version
import module
await module.load('freesurfer/8.0.0')
await module.list()
['freesurfer/8.0.0']
%%capture
!pip install nibabel numpy
Let’s try running the command with the –help flag!#
!recon-all-clinical.sh --help
Recon-all-like stream for clinical scans of arbigrary orientation/resolution/contrast
Use this script to process clinical scans of arbitrary orientation, resolution, and
contrast. It essentially runs a combination of:
* SynthSeg: to obtain a volumetric segmentation and linear registration to Talairach space
* SynthSR: to have a higher resolution 1mm MPRAGE for visualization
* SynthDist: to fit surfaces by predicting the distance maps and reconstructing topologically accurate cortical surfaces
Using this module is very simple: you just provide an input scan, the subject name, the
number of threads you want to use, and (optionally) the subjects directory:
recon-all-clinical.sh INPUT_SCAN SUBJECT_ID THREADS [SUBJECT_DIR]
(the argument [SUBJECT_DIR] is only necessary if the
environment variable SUBJECTS_DIR has not been set
or if you want to override it)
This stream runs a bit faster than the original recon-all, since the volumetric
segmentation is much faster than the iterative Bayesian method in the standard stream
If you use this stream for your analysis, please cite:
K Gopinath, DN Greeve, S Das, S Arnold, C Magdamo, JE Iglesias:
Cortical analysis of heterogeneous clinical brain MRI scans for large-scale neuroimaging studies
https://arxiv.org/abs/2305.01827
B Billot, DN Greve, O Puonti, A Thielscher, K Van Leemput, B Fischl, AV Dalca, JE Iglesias:
SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining
Medical Image Analysis, 83, 102789 (2023)
B Billot, C Magdamo, SE Arnold, S Das, JE Iglesias:
Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets
PNAS, 120(9), e2216399120 (2023)
SynthSR: a public AI tool to turn heterogeneous clinical brain scans into high-resolution T1-weighted images for 3D morphometry
JE Iglesias, B Billot, Y Balbastre, C Magdamo, S Arnold, S Das, B Edlow, D Alexander, P Golland, B Fischl
Science Advances, 9(5), eadd3607 (2023)
📥 Downloading the Data
We will now download a sample brain scan (called mp2rage.nii.gz)
from the Open Science Framework.
- 🌐 This file comes from an open research resource
- 🧠 It is a standard type of MRI scan used for brain structure
- 📂 We will use it today as our example dataset
➡️ Click the cell below, then press Command + Enter (Mac) or Control + Enter (Windows/Linux)
to start the download.
! echo "Downloading File"; mkdir -p ./data/structural && osf -p bt4ez fetch osfstorage/TOMCAT_DIB/sub-01/ses-01_7T/anat/sub-01_ses-01_7T_T1w_defaced.nii.gz ./data/structural/mp2rage.nii.gz
Downloading File
usage: osf fetch [-h] [-f] [-U] remote [local]
osf fetch: error: Local file ./data/structural/mp2rage.nii.gz already exists, not overwriting.
!ls ./data/structural/mp*
./data/structural/mp2rage.nii.gz
🖼️ Viewing mp2rage.nii.gz
We will now open the mp2rage.nii.gz file. This is the patient’s T1-weighted MRI scan that FreeSurfer will change into its own format.
- 🎛️ We display it in grayscale so brain tissue boundaries are clear
- 📐 Brightness/contrast is automatically adjusted (ignores empty space and extreme values)
- ➕ Crosshairs help you line up the same point across axial, coronal, and sagittal slices
- 🧭 The viewer lets you scroll through slices and explore the brain interactively
➡️ Click the cell below, then press Command + Enter (Mac) or Control + Enter.
This will open mp2rage.nii.gz in the interactive viewer.
# Display original file in grayscale
from ipyniivue import NiiVue
from IPython.display import display, Image
import nibabel as nib, numpy as np
T1_PATH = "./data/structural/mp2rage.nii.gz"
# Robust intensity window (ignore zeros and outliers)
t1 = nib.load(T1_PATH).get_fdata()
vals = t1[t1 > 0]
vmin, vmax = np.percentile(vals, [0.5, 99.5]) if vals.size else (None, None)
nv = NiiVue(
height=600,
multiplanar_layout="GRID",
multiplanar_show_render=True,
is_ruler=False,
is_colorbar=True,
is_orient_cube=True,
is_radiological_convention=True,
back_color=(0.1,0.1,0.1,1.0),
)
nv.add_volume({
"path": T1_PATH,
"name": "native",
"opacity": 1.0,
"colormap": "gray",
"cal_min": float(vmin) if vmin is not None else None,
"cal_max": float(vmax) if vmax is not None else None,
})
nv.set_crosshair_color([0,0,0,1])
display(nv)
[HF-patcher] mp2rage: path → url
Run#
🧠 Automated Brain Scan Processing using recon-all clinical
This step prepares our MRI data so it can be processed automatically. Think of it like setting up the folders and tools before we start the real analysis.
- ✔️ Creates a folder where results will be saved
- ✔️ Checks everything is ready before running
- ✔️ Run the command "recon-all-clinical.sh"
In plain words: we are telling the computer:
"Here’s the scan. Put the results in this folder. Run the pipeline."
⚠️ Don’t worry about the code details – they’re just making sure the computer behaves!
➡️ When you are ready, hit Command + Enter (Mac) or Control + Enter (Windows/Linux),
or press the ▶️ play button after clicking on the cell below.
%%bash
#--------------------------------------------
# FreeSurfer recon-all-clinical pipeline
#--------------------------------------------
set -euo pipefail # Stop on unset variables or errors
#----------------------------
# Config
#----------------------------
INPUT_SCAN=./data/structural/mp2rage.nii.gz
SUBJECT_ID=TestSubject
THREADS=2 #adapt if more resources are available
SUBJECT_DIR=./data/structural/recon-all-clinical
# Ensure output folder exists
mkdir -p "$SUBJECT_DIR"
echo "SUBJECT_DIR=$SUBJECT_DIR"
echo "SUBJECT_ID=$SUBJECT_ID"
echo "INPUT_SCAN=$INPUT_SCAN"
echo
#----------------------------
# Allow deeper folder structures in some FreeSurfer builds
#----------------------------
export FS_ALLOW_DEEP=1
export SINGULARITYENV_FS_ALLOW_DEEP=1
export APPTAINERENV_FS_ALLOW_DEEP=1
#----------------------------
# Start pipeline
#----------------------------
# Remove previous "is-running" file if it exists
rm -f "$SUBJECT_DIR/$SUBJECT_ID/scripts/IsRunning.lh+rh"
# Run the actual recon-all-clinical pipeline
recon-all-clinical.sh "$INPUT_SCAN" "$SUBJECT_ID" "$THREADS" "$SUBJECT_DIR"
#----------------------------
# End message
#----------------------------
echo "----- recon-all-clinical.sh completed -----"
echo "Results saved to: $SUBJECT_DIR/$SUBJECT_ID"
SUBJECT_DIR=./data/structural/recon-all-clinical
SUBJECT_ID=TestSubject
INPUT_SCAN=./data/structural/mp2rage.nii.gz
#--------------------------------------------
#@# recon-all-clinical Tue Mar 3 11:10:09 AM UTC 2026
mri_convert ./data/structural/mp2rage.nii.gz /home/jovyan/workspace/books/examples/structural_imagin
g/data/structural/recon-all-clinical/TestSubject/mri/native.mgz
INFO: using NIfTI-1 sform (sform_code=1)
reading from ./data/structural/mp2rage.nii.gz...
TR=4310.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras
= (0.999815, -0.0191912, -0.00103917)
j_ras = (0.019201, 0.999761, 0.0104718)
k_ras = (0.000837961,
-0.0104898, 0.999945)
writing to /home/jovyan/workspace/books/examples/structural_imaging/data/stru
ctural/recon-all-clinical/TestSubject/mri/native.mgz...
SynthSeg-robust 2.0
using CPU, hiding all CUDA_VISIBLE_DEVICES
using 2 threads
addctab True
predict
ing 1/1
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 265s 265s/step
segmentation saved in: /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/mri/synthseg.mgz
volumes saved in: /home/jovyan/workspace/b
ooks/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/stats/synthseg.vol.c
sv
QC scores saved in: /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical/TestSubject/stats/synthseg.qc.csv
#@# mri_synthseg vmpeak 53367216
If you u
se this tool in a publication, please cite:
SynthSeg: Segmentation of brain MRI scans of any contras
t and resolution without retraining
B. Billot, D.N. Greve, O. Puonti, A. Thielscher, K. Van Leemput,
B. Fischl, A.V. Dalca, J.E. Iglesias
Medical Image Analysis, 2023.
Robust machine learning segment
ation for large-scale analysis of heterogeneous clinical brain MRI datasets
B. Billot, C. Magdamo, Y
. Cheng, S.E. Arnold, S. Das, J.E. Iglesias
PNAS, 2023.
using CPU, hiding all CUDA_VISIBLE_DEVICES
Using general model from January 2023 (version 2)
/opt/fr
eesurfer-8.0.0/models/synthsr_v20_230130.h5
using 2 threads
predicting 1/1
Prediction without flippi
ng
1/1
[==============================] - 43s 43s/step
Prediction with flipping
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 43s 43s/step
prediction saved in: /home/jovyan/workspace/books/examples/structural_imaging/data/structural/reco
n-all-clinical/TestSubject/mri/synthSR.raw.mgz
If you use this tool in a publication, please cite:
Joint super-resolution and synthesis of 1 mm isotropic MP-RAGE volumes from clinical
MRI exams wi
th scans of different orientation, resolution and contrast
JE Iglesias, B Billot, Y Balbastre, A Tab
ari, J Conklin, RG Gonzalez, DC Alexander,
P Golland, BL Edlow, B Fischl, for the ADNI
NeuroImage, 1
18206 (2021)
SynthSR: a public AI tool to turn heterogeneous clinical brain scans into
high-reso
lution T1-weighted images for 3D morphometry
JE Iglesias, B Billot, Y Balbastre, C Magdamo, S Arnold
, S Das, B Edlow, D Alexander,
P Golland, B Fischl
Science Advances, 9(5), eadd3607 (2023)
If you
use the low-field (Hyperfine) version, please cite also:
Quantitative Brain Morphometry of Porta
ble Low-Field-Strength MRI Using
Super-Resolution Machine Learning
JE Iglesias, R Schleicher, S Lag
una, B Billot, P Schaefer, B McKaig, JN Goldstein,
KN Sheth, MS Rosen, WT Kimberly
Radiology, 22052
2 (2022)
2026-03-03 11:16:58.553140: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on
your machine, GPU will not be used.
2026-03-03 11:16:58.636296: I tensorflow/tsl/cuda/cudart_stub.cc:28] Could not find cuda drivers on
your machine, GPU will not be used.
2026-03-03 11:16:58.637003: I tensorflow/core/platform/cpu_feature_guard.cc:182] This TensorFlow bin
ary is optimized to use available CPU instructions in performance-critical operations.
To enable the
following instructions: AVX2 FMA, in other operations, rebuild TensorFlow with the appropriate comp
iler flags.
2026-03-03 11:17:01.346348: W tensorflow/compiler/tf2tensorrt/utils/py_utils.cc:38] TF-TRT Warning:
Could not find TensorRT
/opt/freesurfer-8.0.0/python
using CPU, hiding all CUDA_VISIBLE_DEVICES
Reading image
Reading SynthS
eg segmentation / parcellation
Resampling and padding image
Building U-net
Pushing image through U-n
et
1/1 [==============================] - ETA: 0s
1/1 [==============================] - 41s 41s/step
/opt/freesurfer-8.0.0/python/scripts/mri_synth_surf.py:13: DeprecationWarning: Please use `distance_
transform_edt` from the `scipy.ndimage` namespace, the `scipy.ndimage.morphology` namespace is depre
cated.
from scipy.ndimage.morphology import distance_transform_edt
Saving prediction to disk
Resam
pling SynthSeg to space of prediction
Computing Talairach transform
Making synthetic image and other
<<fake>> volumes, in FreeSurfer orientation!
All done!
mri_convert ./synthseg.mgz ./synthseg.resampled.mgz -rl ./synthSR.raw.mgz -rt nearest -odt float
reading from ./synthseg.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.999815, -0.0191
912, -0.00103917)
j_ras = (0.019201, 0.999761, 0.0104718)
k_ras = (0.000837961, -0.0104898, 0.999945
)
reading template info from volume ./synthSR.raw.mgz...
writing to ./synthseg.resampled.mgz...
/opt/freesurfer-8.0.0/python/scripts/norm_synthSR.py:8: DeprecationWarning: Please use `distance_tra
nsform_edt` from the `scipy.ndimage` namespace, the `scipy.ndimage.morphology` namespace is deprecat
ed.
from scipy.ndimage.morphology import distance_transform_edt
/opt/freesurfer-8.0.0/python
Readi
ng inputs
Normalizing and dilating
Writing to disk
Done!
mri_convert ./synthSR.norm.tmp.mgz ./synthSR.norm.mgz -rl ./norm.mgz -odt float
reading from ./synthSR.norm.tmp.mgz...
TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (0.999815,
-0.0191912, -0.00103917)
j_ras = (0.019201, 0.999761, 0.0104718)
k_ras = (0.000837961, -0.0104898,
0.999945)
reading template info from volume ./norm.mgz...
Reslicing using trilinear interpolation
w
riting to ./synthSR.norm.mgz...
8.0.0
--src: norm.mgz src image (geometry).
--trg: /opt/freesurfer-8.0.0/average/mni305.cor.mgz trg image
(geometry).
--inmni: transforms/talairach.xfm input MNI/XFM transform.
--outlta: transforms/talairac
h.xfm.lta output LTA.
--s: fsaverage subject name
--ltavox2vox: output LTA as VOX_TO_VOX transform.
LTA read, type : 1
1.10460 -0.00862 -0.00334 -0.03559;
-0.00180 1.03584 0.25272 -35.48325;
-0.01409 -0.29788 1.10985 47.01420;
0.00000 0.00000 0.00000 1.00000;
setting subject to fsaverage
Writing LTA to file transforms/talairach.xfm.lta...
lta_convert succes
sful.
will read norm from ./synthSR.norm.mgz
will read input aseg from ./aseg.auto_noCCseg.mgz
writing ase
g with cc labels to aseg.presurf.mgz
will write lta as ./transforms/cc_up.lta
reading aseg from /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical/TestSubject/mri/./aseg.auto_noCCseg.mgz
reading norm from /home/jovyan/workspace/books/exa
mples/structural_imaging/data/structural/recon-all-clinical/TestSubject/mri/./synthSR.norm.mgz
19595
8 voxels in left wm, 50361 in right wm, xrange [72, 97]
searching rotation angles z=[-5 9], y=[-8
6]
searching scale 1 Z rot -5.0
searching scale 1 Z rot -4.8
searching scale 1 Z rot -4.5
searching scale 1 Z rot -4.3
searching scale 1 Z rot -4.0
searching scale 1 Z rot -3.8
searching scale 1 Z rot -3.5
searching scale 1 Z rot -3.3
searching scale 1 Z rot -3.0
searching scale 1 Z rot -2.8
searching scale 1 Z rot -2.5
searching scale 1 Z rot -2.3
searching scale 1 Z rot -2.0
searching scale 1 Z rot -1.8
searching scale 1 Z rot -1.5
searching scale 1 Z rot -1.3
searching scale 1 Z rot -1.0
searching scale 1 Z rot -0.8
searching scale 1 Z rot -0.5
searching scale 1 Z rot -0.3
searching scale 1 Z rot -0.0
searching scale 1 Z rot 0.2
searching scale 1 Z rot 0.5
searching scale 1 Z rot 0.7
searching scale 1 Z rot 1.0
searching scale 1 Z rot 1.2
searching scale 1 Z rot 1.5
searching scale 1 Z rot 1.7
searching scale 1 Z rot 2.0
searching scale 1 Z rot 2.2
searching scale 1 Z rot 2.5
searching scale 1 Z rot 2.7
searching scale 1 Z rot 3.0
searching scale 1 Z rot 3.2
searching scale 1 Z rot 3.5
searching scale 1 Z rot 3.7
searching scale 1 Z rot 4.0
searching scale 1 Z rot 4.2
searching scale 1 Z rot 4.5
searching scale 1 Z rot 4.7
searching scale 1 Z rot 5.0
searching scale 1 Z rot 5.2
searching scale 1 Z rot 5.5
searching scale 1 Z rot 5.7
searching scale 1 Z rot 6.0
searching scale 1 Z rot 6.2
searching scale 1 Z rot 6.5
searching scale 1 Z rot 6.7
searching scale 1 Z rot 7.0
searching scale 1 Z rot 7.2
searching scale 1 Z rot 7.5
searching scale 1 Z rot 7.7
searching scale 1 Z rot 8.0
searching scale 1 Z rot 8.2
searching scale 1 Z rot 8.5
global minimum found at slice 76.0, rotations (-0.83, 1.72)
final transformation (x=76.0, yr=-0.827,
zr=1.720):
0.99945 -0.03002 -0.01442 55.66253;
0.03001 0.99955 -0.00043 51.79436;
0.014
43 -0.00000 0.99990 29.91334;
0.00000 0.00000 0.00000 1.00000;
updating x range to be [125, 130] in xformed coordinates
best xformed slice 127
min_x_fornix = 124
m
in_x_fornix = 127
min_x_fornix = 134
min_x_fornix = 154
min_x_fornix = 123
cc center is found at 127
74 97
eigenvectors:
0.00040 -0.00484 0.99999;
-0.08493 -0.99638 -0.00478;
0.99639 -0.08492
-0.00081;
error in mid anterior detected - correcting...
writing aseg with callosum to /home/jovyan/workspace/
books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/mri/aseg.presurf.mg
z...
corpus callosum segmentation took 1.0 minutes
#VMPC# mri_cc VmPeak 246492
mri_cc done
Iteration Number : 1
pass 1 (xy+): 37 found - 37 modified | TOTAL: 37
pass 2 (xy+): 0 found - 37 modified | TOTAL: 37
pass 1 (xy-): 34 found - 34 modified | TOTAL: 71
pass 2 (xy-): 0 found - 34 modified | TOTAL: 71
pass 1 (yz+): 54 found - 54 modified | TOTAL: 125
pass 2 (yz+): 0 found - 54 modified | TOTAL: 125
pass 1 (yz-): 52 found - 52 modified | TOTAL: 177
pass 2 (yz-): 0 found - 52 modified | TOTAL: 177
pass 1 (xz+): 36 found - 36 modified | TOTAL: 213
pass 2 (xz+): 0 found - 36 modified | TOTAL: 213
pass 1 (xz-): 41 found - 41 modified | TOTAL: 254
pass 2 (xz-): 0 found - 41 modified | TOTAL: 254
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 2 found - 2 modified | TOTAL: 2
pass 2 (+++): 0 found - 2 modified | TOTAL: 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 2
pass 1 (+++): 4 found - 4 modified | TOTAL: 6
pass 2 (+++): 0 found - 4 modified | TOTAL: 6
Iteration Number : 1
pass 1 (++): 23 found - 23 modified | TOTAL: 23
pass 2 (++): 0 found - 23 modified | TOTAL: 23
pass 1 (+-): 11 found - 11 modified | TOTAL: 34
pass 2 (+-): 0 found - 11 modified | TOTAL: 34
pass 1 (--): 15 found - 15 modified | TOTAL: 49
pass 2 (--): 0 found - 15 modified | TOTAL: 49
pass 1 (-+): 27 found - 27 modified | TOTAL: 76
pass 2 (-+): 0 found - 27 modified | TOTAL: 76
Iteration Number : 2
pass 1 (xy+): 2 found - 2 modified | TOTAL: 2
pass 2 (xy+): 0 found - 2 modified | TOTAL: 2
pass 1 (xy-): 1 found - 1 modified | TOTAL: 3
pass 2 (xy-): 0 found - 1 modified | TOTAL: 3
pass 1 (yz+): 0 found - 0 modified | TOTAL: 3
pass 1 (yz-): 0 found - 0 modified | TOTAL: 3
pass 1 (xz+): 0 found - 0 modified | TOTAL: 3
pass 1 (xz-): 0 found - 0 modified | TOTAL: 3
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 1 found - 1 modified | TOTAL: 1
pass 2 (++): 0 found - 1 modified | TOTAL: 1
pass 1 (+-): 0 found - 0 modified | TOTAL: 1
pass 1 (--): 0 found - 0 modified | TOTAL: 1
pass 1 (-+): 0 found - 0 modified | TOTAL: 1
Iteration Number : 3
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 340 (out of 553619: 0.061414)
binarizing input wm segmentation...
Ambiguous edge configurations...
mri_pretess done
Iteration Number : 1
pass 1 (xy+): 15 found - 15 modified | TOTAL: 15
pass 2 (xy+): 0 found - 15 modified | TOTAL: 15
pass 1 (xy-): 17 found - 17 modified | TOTAL: 32
pass 2 (xy-): 0 found - 17 modified | TOTAL: 32
pass 1 (yz+): 29 found - 29 modified | TOTAL: 61
pass 2 (yz+): 0 found - 29 modified | TOTAL: 61
pass 1 (yz-): 28 found - 28 modified | TOTAL: 89
pass 2 (yz-): 0 found - 28 modified | TOTAL: 89
pass 1 (xz+): 21 found - 21 modified | TOTAL: 110
pass 2 (xz+): 0 found - 21 modified | TOTAL: 110
pass 1 (xz-): 18 found - 18 modified | TOTAL: 128
pass 2 (xz-): 0 found - 18 modified | TOTAL: 128
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 2 found - 2 modified | TOTAL: 2
pass 2 (+++): 0 found - 2 modified | TOTAL: 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 2
pass 1 (+++): 4 found - 4 modified | TOTAL: 6
pass 2 (+++): 0 found - 4 modified | TOTAL: 6
Iteration Number : 1
pass 1 (++): 7 found - 7 modified | TOTAL: 7
pass 2 (++): 0 found - 7 modified | TOTAL: 7
pass 1 (+-): 8 found - 8 modified | TOTAL: 15
pass 2 (+-): 0 found - 8 modified | TOTAL: 15
pass 1 (--): 6 found - 6 modified | TOTAL: 21
pass 2 (--): 0 found - 6 modified | TOTAL: 21
pass 1 (-+): 12 found - 12 modified | TOTAL: 33
pass 2 (-+): 0 found - 12 modified | TOTAL: 33
Iteration Number : 2
pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
pass 1 (xy-): 1 found - 1 modified | TOTAL: 2
pass 2 (xy-): 0 found - 1 modified | TOTAL: 2
pass 1 (yz+): 0 found - 0 modified | TOTAL: 2
pass 1 (yz-): 0 found - 0 modified | TOTAL: 2
pass 1 (xz+): 0 found - 0 modified | TOTAL: 2
pass 1 (xz-): 0 found - 0 modified | TOTAL: 2
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 1 found - 1 modified | TOTAL: 1
pass 2 (++): 0 found - 1 modified | TOTAL: 1
pass 1 (+-): 0 found - 0 modified | TOTAL: 1
pass 1 (--): 0 found - 0 modified | TOTAL: 1
pass 1 (-+): 0 found - 0 modified | TOTAL: 1
Iteration Number : 3
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 170 (out of 279688: 0.060782)
Ambiguous edge configurations...
mri_pretess done
8.0.0
8.0.0
slice 30: 1793 vertices, 1909 faces
slice 40: 6521 vertices, 6718 faces
slice 50: 13667 vertices, 13
967 faces
slice 60: 22813 vertices, 23150 faces
slice 70: 33144 vertices, 33506 faces
slice 80: 4343
2 vertices, 43777 faces
slice 90: 52552 vertices, 52892 faces
slice 100: 61974 vertices, 62320 faces
slice 110: 71377 vertices, 71717 faces
slice 120: 80466 vertices, 80812 faces
slice 130: 89203 vert
ices, 89508 faces
slice 140: 96262 vertices, 96514 faces
slice 150: 102723 vertices, 102927 faces
sl
ice 160: 107904 vertices, 108093 faces
slice 170: 111920 vertices, 112062 faces
slice 180: 114420 ve
rtices, 114473 faces
slice 190: 114564 vertices, 114582 faces
slice 200: 114564 vertices, 114582 fac
es
slice 210: 114564 vertices, 114582 faces
using the conformed surface RAS to save vertex points...
writing ../surf/lh.orig.nofix
using vox2ras matrix:
-1.00000 0.00000 0.00000 77.50000;
0.000
00 0.00000 1.00000 -106.00000;
0.00000 -1.00000 0.00000 117.50000;
0.00000 0.00000 0
.00000 1.00000;
counting number of connected components...
114564 voxel in cpt #1: X=-18 [v=114564,e=343746,f=229164] located at (-26.720881, -10.154708, 3
4.414169)
For the whole surface: X=-18 [v=114564,e=343746,f=229164]
One single component has been found
nothi
ng to do
done
Iteration Number : 1
pass 1 (xy+): 23 found - 23 modified | TOTAL: 23
pass 2 (xy+): 0 found - 23 modified | TOTAL: 23
pass 1 (xy-): 18 found - 18 modified | TOTAL: 41
pass 2 (xy-): 0 found - 18 modified | TOTAL: 41
pass 1 (yz+): 35 found - 35 modified | TOTAL: 76
pass 2 (yz+): 0 found - 35 modified | TOTAL: 76
pass 1 (yz-): 28 found - 28 modified | TOTAL: 104
pass 2 (yz-): 0 found - 28 modified | TOTAL: 104
pass 1 (xz+): 15 found - 15 modified | TOTAL: 119
pass 2 (xz+): 0 found - 15 modified | TOTAL: 119
pass 1 (xz-): 23 found - 23 modified | TOTAL: 142
pass 2 (xz-): 0 found - 23 modified | TOTAL: 142
Iteration Number : 1
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 1
pass 1 (++): 16 found - 16 modified | TOTAL: 16
pass 2 (++): 0 found - 16 modified | TOTAL: 16
pass 1 (+-): 4 found - 4 modified | TOTAL: 20
pass 2 (+-): 0 found - 4 modified | TOTAL: 20
pass 1 (--): 9 found - 9 modified | TOTAL: 29
pass 2 (--): 0 found - 9 modified | TOTAL: 29
pass 1 (-+): 14 found - 14 modified | TOTAL: 43
pass 2 (-+): 0 found - 14 modified | TOTAL: 43
Iteration Number : 2
pass 1 (xy+): 1 found - 1 modified | TOTAL: 1
pass 2 (xy+): 0 found - 1 modified | TOTAL: 1
pass 1 (xy-): 0 found - 0 modified | TOTAL: 1
pass 1 (yz+): 0 found - 0 modified | TOTAL: 1
pass 1 (yz-): 0 found - 0 modified | TOTAL: 1
pass 1 (xz+): 0 found - 0 modified | TOTAL: 1
pass 1 (xz-): 0 found - 0 modified | TOTAL: 1
Iteration Number : 2
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 2
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (xy+): 0 found - 0 modified | TOTAL: 0
pass 1 (xy-): 0 found - 0 modified | TOTAL: 0
pass 1 (yz+): 0 found - 0 modified | TOTAL: 0
pass 1 (yz-): 0 found - 0 modified | TOTAL: 0
pass 1 (xz+): 0 found - 0 modified | TOTAL: 0
pass 1 (xz-): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
pass 1 (+++): 0 found - 0 modified | TOTAL: 0
Iteration Number : 3
pass 1 (++): 0 found - 0 modified | TOTAL: 0
pass 1 (+-): 0 found - 0 modified | TOTAL: 0
pass 1 (--): 0 found - 0 modified | TOTAL: 0
pass 1 (-+): 0 found - 0 modified | TOTAL: 0
Total Number of Modified Voxels = 186 (out of 273947: 0.067896)
Ambiguous edge configurations...
mri_pretess done
8.0.0
8.0.0
slice 30: 2064 vertices, 2185 faces
slice 40: 7248 vertices, 7486 faces
slice 50: 14919 vertices, 15
232 faces
slice 60: 24127 vertices, 24453 faces
slice 70: 33564 vertices, 33902 faces
slice 80: 4284
7 vertices, 43201 faces
slice 90: 51993 vertices, 52313 faces
slice 100: 60965 vertices, 61292 faces
slice 110: 69472 vertices, 69808 faces
slice 120: 78189 vertices, 78543 faces
slice 130: 86910 vert
ices, 87215 faces
slice 140: 94287 vertices, 94522 faces
slice 150: 100523 vertices, 100751 faces
sl
ice 160: 106084 vertices, 106308 faces
slice 170: 110745 vertices, 110908 faces
slice 180: 113440 ve
rtices, 113518 faces
slice 190: 113640 vertices, 113664 faces
slice 200: 113640 vertices, 113664 fac
es
slice 210: 113640 vertices, 113664 faces
using the conformed surface RAS to save vertex points...
writing ../surf/rh.orig.nofix
using vox2ras matrix:
-1.00000 0.00000 0.00000 77.50000;
0.000
00 0.00000 1.00000 -106.00000;
0.00000 -1.00000 0.00000 117.50000;
0.00000 0.00000 0
.00000 1.00000;
counting number of connected components...
113632 voxel in cpt #1: X=-26 [v=113632,e=340974,f=227316] located at (28.477621, -9.755870, 33.
786083)
8 voxel in cpt #2: X=2 [v=8,e=18,f=12] located at (18.500000, -61.000000, 10.500000)
For the whole surface: X=-24 [v=113640,e=340992,f=227328]
2 components have been found
keeping comp
onent #1 with 113632 vertices
done
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
setting seed for random number generator to 1234
smoothing surface tessellation for 10 iterations...
smoothing complete - recomputing first and second fundamental forms...
Not saving sulc
Reading ./lh.smoothwm.nofix
avg radius = 45.9 mm, total surface area = 62396 mm^2
step 005: RMS=0.110 (target=0.015)
step 010: RMS=0.078 (target=0.015)
step 015: RMS=0.064 (target=0.015)
step 020: RMS=0.054 (target=0.015)
step 025: RMS=0.046 (target=0.015)
step 030: RMS=0.039 (target=0.015)
step 035: RMS=0.034 (target=0.015)
step 040: RMS=0.031 (target=0.015)
step 045: RMS=0.029 (target=0.015)
step 050: RMS=0.028 (target=0.015)
step 055: RMS=0.027 (target=0.015)
step 060: RMS=0.026 (target=0.015) writing inflated surface to ./lh.inflated.nofix
inflation took 0.3 minutes
inflation complete.
Not saving sulc
mris_inflate utimesec 17.236861
m
ris_inflate stimesec 0.939948
mris_inflate ru_maxrss 182980
mris_inflate ru_ixrss 0
mris_inf
late ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 485724
mris_inflate ru_majflt
0
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 8064
mris_inflat
e ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 62
mr
is_inflate ru_nivcsw 99
Not saving sulc
Reading ./rh.smoothwm.nofix
avg radius = 46.7 mm, total surface area = 61806 mm^2
step 005: RMS=0.110 (target=0.015)
step 010: RMS=0.078 (target=0.015)
step 015: RMS=0.065 (target=0.015)
step 020: RMS=0.055 (target=0.015)
step 025: RMS=0.047 (target=0.015)
step 030: RMS=0.041 (target=0.015)
step 035: RMS=0.037 (target=0.015)
step 040: RMS=0.034 (target=0.015)
step 045: RMS=0.031 (target=0.015)
step 050: RMS=0.030 (target=0.015)
step 055: RMS=0.029 (target=0.015)
step 060: RMS=0.028 (target=0.015) writing inflated surface to ./rh.inflated.nofix
inflation took 0.3 minutes
inflation complete.
Not saving sulc
mris_inflate utimesec 17.606393
m
ris_inflate stimesec 0.972383
mris_inflate ru_maxrss 181516
mris_inflate ru_ixrss 0
mris_inf
late ru_idrss 0
mris_inflate ru_isrss 0
mris_inflate ru_minflt 483832
mris_inflate ru_majflt
0
mris_inflate ru_nswap 0
mris_inflate ru_inblock 0
mris_inflate ru_oublock 8000
mris_inflat
e ru_msgsnd 0
mris_inflate ru_msgrcv 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 51
mr
is_inflate ru_nivcsw 158
doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
version: 8.0.0
available threads: 1
scaling brain by 0.339...
inflating...
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.08 +- 0.57 (0.02-->5.32) (max @ vno 70048 --> 70070)
face area 0.03 +- 0.03 (-0.09-->0.42)
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial er
ror=176.315, avgs=0
005/300: dt: 0.9000, rms radial error=176.054, avgs=0
010/300: dt: 0.9000, rms r
adial error=175.492, avgs=0
015/300: dt: 0.9000, rms radial error=174.753, avgs=0
020/300: dt: 0.900
0, rms radial error=173.913, avgs=0
025/300: dt: 0.9000, rms radial error=173.014, avgs=0
030/300: d
t: 0.9000, rms radial error=172.083, avgs=0
035/300: dt: 0.9000, rms radial error=171.137, avgs=0
04
0/300: dt: 0.9000, rms radial error=170.187, avgs=0
045/300: dt: 0.9000, rms radial error=169.240, a
vgs=0
050/300: dt: 0.9000, rms radial error=168.295, avgs=0
055/300: dt: 0.9000, rms radial error=16
7.353, avgs=0
060/300: dt: 0.9000, rms radial error=166.416, avgs=0
065/300: dt: 0.9000, rms radial
error=165.482, avgs=0
070/300: dt: 0.9000, rms radial error=164.554, avgs=0
075/300: dt: 0.9000, rms
radial error=163.632, avgs=0
080/300: dt: 0.9000, rms radial error=162.715, avgs=0
085/300: dt: 0.9
000, rms radial error=161.803, avgs=0
090/300: dt: 0.9000, rms radial error=160.896, avgs=0
095/300:
dt: 0.9000, rms radial error=159.993, avgs=0
100/300: dt: 0.9000, rms radial error=159.096, avgs=0
105/300: dt: 0.9000, rms radial error=158.203, avgs=0
110/300: dt: 0.9000, rms radial error=157.316,
avgs=0
115/300: dt: 0.9000, rms radial error=156.433, avgs=0
120/300: dt: 0.9000, rms radial error=
155.555, avgs=0
125/300: dt: 0.9000, rms radial error=154.682, avgs=0
130/300: dt: 0.9000, rms radia
l error=153.814, avgs=0
135/300: dt: 0.9000, rms radial error=152.950, avgs=0
140/300: dt: 0.9000, r
ms radial error=152.092, avgs=0
145/300: dt: 0.9000, rms radial error=151.238, avgs=0
150/300: dt: 0
.9000, rms radial error=150.389, avgs=0
155/300: dt: 0.9000, rms radial error=149.544, avgs=0
160/30
0: dt: 0.9000, rms radial error=148.705, avgs=0
165/300: dt: 0.9000, rms radial error=147.870, avgs=
0
170/300: dt: 0.9000, rms radial error=147.039, avgs=0
175/300: dt: 0.9000, rms radial error=146.21
3, avgs=0
180/300: dt: 0.9000, rms radial error=145.392, avgs=0
185/300: dt: 0.9000, rms radial erro
r=144.575, avgs=0
190/300: dt: 0.9000, rms radial error=143.763, avgs=0
195/300: dt: 0.9000, rms rad
ial error=142.956, avgs=0
200/300: dt: 0.9000, rms radial error=142.152, avgs=0
205/300: dt: 0.9000,
rms radial error=141.354, avgs=0
210/300: dt: 0.9000, rms radial error=140.559, avgs=0
215/300: dt:
0.9000, rms radial error=139.769, avgs=0
220/300: dt: 0.9000, rms radial error=138.984, avgs=0
225/
300: dt: 0.9000, rms radial error=138.203, avgs=0
230/300: dt: 0.9000, rms radial error=137.426, avg
s=0
235/300: dt: 0.9000, rms radial error=136.653, avgs=0
240/300: dt: 0.9000, rms radial error=135.
885, avgs=0
245/300: dt: 0.9000, rms radial error=135.121, avgs=0
250/300: dt: 0.9000, rms radial er
ror=134.361, avgs=0
255/300: dt: 0.9000, rms radial error=133.606, avgs=0
260/300: dt: 0.9000, rms r
adial error=132.855, avgs=0
265/300: dt: 0.9000, rms radial error=132.108, avgs=0
270/300: dt: 0.900
0, rms radial error=131.365, avgs=0
275/300: dt: 0.9000, rms radial error=130.626, avgs=0
280/300: d
t: 0.9000, rms radial error=129.891, avgs=0
285/300: dt: 0.9000, rms radial error=129.161, avgs=0
29
0/300: dt: 0.9000, rms radial error=128.434, avgs=0
295/300: dt: 0.9000, rms radial error=127.712, a
vgs=0
300/300: dt: 0.9000, rms radial error=126.994, avgs=0
spherical inflation complete.
epoch 1 (
K=10.0), pass 1, starting sse = 12886.21
taking momentum steps...
taking momentum steps...
taking mo
mentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00054
epoch 2
(K=40.0), pass 1, starting sse = 1900.01
taking momentum steps...
taking momentum steps...
taking m
omentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00076
epoch
3 (K=160.0), pass 1, starting sse = 139.83
taking momentum steps...
taking momentum steps...
taking
momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.19/17 = 0.01147
epoch
4 (K=640.0), pass 1, starting sse = 4.19
taking momentum steps...
taking momentum steps...
taki
ng momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.23/24 = 0.00962
fi
nal distance error %100000.00
writing spherical brain to ./lh.qsphere.nofix
spherical transformation took 0.0375 hours
FSRUNTIME@ mris_sphere 0.0375 hours 1 threads
#VMPC# mris_sphere VmPeak 443520
mris_sphere done
doing quick spherical unfolding.
limitting unfolding to 6 passes
using n_averages = 128
setting seed for random number genererator to 1234
version: 8.0.0
available threads: 1
scaling brain by 0.340...
inflating...
projecting onto sphere...
surface projected - minimizing metric distortion...
vertex spacing 1.08 +- 0.58 (0.01-->5.47) (max @ vno 48028 --> 48890)
face area 0.03 +- 0.04 (-0.06-->0.54)
Entering MRISinflateToSphere()
inflating to sphere (rms error < 2.00)
000: dt: 0.0000, rms radial er
ror=176.052, avgs=0
005/300: dt: 0.9000, rms radial error=175.792, avgs=0
010/300: dt: 0.9000, rms r
adial error=175.232, avgs=0
015/300: dt: 0.9000, rms radial error=174.499, avgs=0
020/300: dt: 0.900
0, rms radial error=173.665, avgs=0
025/300: dt: 0.9000, rms radial error=172.774, avgs=0
030/300: d
t: 0.9000, rms radial error=171.852, avgs=0
035/300: dt: 0.9000, rms radial error=170.914, avgs=0
04
0/300: dt: 0.9000, rms radial error=169.969, avgs=0
045/300: dt: 0.9000, rms radial error=169.024, a
vgs=0
050/300: dt: 0.9000, rms radial error=168.080, avgs=0
055/300: dt: 0.9000, rms radial error=16
7.139, avgs=0
060/300: dt: 0.9000, rms radial error=166.202, avgs=0
065/300: dt: 0.9000, rms radial
error=165.273, avgs=0
070/300: dt: 0.9000, rms radial error=164.347, avgs=0
075/300: dt: 0.9000, rms
radial error=163.427, avgs=0
080/300: dt: 0.9000, rms radial error=162.511, avgs=0
085/300: dt: 0.9
000, rms radial error=161.600, avgs=0
090/300: dt: 0.9000, rms radial error=160.694, avgs=0
095/300:
dt: 0.9000, rms radial error=159.793, avgs=0
100/300: dt: 0.9000, rms radial error=158.897, avgs=0
105/300: dt: 0.9000, rms radial error=158.005, avgs=0
110/300: dt: 0.9000, rms radial error=157.119,
avgs=0
115/300: dt: 0.9000, rms radial error=156.237, avgs=0
120/300: dt: 0.9000, rms radial error=
155.360, avgs=0
125/300: dt: 0.9000, rms radial error=154.488, avgs=0
130/300: dt: 0.9000, rms radia
l error=153.620, avgs=0
135/300: dt: 0.9000, rms radial error=152.757, avgs=0
140/300: dt: 0.9000, r
ms radial error=151.899, avgs=0
145/300: dt: 0.9000, rms radial error=151.045, avgs=0
150/300: dt: 0
.9000, rms radial error=150.196, avgs=0
155/300: dt: 0.9000, rms radial error=149.351, avgs=0
160/30
0: dt: 0.9000, rms radial error=148.512, avgs=0
165/300: dt: 0.9000, rms radial error=147.677, avgs=
0
170/300: dt: 0.9000, rms radial error=146.846, avgs=0
175/300: dt: 0.9000, rms radial error=146.02
1, avgs=0
180/300: dt: 0.9000, rms radial error=145.200, avgs=0
185/300: dt: 0.9000, rms radial erro
r=144.383, avgs=0
190/300: dt: 0.9000, rms radial error=143.571, avgs=0
195/300: dt: 0.9000, rms rad
ial error=142.763, avgs=0
200/300: dt: 0.9000, rms radial error=141.960, avgs=0
205/300: dt: 0.9000,
rms radial error=141.162, avgs=0
210/300: dt: 0.9000, rms radial error=140.367, avgs=0
215/300: dt:
0.9000, rms radial error=139.577, avgs=0
220/300: dt: 0.9000, rms radial error=138.792, avgs=0
225/
300: dt: 0.9000, rms radial error=138.011, avgs=0
230/300: dt: 0.9000, rms radial error=137.234, avg
s=0
235/300: dt: 0.9000, rms radial error=136.462, avgs=0
240/300: dt: 0.9000, rms radial error=135.
694, avgs=0
245/300: dt: 0.9000, rms radial error=134.930, avgs=0
250/300: dt: 0.9000, rms radial er
ror=134.170, avgs=0
255/300: dt: 0.9000, rms radial error=133.414, avgs=0
260/300: dt: 0.9000, rms r
adial error=132.663, avgs=0
265/300: dt: 0.9000, rms radial error=131.916, avgs=0
270/300: dt: 0.900
0, rms radial error=131.173, avgs=0
275/300: dt: 0.9000, rms radial error=130.435, avgs=0
280/300: d
t: 0.9000, rms radial error=129.700, avgs=0
285/300: dt: 0.9000, rms radial error=128.970, avgs=0
29
0/300: dt: 0.9000, rms radial error=128.243, avgs=0
295/300: dt: 0.9000, rms radial error=127.521, a
vgs=0
300/300: dt: 0.9000, rms radial error=126.803, avgs=0
spherical inflation complete.
epoch 1 (
K=10.0), pass 1, starting sse = 12774.46
taking momentum steps...
taking momentum steps...
taking mo
mentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00051
epoch 2
(K=40.0), pass 1, starting sse = 1888.78
taking momentum steps...
taking momentum steps...
taking m
omentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.01/13 = 0.00111
epoch
3 (K=160.0), pass 1, starting sse = 144.08
taking momentum steps...
taking momentum steps...
taking
momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.19/18 = 0.01042
epoch
4 (K=640.0), pass 1, starting sse = 6.14
taking momentum steps...
taking momentum steps...
taki
ng momentum steps...
taking momentum steps...
pass 1 complete, delta sse/iter = 0.17/25 = 0.00679
fi
nal distance error %100000.00
writing spherical brain to ./rh.qsphere.nofix
spherical transformation took 0.0376 hours
FSRUNTIME@ mris_sphere 0.0376 hours 1 threads
#VMPC# mris_sphere VmPeak 442052
mris_sphere done
reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nof
ix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
*************************************************************
Topology Correction Parameters
retes
sellation mode: genetic search
number of patches/generation : 10
number of generations :
10
surface mri loglikelihood coefficient : 1.0
volume mri loglikelihood coefficient :
10.0
normal dot loglikelihood coefficient : 1.0
quadratic curvature loglikelihood
coefficient : 1.0
volume resolution : 2
eliminate vertices during search
: 1
initial patch selection : 1
select all defect vertices :
0
ordering dependant retessellation: 0
use precomputed edge table :
0
smooth retessellated patch : 2
match retessellated patch :
1
verbose mode : 0
*******************************
******************************
INFO: assuming .mgz format
writing corrected surface to 'orig.premesh
'
8.0.0
8.0.0
before topology correction, eno=-18 (nv=114564, nf=229164, ne=343746, g=10)
using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology
Finding true center and radius of Spherical Surface...
done
Surface centered at (0,0,0) with radius 100.0 in 11 iterations
marking ambiguous vertices...
807 ambiguous faces found in tessellation
segmenting defects...
12 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
12 defects to be corrected
0 vertices coincident
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/lh.qsphere.nofix...
reading brain volume from brain...
reading wm seg
mentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.
nofix
Computing Initial Surface Statistics
-face loglikelihood: -9.3094 (-4.6547)
-vertex loglikelihood: -6.6149 (-3.30
74)
-normal dot loglikelihood: -3.7133 (-3.7133)
-quad curv loglikelihood: -6.2532 (-
3.1266)
Total Loglikelihood : -25.8907
CORRECTING DEFECT 0 (vertices=5, convex hull=31, v0=862)
After retessellation of defect 0 (v0=862), euler #=-9 (113994,341550,227547) : difference with theor
y (-9) = 0
CORRECTING DEFECT 1 (vertices=79, convex hull=112, v0=2342)
After retessellation of defect 1 (v0=2342), euler #=-8 (114014,341655,227633) : difference with theo
ry (-8) = 0
CORRECTING DEFECT 2 (vertices=56, convex hull=104, v0=2502)
After retessellation of defect 2 (v0=2502), euler #=-7 (114028,341742,227707) : difference with theo
ry (-7) = 0
CORRECTING DEFECT 3 (vertices=5, convex hull=35, v0=3807)
After retessellation of defect 3 (v0=3807), euler #=-6 (114030,341758,227722) : difference with theo
ry (-6) = 0
CORRECTING DEFECT 4 (vertices=25, convex hull=81, v0=4670)
After retessellation of defect 4 (v0=4670), euler #=-5 (114039,341815,227771) : difference with theo
ry (-5) = 0
CORRECTING DEFECT 5 (vertices=73, convex hull=111, v0=8988)
After retessellation of defect 5 (v0=8988), euler #=-4 (114074,341972,227894) : difference with theo
ry (-4) = 0
CORRECTING DEFECT 6 (vertices=64, convex hull=109, v0=10458)
After retessellation of defect 6 (v0=10458), euler #=-3 (114109,342123,228011) : difference with the
ory (-3) = 0
CORRECTING DEFECT 7 (vertices=86, convex hull=139, v0=28658)
After retessellation of defect 7 (v0=28658), euler #=-2 (114172,342373,228199) : difference with the
ory (-2) = 0
CORRECTING DEFECT 8 (vertices=54, convex hull=83, v0=39107)
After retessellation of defect 8 (v0=39107), euler #=-1 (114205,342503,228297) : difference with the
ory (-1) = 0
CORRECTING DEFECT 9 (vertices=28, convex hull=76, v0=48957)
After retessellation of defect 9 (v0=48957), euler #=0 (114222,342587,228365) : difference with theo
ry (0) = 0
CORRECTING DEFECT 10 (vertices=56, convex hull=97, v0=68226)
After retessellation of defect 10 (v0=68226), euler #=1 (114239,342681,228443) : difference with the
ory (1) = 0
CORRECTING DEFECT 11 (vertices=41, convex hull=77, v0=104704)
After retessellation of defect 11 (v0=104704), euler #=2 (114260,342774,228516) : difference with th
eory (2) = 0
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.21 (0.14-->8.03) (max @ vno 11662 --> 13219)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.21 (0.14-->8.03) (max @ vno 11662 --> 13219)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
40 mutations (33.1%), 81 crossovers (66.9%), 56 vertices were eliminated
building final representati
on...
304 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=114260, nf=228516, ne=342774, g=0)
writing corrected surface to /home/jovyan/workspace/books/examples/structural_imaging/data/structura
l/recon-all-clinical/TestSubject/surf/lh.orig.premesh...
0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 82 intersecting
001: 5 intersecting
terminating search with 0 inter
secting
topology fixing took 1.7 minutes
FSRUNTIME@ mris_fix_topology lh 0.0280 hours 1 threads
#VM
PC# mris_fix_topology VmPeak 737832
reading spherical homeomorphism from 'qsphere.nofix'
reading inflated coordinates from 'inflated.nof
ix'
reading original coordinates from 'orig.nofix'
using genetic algorithm with optimized parameters
setting seed for random number genererator to 1234
************************************************
*************
Topology Correction Parameters
retessellation mode: genetic search
number of
patches/generation : 10
number of generations : 10
surface mri loglikelihood coefficient :
1.0
volume mri loglikelihood coefficient : 10.0
normal dot loglikelihood coefficient
: 1.0
quadratic curvature loglikelihood coefficient : 1.0
volume resolution :
2
eliminate vertices during search : 1
initial patch selection :
1
select all defect vertices : 0
ordering dependant retessellatio
n: 0
use precomputed edge table : 0
smooth retessellated patch :
2
match retessellated patch : 1
verbose mode :
0
*************************************************************
INFO: assuming .mgz
format
writing corrected surface to 'orig.premesh'
8.0.0
8.0.0
before topology correction, eno=-26 (nv=113632, nf=227316, ne=340974, g=14)
using quasi-homeomorphic spherical map to tessellate cortical surface...
Correction of the Topology
Finding true center and radius of Spherical Surface...
done
Surface centered at (0,0,0) with radius 100.0 in 8 iterations
marking ambiguous vertices...
2126 ambiguous faces found in tessellation
segmenting defects...
12 defects found, arbitrating ambiguous regions...
analyzing neighboring defects...
12 defects to be corrected
0 vertices coincident
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/rh.qsphere.nofix...
reading brain volume from brain...
reading wm seg
mentation from wm...
Reading original properties of orig.nofix
Reading vertex positions of inflated.
nofix
Computing Initial Surface Statistics
-face loglikelihood: -9.3162 (-4.6581)
-vertex loglikelihood: -6.5417 (-3.27
09)
-normal dot loglikelihood: -3.6684 (-3.6684)
-quad curv loglikelihood: -6.2088 (-
3.1044)
Total Loglikelihood : -25.7350
CORRECTING DEFECT 0 (vertices=312, convex hull=229, v0=15)
After retessellation of defect 0 (v0=15), euler #=-9 (112273,336251,223969) : difference with theory
(-9) = 0
CORRECTING DEFECT 1 (vertices=76, convex hull=125, v0=1426)
After retessellation of defect 1 (v0=1426), euler #=-8 (112320,336443,224115) : difference with theo
ry (-8) = 0
CORRECTING DEFECT 2 (vertices=139, convex hull=109, v0=1515)
After retessellation of defect 2 (v0=1515), euler #=-7 (112356,336610,224247) : difference with theo
ry (-7) = 0
CORRECTING DEFECT 3 (vertices=139, convex hull=174, v0=3361)
After retessellation of defect 3 (v0=3361), euler #=-6 (112429,336907,224472) : difference with theo
ry (-6) = 0
CORRECTING DEFECT 4 (vertices=127, convex hull=112, v0=13030)
After retessellation of defect 4 (v0=13030), euler #=-5 (112475,337099,224619) : difference with the
ory (-5) = 0
CORRECTING DEFECT 5 (vertices=55, convex hull=90, v0=15297)
After retessellation of defect 5 (v0=15297), euler #=-4 (112486,337167,224677) : difference with the
ory (-4) = 0
CORRECTING DEFECT 6 (vertices=70, convex hull=107, v0=17663)
After retessellation of defect 6 (v0=17663), euler #=-3 (112523,337322,224796) : difference with the
ory (-3) = 0
CORRECTING DEFECT 7 (vertices=45, convex hull=70, v0=19066)
After retessellation of defect 7 (v0=19066), euler #=-2 (112532,337379,224845) : difference with the
ory (-2) = 0
CORRECTING DEFECT 8 (vertices=191, convex hull=194, v0=55731)
After retessellation of defect 8 (v0=55731), euler #=-1 (112624,337748,225123) : difference with the
ory (-1) = 0
CORRECTING DEFECT 9 (vertices=16, convex hull=36, v0=60760)
After retessellation of defect 9 (v0=60760), euler #=0 (112628,337772,225144) : difference with theo
ry (0) = 0
CORRECTING DEFECT 10 (vertices=123, convex hull=131, v0=98009)
After retessellation of defect 10 (v0=98009), euler #=1 (112646,337884,225239) : difference with the
ory (1) = 0
CORRECTING DEFECT 11 (vertices=75, convex hull=112, v0=102371)
After retessellation of defect 11 (v0=102371), euler #=2 (112693,338073,225382) : difference with th
eory (2) = 0
computing original vertex metric properties...
storing new metric properties...
computing tessellation statistics...
vertex spacing 0.89 +- 0.23 (0.10-->10.65) (max @ vno 88 --> 1304)
face area -nan +- -nan (1000.00-->-1.00)
performing soap bubble on retessellated vertices for 0 iterations...
vertex spacing 0.89 +- 0.23 (0.10-->10.65) (max @ vno 88 --> 1304)
face area -nan +- -nan (1000.00-->-1.00)
tessellation finished, orienting corrected surface...
44 mutations (31.2%), 97 crossovers (68.8%), 191 vertices were eliminated
building final representat
ion...
939 vertices and 0 faces have been removed from triangulation
after topology correction, eno=2 (nv=112693, nf=225382, ne=338073, g=0)
writing corrected surface to /home/jovyan/workspace/books/examples/structural_imaging/data/structura
l/recon-all-clinical/TestSubject/surf/rh.orig.premesh...
0.000 % of the vertices (0 vertices) exhibit an orientation change
removing intersecting faces
000: 146 intersecting
terminating search with 0 intersecting
topology fi
xing took 3.6 minutes
FSRUNTIME@ mris_fix_topology rh 0.0600 hours 1 threads
#VMPC# mris_fix_topolo
gy VmPeak 736896
euler # = v-e+f = 2g-2: 114260 - 342774 + 228516 = 2 --> 0 holes
F =2V-4: 228516 = 22
8520-4 (0)
2E=3F: 685548 = 685548 (0)
total defect index = 0
euler # = v-e+f = 2g-2: 112693 - 338073 + 225382 = 2 --> 0 holes
F =2V-4: 225382 = 22
5386-4 (0)
2E=3F: 676146 = 676146 (0)
total defect index = 0
iters = 3
standard remeshing without target
adjusted l: 0.709834
remeshing to edge length 0.709834 with 3 iterations
avg qual before : 0.892131 after: 0.970905
Removing intersections
Remeshed surface quality stats nv0 = 114260 nv = 119704 1.04765
Area 239404 0.30158 0.03374 0
.075405 0.4740
Corner 718212 60.00000 8.85452 15.843892 147.9050
Edge 359106 0.84259 0.0825
9 0.458977 1.2503
Hinge 359106 9.31227 9.26826 0.000000 115.9328
mris_remesh done
iters = 3
standard remeshing without target
adjusted l: 0.711021
remeshing to edge length 0.711021 with 3 iterations
avg qual before : 0.892039 after: 0.971146
Removing intersections
Remeshed surface quality stats nv0 = 112693 nv = 118059 1.04762
Area 236114 0.30260 0.03361 0
.094241 0.4689
Corner 708342 60.00000 8.80318 20.525221 137.6196
Edge 354171 0.84394 0.0823
8 0.472233 1.2928
Hinge 354171 9.38191 9.45202 0.000000 148.3136
mris_remesh done
intersection removal took 0.00 hours
Found 0 intersections
writing corrected surface to ./lh.orig
intersection removal took 0.00 hours
Found 0 intersections
writing corrected surface to ./rh.orig
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinica
l/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/
structural/recon-all-clinical
mris_autodet_gwstats --o ../surf/autodet.gw.stats.lh.dat --i brain.mgz
--wm wm.mgz --surf ../surf/lh.orig.premesh
border white: 208355 voxels (2.70%)
border gray 225270 voxels (2.92%)
Reading in intensity volume brain.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/lh.orig.pr
emesh
Auto detecting stats
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
Binarizing thresholding
at 5
computing class statistics... low=30, hi=110.000000
CCS WM (106.0): 100.9 +- 10.6 [70.0 --> 109
.0]
CCS GM (70.0) : 73.0 +- 10.5 [30.0 --> 109.0]
white_mean = 100.922 +/- 10.5831, gray_mean = 72.9
75 +/- 10.5025
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassMode
s(): min=0 max=109 nbins=110
intensity peaks found at WM=108+-0.9, GM=69+-2.6
white_mode = 108, g
ray_mode = 69
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_B
ORDER to 58.5 (was 70.000000)
setting MAX_BORDER_WHITE to 118.6 (was 105.000000)
setting MIN_BORDER_
WHITE to 69.0 (was 85.000000)
setting MAX_CSF to 48.0 (was 40.000000)
setting MAX_GRAY to 97.4 (was
95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 58.5 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to
37.5 (was 40.000000)
When placing the white surface
white_border_hi = 118.583;
white_border_lo
w = 69;
white_outside_low = 58.4975;
white_inside_hi = 120;
white_outside_hi = 118.583;
Wh
en placing the pial surface
pial_border_hi = 58.4975;
pial_border_low = 37.4926;
pial_outsi
de_low = 10;
pial_inside_hi = 97.4169;
pial_outside_hi = 53.2463;
#VMPC# mris_autodet_gwstats
VmPeak 226196
mris_autodet_gwstats done
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinica
l/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/
structural/recon-all-clinical
mris_autodet_gwstats --o ../surf/autodet.gw.stats.rh.dat --i brain.mgz
--wm wm.mgz --surf ../surf/rh.orig.premesh
border white: 208355 voxels (2.70%)
border gray 225270 voxels (2.92%)
Reading in intensity volume brain.mgz
Reading in wm volume wm.mgz
Reading in surf ../surf/rh.orig.pr
emesh
Auto detecting stats
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
Binarizing thresholding
at 5
computing class statistics... low=30, hi=110.000000
CCS WM (106.0): 100.9 +- 10.6 [70.0 --> 109
.0]
CCS GM (70.0) : 73.0 +- 10.5 [30.0 --> 109.0]
white_mean = 100.922 +/- 10.5831, gray_mean = 72.9
75 +/- 10.5025
using class modes intead of means, discounting robust sigmas....
MRIScomputeClassMode
s(): min=0 max=109 nbins=110
intensity peaks found at WM=108+-0.9, GM=69+-2.6
white_mode = 108, g
ray_mode = 69
std_scale = 1
Applying sanity checks, max_scale_down = 0.2
setting MIN_GRAY_AT_WHITE_B
ORDER to 58.5 (was 70.000000)
setting MAX_BORDER_WHITE to 118.6 (was 105.000000)
setting MIN_BORDER_
WHITE to 69.0 (was 85.000000)
setting MAX_CSF to 48.0 (was 40.000000)
setting MAX_GRAY to 97.4 (was
95.000000)
setting MAX_GRAY_AT_CSF_BORDER to 58.5 (was 75.000000)
setting MIN_GRAY_AT_CSF_BORDER to
37.5 (was 40.000000)
When placing the white surface
white_border_hi = 118.583;
white_border_lo
w = 69;
white_outside_low = 58.4975;
white_inside_hi = 120;
white_outside_hi = 118.583;
Wh
en placing the pial surface
pial_border_hi = 58.4975;
pial_border_low = 37.4926;
pial_outsi
de_low = 10;
pial_inside_hi = 97.4169;
pial_outside_hi = 53.2463;
#VMPC# mris_autodet_gwstats
VmPeak 224076
mris_autodet_gwstats done
8.0.0
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --
wm wm.mgz --threads 2 --invol brain.mgz --lh --i ../surf/lh.orig --o ../surf/lh.white.preaparc --whi
te --seg aseg.presurf.mgz --nsmooth 5
Reading in input surface ../surf/lh.orig
Smoothing surface before ripping with 5 iterations
Area
239404 0.26869 0.06111 0.028228 0.5937
Corner 718212 60.00000 9.11664 18.026135 141.5662
Edge
359106 0.79138 0.11057 0.179387 1.2892
Hinge 359106 6.35484 6.01539 0.000011 98.7051
Not reading in aparc
Reading in input volume brain.mgz
Reading in seg volume aseg.presurf.mgz
Readin
g in wm volume wm.mgz
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
MRIfindBrightNonWM(): 0 brigh
t non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRIm
ask(): AllowDiffGeom = 1
Ripping frozen voxels
INFO: rip surface needed but not specified, so using
input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=0
#FML# MRISripMidline(): nmarked=6210, nmarked2=0, nripped=6210
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs()
: -2 2 0.5 ripped 0
opt weights int=0.2 loc=0 rep=5 nspr=0.3 curv=1
vertex 59852: xyz = (-45.2538,1.
4555,32.8787) oxyz = (-45.2538,1.4555,32.8787) wxzy = (-45.2538,1.4555,32.8787) pxyz = (0,0,0)
CBVO Creating mask 119704
n_averages 4
Iteration 0 =========================================
n_avera
ges=4, current_sigma=2
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed bu
t not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhi
biting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0
# MRISripMidline(): nripped=6210
#FML# MRISripMidline(): nmarked=6210, nmarked2=0, nripped=6210
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247
MRISripSe
gs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
i
nside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low =
58.4975320;
outside_hi = 118.5830610;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP
_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nv
ertices=119704
Gdiag_no=-1
VMPeak = 823116
vno start=0, stop=119704
#SI# sigma=2 had to be inc
reased for 390 vertices, nripped=6210
mean border=78.3, 572 (572) missing vertices, mean dist 0.3 [0
.8 (%32.4)->0.8 (%67.6))]
%60 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignore
d
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1207 min
Finding expansion regions
mean absolute distance = 0.83 +- 1.02
3700 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=05768, nav=4, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat
0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisph
ere 0
randomSeed 0
000: dt: 0.0000, sse=5829538.5, rms=15.886
001: dt: 0.5000, sse=3724957.5, rms=12.621 (20.553%)
002: dt: 0.5000, sse=2473216.2, rms=10.193 (19.238%)
003: dt: 0.5000, sse=1698042.9, rms=8.339 (18.187%)
004: dt: 0.5000, sse=1214845.2, rms=6.935 (16.843%)
005: dt: 0.5000, sse=922419.0, rms=5.918 (14.661%)
006: dt: 0.5000, sse=746662.6, rms=5.211 (11.941%)
007: dt: 0.5000, sse=642532.2, rms=4.738 (9.084%)
008: dt: 0.5000, sse=586274.3, rms=4.434 (6.414%)
009: dt: 0.5000, sse=558887.8, rms=4.240 (4.383%)
010: dt: 0.5000, sse=526061.4, rms=4.113 (2.983%)
011: dt: 0.5000, sse=508132.2, rms=4.021 (2.235%)
012: dt: 0.5000, sse=497951.7, rms=3.954 (1.688%)
013: dt: 0.5000, sse=488695.9, rms=3.895 (1.468%)
rms = 3.8568/3.8955, sse=478717.1/488695.9, time step reduction 1 of 3 to 0.250 0 0 1
014: dt: 0.50
00, sse=478717.1, rms=3.857 (0.992%)
015: dt: 0.2500, sse=295677.9, rms=2.536 (34.259%)
016: dt: 0.2500, sse=255924.5, rms=2.164 (14.667%)
017: dt: 0.2500, sse=239810.0, rms=2.052 (5.177%)
018: dt: 0.2500, sse=233818.4, rms=1.976 (3.670%)
rms = 1.9432/1.9763, sse=230829.1/233818.4, time step reduction 2 of 3 to 0.125 0 0 1
019: dt: 0.25
00, sse=230829.1, rms=1.943 (1.675%)
020: dt: 0.1250, sse=225730.6, rms=1.892 (2.636%)
rms = 1.8811/1.8920, sse=226920.1/225730.6, time step reduction 3 of 3 to 0.062 0 1 1
021: dt: 0.12
50, sse=226920.1, rms=1.881 (0.576%)
maximum number of reductions reached, breaking from loop
positioning took 2.3 minutes
done positioning surface
Iteration 1 ================================
=========
n_averages=2, current_sigma=1
Freezing midline and others
Ripping frozen voxels
INFO: rip
surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6210
removing 4 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6401, nmarked2=0, nripped=6401
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247
MRISr
ipSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_lo
w = 58.4975320;
outside_hi = 118.5830610;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdiag_no=-1
VMPeak = 1690176
vno start=0, stop=119704
#SI# sigma=1 had to b
e increased for 208 vertices, nripped=6401
mean border=84.9, 574 (465) missing vertices, mean dist -
0.3 [0.4 (%90.0)->0.2 (%10.0))]
%81 local maxima, %13 large gradients and % 0 min vals, 0 gradients
ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0798 min
Finding expansion regi
ons
mean absolute distance = 0.35 +- 0.42
910 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=05768, nav=2, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=1704703.6, rms=8.189
022: dt: 0.5000, sse=806814.8, rms=5.198 (36.525%)
023: dt: 0.5000, sse=638929.2, rms=4.458 (14.235%)
rms = 4.4201/4.4577, sse=633981.4/638929.2, time step reduction 1 of 3 to 0.250 0 0 1
024: dt: 0.50
00, sse=633981.4, rms=4.420 (0.844%)
025: dt: 0.2500, sse=343680.8, rms=2.584 (41.539%)
026: dt: 0.2500, sse=296055.9, rms=2.066 (20.061%)
027: dt: 0.2500, sse=281494.5, rms=1.937 (6.247%)
028: dt: 0.2500, sse=279233.4, rms=1.841 (4.938%)
rms = 1.8113/1.8410, sse=283181.8/279233.4, time step reduction 2 of 3 to 0.125 0 1 1
029: dt: 0.25
00, sse=283181.8, rms=1.811 (1.616%)
030: dt: 0.1250, sse=277064.1, rms=1.732 (4.391%)
rms = 1.7234/1.7317, sse=289166.7/277064.1, time step reduction 3 of 3 to 0.062 0 1 1
031: dt: 0.12
50, sse=289166.7, rms=1.723 (0.478%)
maximum number of reductions reached, breaking from loop
positioning took 1.1 minutes
done positioning surface
Iteration 2 ================================
=========
n_averages=1, current_sigma=0.5
Freezing midline and others
Ripping frozen voxels
INFO: ri
p surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6401
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6455, nmarked2=0, nripped=6455
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247
M
RISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new
():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outsid
e_low = 58.4975320;
outside_hi = 118.5830610;
sigma = 0.5;
max_thickness = 10;
step_size=0
.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPea
kD2=0
nvertices=119704
Gdiag_no=-1
VMPeak = 1853412
vno start=0, stop=119704
#SI# sigma=0.5
had to be increased for 207 vertices, nripped=6455
mean border=87.9, 600 (441) missing vertices, mea
n dist -0.1 [0.1 (%83.9)->0.1 (%16.1))]
%90 local maxima, % 4 large gradients and % 0 min vals, 0 gr
adients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0503 min
Finding expans
ion regions
mean absolute distance = 0.14 +- 0.22
672 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=05768, nav=1, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=563330.1, rms=3.919
032: dt: 0.5000, sse=540470.8, rms=3.810 (2.783%)
rms = 4.2058/3.8104, sse=598107.7/540470.8, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
033: dt: 0.2500, sse=344948.0, rms=2.515 (33.997%)
034: dt: 0.2500, sse=301181.1, rms=1.981 (21.233%)
035: dt: 0.2500, sse=286580.6, rms=1.833 (7.489%)
036: dt: 0.2500, sse=271211.7, rms=1.782 (2.761%)
rms = 1.7667/1.7820, sse=268138.4/271211.7, time step reduction 2 of 3 to 0.125 0 0 1
037: dt: 0.25
00, sse=268138.3, rms=1.767 (0.856%)
038: dt: 0.1250, sse=267340.6, rms=1.697 (3.959%)
rms = 1.6956/1.6968, sse=268880.2/267340.6, time step reduction 3 of 3 to 0.062 0 1 1
039: dt: 0.12
50, sse=268880.2, rms=1.696 (0.072%)
maximum number of reductions reached, breaking from loop
positioning took 0.9 minutes
done positioning surface
Iteration 3 ================================
=========
n_averages=0, current_sigma=0.25
Freezing midline and others
Ripping frozen voxels
INFO: r
ip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6455
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6471, nmarked2=0, nripped=6471
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 24
7
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues
_new():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
ou
tside_low = 58.4975320;
outside_hi = 118.5830610;
sigma = 0.25;
max_thickness = 10;
step_s
ize=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFir
stPeakD2=0
nvertices=119704
Gdiag_no=-1
VMPeak = 1998052
vno start=0, stop=119704
#SI# sigma
=0.25 had to be increased for 172 vertices, nripped=6471
mean border=88.3, 634 (426) missing vertice
s, mean dist -0.0 [0.1 (%56.0)->0.1 (%44.0))]
%92 local maxima, % 3 large gradients and % 0 min vals
, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0373 min
Finding expansion regions
mean absolute distance = 0.09 +- 0.16
928 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=05768, nav=0, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=274098.7, rms=1.773
rms = 2.1562/1.7727, sse=316265.9/274098.7, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
040: dt: 0.2500, sse=258367.5, rms=1.580 (10.875%)
rms = 1.5568/1.5800, sse=262152.4/258367.5, time step reduction 2 of 3 to 0.125 0 1 1
041: dt: 0.25
00, sse=262152.4, rms=1.557 (1.464%)
rms = 1.5396/1.5568, sse=252327.8/262152.4, time step reduction 3 of 3 to 0.062 0 0 1
042: dt: 0.12
50, sse=252327.8, rms=1.540 (1.108%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface 5.04 minutes
Writing output to ../surf/lh.white.preaparc
#VMPC# mris_plac
e_surfaces VmPeak 2034912
mris_place_surface done
8.0.0
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --
wm wm.mgz --threads 2 --invol brain.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --whi
te --seg aseg.presurf.mgz --nsmooth 5
Reading in input surface ../surf/rh.orig
Smoothing surface before ripping with 5 iterations
Area
236114 0.26906 0.06155 0.019796 0.5839
Corner 708342 60.00000 9.16405 14.150339 132.9291
Edge
354171 0.79190 0.11130 0.126426 1.4359
Hinge 354171 6.38883 6.12254 0.000028 109.3791
Not reading in aparc
Reading in input volume brain.mgz
Reading in seg volume aseg.presurf.mgz
Readin
g in wm volume wm.mgz
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
MRIfindBrightNonWM(): 0 brigh
t non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRIm
ask(): AllowDiffGeom = 1
Ripping frozen voxels
INFO: rip surface needed but not specified, so using
input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6253, nmarked2=0, nripped=6253
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs()
: -2 2 0.5 ripped 0
opt weights int=0.2 loc=0 rep=5 nspr=0.3 curv=1
vertex 59030: xyz = (47.7904,3.4
8663,45.999) oxyz = (47.7904,3.48663,45.999) wxzy = (47.7904,3.48663,45.999) pxyz = (0,0,0)
CBVO Creating mask 118059
n_averages 4
Iteration 0 =========================================
n_avera
ges=4, current_sigma=2
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed bu
t not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhi
biting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0
# MRISripMidline(): nripped=6253
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6253, nmarked2=0, nripped=6253
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247
MRISripSe
gs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
i
nside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low =
58.4975320;
outside_hi = 118.5830610;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP
_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nv
ertices=118059
Gdiag_no=-1
VMPeak = 819112
vno start=0, stop=118059
#SI# sigma=2 had to be inc
reased for 297 vertices, nripped=6253
mean border=78.2, 504 (504) missing vertices, mean dist 0.4 [0
.7 (%33.3)->0.9 (%66.7))]
%63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignore
d
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1260 min
Finding expansion regions
mean absolute distance = 0.82 +- 0.96
4004 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=05768, nav=4, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat
0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisph
ere 1
randomSeed 0
000: dt: 0.0000, sse=5340391.5, rms=15.302
001: dt: 0.5000, sse=3277513.5, rms=11.899 (22.241%)
002: dt: 0.5000, sse=2071056.0, rms=9.345 (21.460%)
003: dt: 0.5000, sse=1377465.0, rms=7.495 (19.804%)
004: dt: 0.5000, sse=986948.8, rms=6.202 (17.240%)
005: dt: 0.5000, sse=762341.6, rms=5.335 (13.987%)
006: dt: 0.5000, sse=634469.4, rms=4.754 (10.888%)
007: dt: 0.5000, sse=564188.5, rms=4.387 (7.727%)
008: dt: 0.5000, sse=518159.7, rms=4.148 (5.438%)
009: dt: 0.5000, sse=492851.1, rms=4.015 (3.204%)
010: dt: 0.5000, sse=479454.6, rms=3.922 (2.314%)
rms = 3.8790/3.9223, sse=475528.8/479454.6, time step reduction 1 of 3 to 0.250 0 0 1
011: dt: 0.50
00, sse=475528.8, rms=3.879 (1.104%)
012: dt: 0.2500, sse=293265.3, rms=2.600 (32.974%)
013: dt: 0.2500, sse=250123.5, rms=2.232 (14.155%)
014: dt: 0.2500, sse=237809.3, rms=2.117 (5.159%)
015: dt: 0.2500, sse=231912.0, rms=2.040 (3.621%)
rms = 1.9945/2.0401, sse=228334.8/231912.0, time step reduction 2 of 3 to 0.125 0 0 1
016: dt: 0.25
00, sse=228334.8, rms=1.995 (2.236%)
017: dt: 0.1250, sse=222814.7, rms=1.940 (2.756%)
rms = 1.9211/1.9395, sse=221731.0/222814.7, time step reduction 3 of 3 to 0.062 0 0 1
018: dt: 0.12
50, sse=221731.0, rms=1.921 (0.952%)
maximum number of reductions reached, breaking from loop
positioning took 2.0 minutes
done positioning surface
Iteration 1 ================================
=========
n_averages=2, current_sigma=1
Freezing midline and others
Ripping frozen voxels
INFO: rip
surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6253
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6370, nmarked2=0,
nripped=6370
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247
MRISr
ipSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_lo
w = 58.4975320;
outside_hi = 118.5830610;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdiag_no=-1
VMPeak = 1635988
vno start=0, stop=118059
#SI# sigma=1 had to b
e increased for 201 vertices, nripped=6370
mean border=85.1, 500 (425) missing vertices, mean dist -
0.3 [0.4 (%90.8)->0.2 (%9.2))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients i
gnored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0830 min
Finding expansion regions
mean absolute distance = 0.35 +- 0.39
1425 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=05768, nav=2, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=1738170.6, rms=8.358
019: dt: 0.5000, sse=814981.6, rms=5.291 (36.689%)
020: dt: 0.5000, sse=635876.1, rms=4.495 (15.040%)
021: dt: 0.5000, sse=611513.5, rms=4.384 (2.482%)
rms = 4.4389/4.3839, sse=623207.9/611513.5, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
022: dt: 0.2500, sse=369022.1, rms=2.882 (34.256%)
023: dt: 0.2500, sse=288840.2, rms=2.159 (25.086%)
024: dt: 0.2500, sse=268470.0, rms=1.927 (10.735%)
025: dt: 0.2500, sse=262671.4, rms=1.851 (3.941%)
rms = 1.8030/1.8514, sse=259058.1/262671.4, time step reduction 2 of 3 to 0.125 0 0 1
026: dt: 0.25
00, sse=259058.1, rms=1.803 (2.613%)
027: dt: 0.1250, sse=251677.8, rms=1.730 (4.067%)
rms = 1.7215/1.7297, sse=251121.2/251677.8, time step reduction 3 of 3 to 0.062 0 0 1
028: dt: 0.12
50, sse=251121.2, rms=1.722 (0.471%)
maximum number of reductions reached, breaking from loop
positioning took 1.1 minutes
done positioning surface
Iteration 2 ================================
=========
n_averages=1, current_sigma=0.5
Freezing midline and others
Ripping frozen voxels
INFO: ri
p surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6370
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6404, nmarked2=0,
nripped=6404
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247
M
RISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new
():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outsid
e_low = 58.4975320;
outside_hi = 118.5830610;
sigma = 0.5;
max_thickness = 10;
step_size=0
.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPea
kD2=0
nvertices=118059
Gdiag_no=-1
VMPeak = 1832908
vno start=0, stop=118059
#SI# sigma=0.5
had to be increased for 139 vertices, nripped=6404
mean border=87.9, 525 (416) missing vertices, mea
n dist -0.1 [0.1 (%82.7)->0.1 (%17.3))]
%91 local maxima, % 3 large gradients and % 0 min vals, 0 gr
adients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0474 min
Finding expans
ion regions
mean absolute distance = 0.13 +- 0.20
763 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=05768, nav=1, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=477859.8, rms=3.662
rms = 3.6767/3.6617, sse=504978.9/477859.8, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
029: dt: 0.2500, sse=322261.9, rms=2.514 (31.349%)
030: dt: 0.2500, sse=247583.4, rms=1.701 (32.315%)
031: dt: 0.2500, sse=239242.8, rms=1.603 (5.814%)
032: dt: 0.2500, sse=237037.3, rms=1.550 (3.261%)
rms = 1.5382/1.5503, sse=237369.0/237037.3, time step reduction 2 of 3 to 0.125 0 1 1
033: dt: 0.25
00, sse=237369.0, rms=1.538 (0.781%)
034: dt: 0.1250, sse=233170.9, rms=1.468 (4.552%)
rms = 1.4649/1.4682, sse=234271.0/233170.9, time step reduction 3 of 3 to 0.062 0 1 1
035: dt: 0.12
50, sse=234271.0, rms=1.465 (0.221%)
maximum number of reductions reached, breaking from loop
positioning took 0.8 minutes
done positioning surface
Iteration 3 ================================
=========
n_averages=0, current_sigma=0.25
Freezing midline and others
Ripping frozen voxels
INFO: r
ip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6404
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6419, nmarked2=0,
nripped=6419
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 24
7
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues
_new():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
ou
tside_low = 58.4975320;
outside_hi = 118.5830610;
sigma = 0.25;
max_thickness = 10;
step_s
ize=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFir
stPeakD2=0
nvertices=118059
Gdiag_no=-1
VMPeak = 1940492
vno start=0, stop=118059
#SI# sigma
=0.25 had to be increased for 112 vertices, nripped=6419
mean border=88.3, 534 (413) missing vertice
s, mean dist -0.0 [0.1 (%55.2)->0.1 (%44.8))]
%92 local maxima, % 2 large gradients and % 0 min vals
, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0349 min
Finding
expansion regions
mean absolute distance = 0.09 +- 0.14
897 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=05768, nav=0, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=231827.9, rms=1.441
rms = 1.8684/1.4406, sse=266453.7/231827.9, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
036: dt: 0.2500, sse=217051.8, rms=1.201 (16.635%)
rms = 1.1631/1.2009, sse=223511.9/217051.8, time step reduction 2 of 3 to 0.125 0 1 1
037: dt: 0.25
00, sse=223511.9, rms=1.163 (3.149%)
rms = 1.1428/1.1631, sse=226263.1/223511.9, time step reduction 3 of 3 to 0.062 0 1 1
038: dt: 0.12
50, sse=226263.1, rms=1.143 (1.750%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface 4.60 minutes
Writing output to ../surf/rh.white.preaparc
#VMPC# mris_plac
e_surfaces VmPeak 1977276
mris_place_surface done
8.0.0
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --
wm wm.mgz --threads 2 --invol brain.mgz --rh --i ../surf/rh.orig --o ../surf/rh.white.preaparc --whi
te --seg aseg.presurf.mgz --nsmooth 5
Reading in input surface ../surf/rh.orig
Smoothing surface before ripping with 5 iterations
Area
236114 0.26906 0.06155 0.019796 0.5839
Corner 708342 60.00000 9.16405 14.150339 132.9291
Edge
354171 0.79190 0.11130 0.126426 1.4359
Hinge 354171 6.38883 6.12254 0.000028 109.3791
Not reading in aparc
Reading in input volume brain.mgz
Reading in seg volume aseg.presurf.mgz
Readin
g in wm volume wm.mgz
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
MRIfindBrightNonWM(): 0 brigh
t non-wm voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRIm
ask(): AllowDiffGeom = 1
Ripping frozen voxels
INFO: rip surface needed but not specified, so using
input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6253, nmarked2=0, nripped=6253
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs()
: -2 2 0.5 ripped 0
opt weights int=0.2 loc=0 rep=5 nspr=0.3 curv=1
vertex 59030: xyz = (47.7904,3.4
8663,45.999) oxyz = (47.7904,3.48663,45.999) wxzy = (47.7904,3.48663,45.999) pxyz = (0,0,0)
CBVO Creating mask 118059
n_averages 4
Iteration 0 =========================================
n_avera
ges=4, current_sigma=2
Freezing midline and others
Ripping frozen voxels
INFO: rip surface needed bu
t not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhi
biting deformation at non-cortical midline structures...
which=1, fix_mtl=0, using annot = 0
#FML0
# MRISripMidline(): nripped=6253
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6253, nmarked2=0, nripped=6253
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247
MRISripSe
gs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
i
nside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low =
58.4975320;
outside_hi = 118.5830610;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP
_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nv
ertices=118059
Gdiag_no=-1
VMPeak = 819108
vno start=0, stop=118059
#SI# sigma=2 had to be inc
reased for 297 vertices, nripped=6253
mean border=78.2, 504 (504) missing vertices, mean dist 0.4 [0
.7 (%33.3)->0.9 (%66.7))]
%63 local maxima, %31 large gradients and % 0 min vals, 0 gradients ignore
d
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1291 min
Finding expansion regions
mean absolute distance = 0.82 +- 0.96
4004 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=05768, nav=4, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat
0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisph
ere 1
randomSeed 0
000: dt: 0.0000, sse=5340391.5, rms=15.302
001: dt: 0.5000, sse=3277513.5, rms=11.899 (22.241%)
002: dt: 0.5000, sse=2071056.0, rms=9.345 (21.460%)
003: dt: 0.5000, sse=1377465.0, rms=7.495 (19.804%)
004: dt: 0.5000, sse=986948.8, rms=6.202 (17.240%)
005: dt: 0.5000, sse=762341.6, rms=5.335 (13.987%)
006: dt: 0.5000, sse=634469.4, rms=4.754 (10.888%)
007: dt: 0.5000, sse=564188.5, rms=4.387 (7.727%)
008: dt: 0.5000, sse=518159.7, rms=4.148 (5.438%)
009: dt: 0.5000, sse=492851.1, rms=4.015 (3.204%)
010: dt: 0.5000, sse=479454.6, rms=3.922 (2.314%)
rms = 3.8790/3.9223, sse=475528.8/479454.6, time step reduction 1 of 3 to 0.250 0 0 1
011: dt: 0.50
00, sse=475528.8, rms=3.879 (1.104%)
012: dt: 0.2500, sse=293265.3, rms=2.600 (32.974%)
013: dt: 0.2500, sse=250123.5, rms=2.232 (14.155%)
014: dt: 0.2500, sse=237809.3, rms=2.117 (5.159%)
015: dt: 0.2500, sse=231912.0, rms=2.040 (3.621%)
rms = 1.9945/2.0401, sse=228334.8/231912.0, time step reduction 2 of 3 to 0.125 0 0 1
016: dt: 0.25
00, sse=228334.8, rms=1.995 (2.236%)
017: dt: 0.1250, sse=222814.7, rms=1.940 (2.756%)
rms = 1.9211/1.9395, sse=221731.0/222814.7, time step reduction 3 of 3 to 0.062 0 0 1
018: dt: 0.12
50, sse=221731.0, rms=1.921 (0.952%)
maximum number of reductions reached, breaking from loop
positioning took 2.0 minutes
done positioning surface
Iteration 1 ================================
=========
n_averages=2, current_sigma=1
Freezing midline and others
Ripping frozen voxels
INFO: rip
surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6253
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6370, nmarked2=0,
nripped=6370
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247
MRISr
ipSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_lo
w = 58.4975320;
outside_hi = 118.5830610;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdiag_no=-1
VMPeak = 1636028
vno start=0, stop=118059
#SI# sigma=1 had to b
e increased for 201 vertices, nripped=6370
mean border=85.1, 500 (425) missing vertices, mean dist -
0.3 [0.4 (%90.8)->0.2 (%9.2))]
%84 local maxima, %11 large gradients and % 0 min vals, 0 gradients i
gnored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0832 min
Finding expansion regions
mean absolute distance = 0.35 +- 0.39
1425 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=05768, nav=2, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=1738170.6, rms=8.358
019: dt: 0.5000, sse=814981.6, rms=5.291 (36.689%)
020: dt: 0.5000, sse=635876.1, rms=4.495 (15.040%)
021: dt: 0.5000, sse=611513.5, rms=4.384 (2.482%)
rms = 4.4389/4.3839, sse=623207.9/611513.5, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
022: dt: 0.2500, sse=369022.1, rms=2.882 (34.256%)
023: dt: 0.2500, sse=288840.2, rms=2.159 (25.086%)
024: dt: 0.2500, sse=268470.0, rms=1.927 (10.735%)
025: dt: 0.2500, sse=262671.4, rms=1.851 (3.941%)
rms = 1.8030/1.8514, sse=259058.1/262671.4, time step reduction 2 of 3 to 0.125 0 0 1
026: dt: 0.25
00, sse=259058.1, rms=1.803 (2.613%)
027: dt: 0.1250, sse=251677.8, rms=1.730 (4.067%)
rms = 1.7215/1.7297, sse=251121.2/251677.8, time step reduction 3 of 3 to 0.062 0 0 1
028: dt: 0.12
50, sse=251121.2, rms=1.722 (0.471%)
maximum number of reductions reached, breaking from loop
positioning took 1.1 minutes
done positioning surface
Iteration 2 ================================
=========
n_averages=1, current_sigma=0.5
Freezing midline and others
Ripping frozen voxels
INFO: ri
p surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6370
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6404, nmarked2=0,
nripped=6404
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247
M
RISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues_new
():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
outsid
e_low = 58.4975320;
outside_hi = 118.5830610;
sigma = 0.5;
max_thickness = 10;
step_size=0
.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPea
kD2=0
nvertices=118059
Gdiag_no=-1
VMPeak = 1865032
vno start=0, stop=118059
#SI# sigma=0.5
had to be increased for 139 vertices, nripped=6404
mean border=87.9, 525 (416) missing vertices, mea
n dist -0.1 [0.1 (%82.7)->0.1 (%17.3))]
%91 local maxima, % 3 large gradients and % 0 min vals, 0 gr
adients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0515 min
Finding expans
ion regions
mean absolute distance = 0.13 +- 0.20
763 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=05768, nav=1, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=477859.8, rms=3.662
rms = 3.6767/3.6617, sse=504978.9/477859.8, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
029: dt: 0.2500, sse=322261.9, rms=2.514 (31.349%)
030: dt: 0.2500, sse=247583.4, rms=1.701 (32.315%)
031: dt: 0.2500, sse=239242.8, rms=1.603 (5.814%)
032: dt: 0.2500, sse=237037.3, rms=1.550 (3.261%)
rms = 1.5382/1.5503, sse=237369.0/237037.3, time step reduction 2 of 3 to 0.125 0 1 1
033: dt: 0.25
00, sse=237369.0, rms=1.538 (0.781%)
034: dt: 0.1250, sse=233170.9, rms=1.468 (4.552%)
rms = 1.4649/1.4682, sse=234271.0/233170.9, time step reduction 3 of 3 to 0.062 0 1 1
035: dt: 0.12
50, sse=234271.0, rms=1.465 (0.221%)
maximum number of reductions reached, breaking from loop
positioning took 0.8 minutes
done positioning surface
Iteration 3 ================================
=========
n_averages=0, current_sigma=0.25
Freezing midline and others
Ripping frozen voxels
INFO: r
ip surface needed but not specified, so using input surface
Freezing midline and others
Entering: MRISripMidline(): inhibiting deformation at non-cortical midline structures...
which=1,
fix_mtl=0, using annot = 0
#FML0# MRISripMidline(): nripped=6404
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 2 vertices from ripped group in thread:0
removing 3 vertices from ripped group in thread:0
removing 4 vertices from ripped group in thread:0
#FML# MRISripMidline(): nmarked=6419, nmarked2=0,
nripped=6419
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247 247 247 247 24
7
MRISripSegs(): -2 2 0.5 ripped 0
Computing target border values
Entering MRIScomputeBorderValues
_new():
inside_hi = 120.0000000;
border_hi = 118.5830610;
border_low = 69.0000000;
ou
tside_low = 58.4975320;
outside_hi = 118.5830610;
sigma = 0.25;
max_thickness = 10;
step_s
ize=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFir
stPeakD2=0
nvertices=118059
Gdiag_no=-1
VMPeak = 1944136
vno start=0, stop=118059
#SI# sigma
=0.25 had to be increased for 112 vertices, nripped=6419
mean border=88.3, 534 (413) missing vertice
s, mean dist -0.0 [0.1 (%55.2)->0.1 (%44.8))]
%92 local maxima, % 2 large gradients and % 0 min vals
, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0359 min
Finding
expansion regions
mean absolute distance = 0.09 +- 0.14
897 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=05768, nav=0, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=231827.9, rms=1.441
rms = 1.8684/1.4406, sse=266453.7/231827.9, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
036: dt: 0.2500, sse=217051.8, rms=1.201 (16.635%)
rms = 1.1631/1.2009, sse=223511.9/217051.8, time step reduction 2 of 3 to 0.125 0 1 1
037: dt: 0.25
00, sse=223511.9, rms=1.163 (3.149%)
rms = 1.1428/1.1631, sse=226263.1/223511.9, time step reduction 3 of 3 to 0.062 0 1 1
038: dt: 0.12
50, sse=226263.1, rms=1.143 (1.750%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface 4.59 minutes
Writing output to ../surf/rh.white.preaparc
#VMPC# mris_plac
e_surfaces VmPeak 1980920
mris_place_surface done
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
3 non-cortica
l segments detected
only using segment with 6127 vertices
erasing segment 1 (vno[0] = 62774)
erasing
segment 2 (vno[0] = 71041)
Generating cortex label... RemoveHipAmgy=1
NucAccIsMedialWall=0
mris->useRealRAS=0
5 non-cortica
l segments detected
only using segment with 5373 vertices
erasing segment 1 (vno[0] = 39713)
erasing
segment 2 (vno[0] = 60839)
erasing segment 3 (vno[0] = 62774)
erasing segment 4 (vno[0] = 71041)
Generating cortex label... RemoveHipAmgy=0
NucAccIsMedialWall=0
mris->useRealRAS=0
4 non-cortica
l segments detected
only using segment with 6084 vertices
erasing segment 1 (vno[0] = 65320)
erasing
segment 2 (vno[0] = 67625)
erasing segment 3 (vno[0] = 70131)
Generating cortex label... RemoveHipAmgy=1
NucAccIsMedialWall=0
mris->useRealRAS=0
6 non-cortica
l segments detected
only using segment with 5245 vertices
erasing segment 1 (vno[0] = 49754)
erasing
segment 2 (vno[0] = 51201)
erasing segment 3 (vno[0] = 65320)
erasing segment 4 (vno[0] = 70131)
er
asing segment 5 (vno[0] = 115512)
smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
smoothing for 3 iterations
setting seed for random number generator to 1234
smoothing surface tessellation for 3 iterations...
smoothing complete - recomputing first and second fundamental forms...
Reading ./lh.smoothwm
avg radius = 46.0 mm, total surface area = 74957 mm^2
step 005: RMS=0.114 (target=0.015)
step 010: RMS=0.086 (target=0.015)
step 015: RMS=0.070 (target=0.015)
step 020: RMS=0.058 (target=0.015)
step 025: RMS=0.048 (target=0.015)
step 030: RMS=0.039 (target=0.015)
step 035: RMS=0.032 (target=0.015)
step 040: RMS=0.027 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.021 (target=0.015)
step 055: RMS=0.020 (target=0.015)
step 060: RMS=0.019 (target=0.015) writing inflated surface to ./lh.inflated
writing sulcal depths to ./lh.sulc
inflation complete.
inflation took 0.4 minutes
mris_inflate utimesec 22.313692
mris_inflate stimesec 0.839264
mris
_inflate ru_maxrss 185052
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_is
rss 0
mris_inflate ru_minflt 474901
mris_inflate ru_majflt 1
mris_inflate ru_nswap 0
mris_
inflate ru_inblock 0
mris_inflate ru_oublock 9360
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrc
v 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 58
mris_inflate ru_nivcsw 379
Reading ./rh.smoothwm
avg radius = 46.7 mm, total surface area = 73982 mm^2
step 005: RMS=0.114 (target=0.015)
step 010: RMS=0.084 (target=0.015)
step 015: RMS=0.070 (target=0.015)
step 020: RMS=0.057 (target=0.015)
step 025: RMS=0.047 (target=0.015)
step 030: RMS=0.038 (target=0.015)
step 035: RMS=0.032 (target=0.015)
step 040: RMS=0.028 (target=0.015)
step 045: RMS=0.024 (target=0.015)
step 050: RMS=0.022 (target=0.015)
step 055: RMS=0.020 (target=0.015)
step 060: RMS=0.018 (target=0.015) writing inflated surface to ./rh.inflated
writing sulcal depths to ./rh.sulc
inflation complete.
inflation took 0.4 minutes
mris_inflate utimesec 20.806546
mris_inflate stimesec 0.971749
mris
_inflate ru_maxrss 182512
mris_inflate ru_ixrss 0
mris_inflate ru_idrss 0
mris_inflate ru_is
rss 0
mris_inflate ru_minflt 483171
mris_inflate ru_majflt 0
mris_inflate ru_nswap 0
mris_
inflate ru_inblock 0
mris_inflate ru_oublock 9240
mris_inflate ru_msgsnd 0
mris_inflate ru_msgrc
v 0
mris_inflate ru_nsignals 0
mris_inflate ru_nvcsw 56
mris_inflate ru_nivcsw 229
setting seed for random number generator to 1234
total integrated curvature = 29.600*4pi (371.967) --> -29 handles
ICI = 123.8, FI = 1203.4, variation=18776.865
writing Gaussian curvature to ./lh.white.preaparc.K...
done.
writing mean curvature to ./lh.white.preaparc.H...
lh.white.preaparc.H
mris_curvature done.
setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature patterns 5 times.
sampling 10 neighbors out to a d
istance of 10 mm
200 vertices thresholded to be in k1 ~ [-0.19 0.32], k2 ~ [-0.11 0.05]
total integrated curvature =
0.680*4pi (8.542) --> 0 handles
ICI = 1.4, FI = 7.1, variation=126.409
112 vertices thresholded to be in [-0.00 0.02]
writing Gaussian curvature to ./lh.inflated.K...
thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
150 vertices thresholded to be in [-0.11 0.16]
done.
writing mean curvature to ./lh.inflated.H...
curvature mean = -0.016, std = 0.020
lh.inflated.
H
mris_curvature done.
setting seed for random number generator to 1234
total integrated curvature = 30.382*4pi (381.797) --> -29 handles
ICI = 124.0, FI = 1199.0, variation=18724.514
writing Gaussian curvature to ./rh.white.preaparc.K...
done.
writing mean curvature to ./rh.white.preaparc.H...
rh.white.preaparc.H
mris_curvature done.
setting seed for random number generator to 1234
normalizing curvature values.
averaging curvature p
atterns 5 times.
sampling 10 neighbors out to a distance of 10 mm
230 vertices thresholded to be in k1 ~ [-0.20 0.32], k2 ~ [-0.08 0.06]
total integrated curvature =
0.708*4pi (8.902) --> 0 handles
ICI = 1.4, FI = 7.5, variation=132.108
120 vertices thresholded to be in [-0.00 0.01]
writing Gaussian curvature to ./rh.inflated.K...
thresholding curvature at 99.90% level
curvature mean = 0.000, std = 0.001
145 vertices thresholded to be in [-0.13 0.16]
done.
writing mean curvature to ./rh.inflated.H...
curvature mean = -0.017, std = 0.021
rh.inflated.
H
mris_curvature done.
setting seed for random number genererator to 1234
version: 8.0.0
available threads: 1
reading original vertex positions...
projecting onto sphere...
surface projected - minimizing metric distortion...
scaling brain by 0.307...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=05768, na
v=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
s
cale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
n
surfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphe
re 0
randomSeed 1234
--------------------
mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %39.27
pass 1: epoch 2 of 3 starting distance error %18.63
unfolding complete - removing small folds...
sta
rting distance error %18.59
removing remaining folds...
final distance error %18.62
MRISunfold() ret
urn, current seed 1234
-01: dt=0.0000, 0 negative triangles VmPeak 503360
writing spherical brain to ../surf/lh.sphere
spherical transformation took 0.1075 hours
FSRUNTIME@ mris_sphere 0.1075 hours 1 threads
#VMPC# mri
s_sphere VmPeak 503360
mris_sphere done
setting seed for random number genererator to 1234
version: 8.0.0
available threads: 1
reading original vertex positions...
projecting onto sphere...
surface projected - minimizing metric distortion...
scaling brain by 0.307...
MRISunfold() max_passes = 1 -------
tol=5.0e-01, sigma=0.0, host=05768, na
v=1024, nbrs=2, l_area=1.000, l_dist=1.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
s
cale 1.000000
desired_rms_height -1.000000
momentum 0.900000
nbhd_size 7
max_nbrs 8
niterations 25
n
surfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphe
re 1
randomSeed 1234
--------------------
mrisRemoveNegativeArea()
pass 1: epoch 1 of 3 starting distance error %40.62
pass 1: epoch 2 of 3 starting distance error %18.75
unfolding complete - removing small folds...
sta
rting distance error %18.69
removing remaining folds...
final distance error %18.73
MRISunfold() ret
urn, current seed 1234
-01: dt=0.0000, 0 negative triangles VmPeak 500040
writing spherical brain to ../surf/rh.sphere
spherical transformation took 0.1068 hours
FSRUNTIME@ mris_sphere 0.1068 hours 1 threads
#VMPC# mri
s_sphere VmPeak 500040
mris_sphere done
using smoothwm curvature for final alignment
cwd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/Tes
tSubject/surf
cmdline mris_register -curv ./lh.sphere /opt/freesurfer-8.0.0/average/lh.folding.atlas
.acfb40.noaparc.i12.2016-08-02.tif ./lh.sphere.reg -threads 2
0 inflated.H
1 sulc
2 smoothwm (comp
uted)
8.0.0
8.0.0
reading surface from ./lh.sphere...
reading template parameterization from /opt/freesurfer-8.0.0/average/lh.folding.atlas.acfb40.noaparc
.i12.2016-08-02.tif...
MRISregister() -------
max_passes = 4
min_degrees = 0.500000
max_degrees = 64.000000
nangles = 8
tol=5.0e-01, sigma=0.0, host=05768, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1
.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smo
oth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000
000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurface
s 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 0
randomSeed 0
tol=5.0e-01, sigma=0.0, host=05768, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.
000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading lh.sulc
tol=1.0e+00, sigma=0.5, host=05768, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.
000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
curvature mean = 0.000, std = 5.440
curvature mean = 0.030, std = 0.819
curvature mean = 0.014, std
= 0.875
Starting MRISrigidBodyAlignGlobal()
Starting new MRISrigidBodyAlignGlobal_findMinSSE()
new
MRISrigidBodyAlignGlobal_findMinSSE min @ (4.50, -7.00, -0.50) sse = 213303.4, elapsed since starti
ng=0.3674 min
MRISrigidBodyAlignGlobal() done 0.37 min
curvature mean = 0.015, std = 0.836
curvatu
re mean = 0.006, std = 0.954
curvature mean = 0.012, std = 0.844
curvature mean = 0.002, std = 0.982
curvature mean = 0.012, std = 0.847
curvature mean = 0.001, std = 0.993
2 Reading smoothwm
curvatur
e mean = -0.020, std = 0.249
curvature mean = 0.045, std = 0.246
curvature mean = 0.059, std = 0.416
curvature mean = 0.040, std = 0.304
curvature mean = 0.027, std = 0.623
curvature mean = 0.040, std
= 0.330
curvature mean = 0.013, std = 0.762
curvature mean = 0.040, std = 0.342
curvature mean = 0.
003, std = 0.858
MRISregister() return, current seed 0
writing registered surface to ./lh.sphere.reg...
-01: dt=0.0000, 0 negative triangles VmPeak 493000
registration took 0.13 hours
#VMPC# mris_regis
ter VmPeak 493000
FSRUNTIME@ mris_register 0.1325 hours 1 threads
using smoothwm curvature for final alignment
cwd /home/jovyan/workspace/books/examples/structural_i
maging/data/structural/recon-all-clinical/TestSubject/surf
cmdline mris_register -curv ./rh.sphere /
opt/freesurfer-8.0.0/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ./rh.sphere.reg -thr
eads 2
0 inflated.H
1 sulc
2 smoothwm (computed)
8.0.0
8.0.0
reading surface from ./rh.sphere...
reading template parameterization from /opt/freesurfer-8.0.0/average/rh.folding.atlas.acfb40.noaparc
.i12.2016-08-02.tif...
MRISregister() -------
max_passes = 4
min_degrees = 0.500000
max_degrees = 64.000000
nangles = 8
tol=5.0e-01, sigma=0.0, host=05768, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1
.000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smo
oth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000
000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurface
s 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 1
randomSeed 0
tol=5.0e-01, sigma=0.0, host=05768, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.
000, l_corr=1.000, l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading rh.sulc
tol=1.0e+00, sigma=0.5, host=05768, nav=1024, nbrs=1, l_extern=10000.000, l_parea=0.200, l_nlarea=1.
000, l_corr=0.050, l_spring=0.500, l_dist=5.000
using quadratic fit line minimization
curvature mean = -0.000, std = 5.334
curvature mean = 0.038, std = 0.810
curvature mean = 0.013, std
= 0.879
Starting MRISrigidBodyAlignGlobal()
Starting new MRISrigidBodyAlignGlobal_findMinSSE()
ne
w MRISrigidBodyAlignGlobal_findMinSSE min @ (6.00, -4.50, 1.50) sse = 223942.8, elapsed since starti
ng=0.3880 min
MRISrigidBodyAlignGlobal() done 0.39 min
curvature mean = 0.004, std = 0.819
curvatu
re mean = 0.005, std = 0.954
curvature mean = -0.001, std = 0.826
curvature mean = 0.002, std = 0.98
2
curvature mean = -0.001, std = 0.829
curvature mean = 0.000, std = 0.993
2 Reading smoothwm
curvat
ure mean = -0.022, std = 0.253
curvature mean = 0.039, std = 0.239
curvature mean = 0.059, std = 0.4
12
curvature mean = 0.034, std = 0.296
curvature mean = 0.028, std = 0.620
curvature mean = 0.033, s
td = 0.322
curvature mean = 0.012, std = 0.762
curvature mean = 0.033, std = 0.334
curvature mean =
0.003, std = 0.858
MRISregister() return, current seed 0
writing registered surface to ./rh.sphere.reg...
-01: dt=0.0000, 0 negative triangles VmPeak 491644
registration took 0.11 hours
#VMPC# mris_regis
ter VmPeak 491644
FSRUNTIME@ mris_register 0.1114 hours 1 threads
reading surface from ./lh.white.preaparc...
writing curvature file ./lh.jacobian_white type -1
reading surface from ./rh.white.preaparc...
writing curvature file ./rh.jacobian_white type -1
averaging curvature patterns 5 times...
reading surface from ./lh.sphere.reg...
reading template parameterization from /opt/freesurfer-8.0.0/average/lh.folding.atlas.acfb40.noaparc
.i12.2016-08-02.tif...
writing curvature file to ./lh.avg_curv...
averaging curvature patterns 5 times...
reading surface from ./rh.sphere.reg...
reading template parameterization from /opt/freesurfer-8.0.0/average/rh.folding.atlas.acfb40.noaparc
.i12.2016-08-02.tif...
writing curvature file to ./rh.avg_curv...
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correc
t midline
8.0.0
8.0.0
reading atlas from /opt/freesurfer-8.0.0/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs.
..
reading color table from GCSA file....
average std = 0.8 using min determinant for regularizati
on = 0.006
0 singular and 342 ill-conditioned covariance matrices regularized
reading surface from /
home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubje
ct/surf/lh.smoothwm...
set_atable_from_ctable(): 36 entries
GCSA::load_default_data(): ninputs=1 su
lc_only=0 which_norm=0
labeling surface...
1104 labels changed using aseg
relabeling using gibbs priors...
000: 2831 changed, 119704 examined
...
001: 615 changed, 11918 examined...
002: 146 changed, 3452 examined...
003: 41 changed
, 881 examined...
004: 19 changed, 259 examined...
005: 8 changed, 119 examined...
006:
2 changed, 47 examined...
007: 1 changed, 12 examined...
008: 3 changed, 8 examined...
0
09: 1 changed, 13 examined...
010: 0 changed, 7 examined...
222 labels changed using aseg
000: 111 total segments, 55 labels (135 vertices) changed
001: 56 tota
l segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 3 changed)
ra
tionalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallo
sum label...
1693 vertices marked for relabeling...
1693 labels changed in reclassification.
writing output to ../label/lh.aparc.annot...
classification
took 0 minutes and 11 seconds.
setting seed for random number generator to 1234
using ../mri/aseg.presurf.mgz aseg volume to correc
t midline
8.0.0
8.0.0
reading atlas from /opt/freesurfer-8.0.0/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs.
..
reading color table from GCSA file....
average std = 0.7 using min determinant for regularizati
on = 0.004
0 singular and 309 ill-conditioned covariance matrices regularized
reading surface from /
home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubje
ct/surf/rh.smoothwm...
set_atable_from_ctable(): 36 entries
GCSA::load_default_data(): ninputs=1 su
lc_only=0 which_norm=0
labeling surface...
936 labels changed using aseg
relabeling using gibbs priors...
000: 2448 changed, 118059 examined.
..
001: 585 changed, 10604 examined...
002: 130 changed, 3353 examined...
003: 36 changed,
820 examined...
004: 14 changed, 231 examined...
005: 6 changed, 85 examined...
006:
0 changed, 38 examined...
198 labels changed using aseg
000: 81 total segments, 41 labels (104 vertices) changed
001: 40 total
segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 6 changed)
rat
ionalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallos
um label...
1536 vertices marked for relabeling...
1536 labels changed in reclassification.
writing output to ../label/rh.aparc.annot...
classification
took 0 minutes and 10 seconds.
8.0.0
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --
seg aseg.presurf.mgz --threads 2 --wm wm.mgz --invol brain.mgz --lh --i ../surf/lh.white.preaparc --
o ../surf/lh.white --white --nsmooth 0 --rip-label ../label/lh.cortex.label --rip-bg --rip-surf ../s
urf/lh.white.preaparc --aparc ../label/lh.aparc.annot
Reading in input surface ../surf/lh.white.preaparc
Not smoothing input surface
Area 239404 0.343
57 0.14060 0.003306 3.6449
Corner 718212 60.00000 14.48119 0.500695 177.1350
Edge 359106 0.9
0394 0.23231 0.028454 4.1785
Hinge 359106 9.99433 11.20261 0.000001 179.9892
Reading in aparc ../label/lh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entrie
s_to_read=36
Reading in input volume brain.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm
volume wm.mgz
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
MRIfindBrightNonWM(): 0 bright non-wm
voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): A
llowDiffGeom = 1
Ripping frozen voxels
Ripping vertices not in label ../label/lh.cortex.label
MRISri
pNotLabel() ripped 6447/119704 vertices (113257 unripped)
Reading in ripping surface ../surf/lh.whit
e.preaparc
Reading in aparc ../label/lh.aparc.annot for ripsurf
[DEBUG] CTABreadFromBinaryV2(): ct->
nentries=36, num_entries_to_read=36
Ripping BG
MRISripBasalGanglia(): 1 -2 2 0.5
MRISripBasalGanglia
(): 1 -2 2 0.5 ripped 619
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5)
segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
opt weights int=0.2 loc=0 rep=5 nspr=0.3 curv=1
vertex
59852: xyz = (-45.1845,1.55112,32.7057) oxyz = (-45.1845,1.55112,32.7057) wxzy = (-45.1845,1.55112,
32.7057) pxyz = (0,0,0)
CBVO Creating mask 119704
n_averages 4
Iteration 0 =========================================
n_avera
ges=4, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000
;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low = 58.4975320;
outside_h
i = 118.5830610;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdiag_n
o=-1
VMPeak = 913008
vno start=0, stop=119704
#SI# sigma=2 had to be increased for 98 vertices,
nripped=7066
mean border=78.0, 95 (95) missing vertices, mean dist 0.4 [2.0 (%5.3)->0.6 (%94.7))]
%5
7 local maxima, %37 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScompute
BorderValues_new() finished in 0.1281 min
Finding expansion regions
mean absolute distance = 0.65 +- 0.82
1219 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=05768, nav=4, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat
0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisph
ere 0
randomSeed 0
000: dt: 0.0000, sse=3275800.5, rms=11.695
001: dt: 0.5000, sse=1011866.8, rms=6.058 (48.195%)
002: dt: 0.5000, sse=543619.8, rms=3.992 (34.112%)
003: dt: 0.5000, sse=495977.8, rms=3.741 (6.285%)
004: dt: 0.5000, sse=471125.3, rms=3.566 (4.662%)
rms = 3.6832/3.5665, sse=492422.9/471125.3, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
005: dt: 0.2500, sse=334028.9, rms=2.581 (27.622%)
006: dt: 0.2500, sse=296467.6, rms=2.123 (17.771%)
007: dt: 0.2500, sse=282236.2, rms=1.950 (8.120%)
rms = 1.9109/1.9502, sse=271680.4/282236.2, time step reduction 2 of 3 to 0.125 0 0 1
008: dt: 0.25
00, sse=271680.4, rms=1.911 (2.018%)
009: dt: 0.1250, sse=266361.1, rms=1.857 (2.801%)
rms = 1.8440/1.8574, sse=264967.0/266361.1, time step reduction 3 of 3 to 0.062 0 0 1
010: dt: 0.12
50, sse=264967.0, rms=1.844 (0.719%)
maximum number of reductions reached, breaking from loop
positioning took 1.1 minutes
done positioning surface
Iteration 1 ================================
=========
n_averages=2, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000
;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low = 58.4975320;
outside_h
i = 118.5830610;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdiag_n
o=-1
VMPeak = 1597508
vno start=0, stop=119704
#SI# sigma=1 had to be increased for 82 vertices,
nripped=7066
mean border=84.9, 69 (36) missing vertices, mean dist -0.3 [0.4 (%90.3)->0.2 (%9.7))]
%81 local maxima, %13 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScompu
teBorderValues_new() finished in 0.0876 min
Finding expansion regions
mean absolute distance = 0.36 +- 0.41
775 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=05768, nav=2, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=1731440.4, rms=8.250
011: dt: 0.5000, sse=833712.3, rms=5.289 (35.894%)
012: dt: 0.5000, sse=639151.0, rms=4.411 (16.591%)
013: dt: 0.5000, sse=617923.3, rms=4.325 (1.969%)
rms = 4.4018/4.3245, sse=634381.7/617923.3, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
014: dt: 0.2500, sse=375433.4, rms=2.795 (35.362%)
015: dt: 0.2500, sse=299041.9, rms=2.068 (26.014%)
016: dt: 0.2500, sse=275089.9, rms=1.823 (11.860%)
017: dt: 0.2500, sse=268585.9, rms=1.740 (4.569%)
rms = 1.6948/1.7396, sse=264534.4/268585.9, time step reduction 2 of 3 to 0.125 0 0 1
018: dt: 0.25
00, sse=264534.3, rms=1.695 (2.572%)
019: dt: 0.1250, sse=256556.0, rms=1.618 (4.511%)
rms = 1.6083/1.6184, sse=260066.2/256556.0, time step reduction 3 of 3 to 0.062 0 1 1
020: dt: 0.12
50, sse=260066.2, rms=1.608 (0.626%)
maximum number of reductions reached, breaking from loop
positioning took 1.1 minutes
done positioning surface
Iteration 2 ================================
=========
n_averages=1, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000
;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low = 58.4975320;
outside_h
i = 118.5830610;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdiag
_no=-1
VMPeak = 1807456
vno start=0, stop=119704
#SI# sigma=0.5 had to be increased for 67 verti
ces, nripped=7066
mean border=87.8, 100 (27) missing vertices, mean dist -0.1 [0.1 (%84.3)->0.1 (%15
.7))]
%90 local maxima, % 4 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0496 min
Finding expansion regions
mean absolute distance = 0.14 +- 0.22
531 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=05768, nav=1, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=537026.6, rms=3.903
021: dt: 0.5000, sse=522406.3, rms=3.769 (3.438%)
rms = 4.1483/3.7690, sse=583631.7/522406.3, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
022: dt: 0.2500, sse=331022.1, rms=2.442 (35.198%)
023: dt: 0.2500, sse=282425.6, rms=1.881 (23.005%)
024: dt: 0.2500, sse=261649.5, rms=1.738 (7.577%)
025: dt: 0.2500, sse=258869.2, rms=1.684 (3.131%)
rms = 1.6707/1.6836, sse=260582.9/258869.2, time step reduction 2 of 3 to 0.125 0 1 1
026: dt: 0.25
00, sse=260582.9, rms=1.671 (0.768%)
027: dt: 0.1250, sse=250166.0, rms=1.603 (4.055%)
rms = 1.6000/1.6029, sse=250475.8/250166.0, time step reduction 3 of 3 to 0.062 0 1 1
028: dt: 0.12
50, sse=250475.8, rms=1.600 (0.183%)
maximum number of reductions reached, breaking from loop
positioning took 0.9 minutes
done positioning surface
Iteration 3 ================================
=========
n_averages=0, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000
;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low = 58.4975320;
outside_h
i = 118.5830610;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which =
1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdia
g_no=-1
VMPeak = 1849928
vno start=0, stop=119704
#SI# sigma=0.25 had to be increased for 43 ver
tices, nripped=7066
mean border=88.3, 147 (27) missing vertices, mean dist -0.0 [0.1 (%56.1)->0.1 (%
43.9))]
%91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0350 min
Finding expansion regions
mean absolute distance = 0.09 +- 0.15
737 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=05768, nav=0, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=254828.0, rms=1.674
rms = 2.1163/1.6743, sse=301593.4/254828.1, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
029: dt: 0.2500, sse=241194.4, rms=1.474 (11.965%)
rms = 1.4587/1.4739, sse=240520.7/241194.4, time step reduction 2 of 3 to 0.125 0 0 1
030: dt: 0.25
00, sse=240520.7, rms=1.459 (1.032%)
rms = 1.4473/1.4587, sse=238959.7/240520.7, time step reduction 3 of 3 to 0.062 0 0 1
031: dt: 0.12
50, sse=238959.7, rms=1.447 (0.782%)
maximum number of reductions reached, breaking from loop
positioning took 0.4 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface 3.90 minutes
Writing output to ../surf/lh.white
#VMPC# mris_place_surface
s VmPeak 1918036
mris_place_surface done
8.0.0
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --
seg aseg.presurf.mgz --threads 2 --wm wm.mgz --invol brain.mgz --rh --i ../surf/rh.white.preaparc --
o ../surf/rh.white --white --nsmooth 0 --rip-label ../label/rh.cortex.label --rip-bg --rip-surf ../s
urf/rh.white.preaparc --aparc ../label/rh.aparc.annot
Reading in input surface ../surf/rh.white.preaparc
Not smoothing input surface
Area 236114 0.344
20 0.13267 0.001689 2.7651
Corner 708342 60.00000 14.25330 0.711754 177.0980
Edge 354171 0.9
0431 0.22044 0.014164 4.2099
Hinge 354171 10.02385 10.86290 0.000012 179.8630
Reading in aparc ../label/rh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentries=36, num_entrie
s_to_read=36
Reading in input volume brain.mgz
Reading in seg volume aseg.presurf.mgz
Reading in wm
volume wm.mgz
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
MRIfindBrightNonWM(): 0 bright non-wm
voxels segmented.
Masking bright non-wm for white surface
MRImask(): AllowDiffGeom = 1
MRImask(): A
llowDiffGeom = 1
Ripping frozen voxels
Ripping vertices not in label ../label/rh.cortex.label
MRISri
pNotLabel() ripped 6430/118059 vertices (111629 unripped)
Reading in ripping surface ../surf/rh.whit
e.preaparc
Reading in aparc ../label/rh.aparc.annot for ripsurf
[DEBUG] CTABreadFromBinaryV2(): ct->
nentries=36, num_entries_to_read=36
Ripping BG
MRISripBasalGanglia(): 1 -2 2 0.5
MRISripBasalGanglia
(): 1 -2 2 0.5 ripped 542
Ripping segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5)
segnos: 247
MRISripSegs(): -2 2 0.5 ripped 0
opt weights int=0.2 loc=0 rep=5 nspr=0.3 curv=1
vertex
59030: xyz = (47.2951,4.23909,45.751) oxyz = (47.2951,4.23909,45.751) wxzy = (47.2951,4.23909,45.75
1) pxyz = (0,0,0)
CBVO Creating mask 118059
n_averages 4
Iteration 0 =========================================
n_avera
ges=4, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000
;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low = 58.4975320;
outside_h
i = 118.5830610;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdiag_n
o=-1
VMPeak = 908080
vno start=0, stop=118059
#SI# sigma=2 had to be increased for 57 vertices,
nripped=6972
mean border=78.0, 63 (63) missing vertices, mean dist 0.5 [1.9 (%4.9)->0.6 (%95.1))]
%6
0 local maxima, %34 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.1158 min
Finding expansion regions
mean
absolute distance = 0.65 +- 0.78
1049 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=05768, nav=4, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat
0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
flags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisph
ere 1
randomSeed 0
000: dt: 0.0000, sse=3207295.2, rms=11.645
001: dt: 0.5000, sse=973610.2, rms=5.980 (48.650%)
002: dt: 0.5000, sse=500610.8, rms=3.816 (36.186%)
003: dt: 0.5000, sse=453513.4, rms=3.534 (7.390%)
004: dt: 0.5000, sse=433009.1, rms=3.374 (4.536%)
rms = 3.5022/3.3736, sse=450453.5/433009.1, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
005: dt: 0.2500, sse=298406.9, rms=2.342 (30.592%)
006: dt: 0.2500, sse=258924.4, rms=1.836 (21.596%)
007: dt: 0.2500, sse=239544.2, rms=1.650 (10.101%)
rms = 1.6067/1.6504, sse=235578.7/239544.2, time step reduction 2 of 3 to 0.125 0 0 1
008: dt: 0.25
00, sse=235578.7, rms=1.607 (2.645%)
009: dt: 0.1250, sse=232703.3, rms=1.550 (3.558%)
rms = 1.5395/1.5496, sse=231644.7/232703.3, time step reduction 3 of 3 to 0.062 0 0 1
010: dt: 0.12
50, sse=231644.7, rms=1.539 (0.651%)
maximum number of reductions reached, breaking from loop
positioning took 1.2 minutes
done positioning surface
Iteration 1 ================================
=========
n_averages=2, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000
;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low = 58.4975320;
outside_h
i = 118.5830610;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdiag_n
o=-1
VMPeak = 1565324
vno start=0, stop=118059
#SI# sigma=1 had to be increased for 51 vertices,
nripped=6972
mean border=85.0, 68 (30) missing vertices, mean dist -0.3 [0.4 (%90.8)->0.2 (%9.2))]
%83 local maxima, %11 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScompu
teBorderValues_new() finished in 0.1003 min
Finding expansion regions
mean absolute distance = 0.36 +- 0.38
1381 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=05768, nav=2, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=1758609.2, rms=8.404
011: dt: 0.5000, sse=834370.7, rms=5.358 (36.245%)
012: dt: 0.5000, sse=617336.4, rms=4.380 (18.244%)
013: dt: 0.5000, sse=582868.5, rms=4.180 (4.571%)
rms = 4.2709/4.1801, sse=602911.9/582868.5, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
014: dt: 0.2500, sse=343167.8, rms=2.590 (38.028%)
015: dt: 0.2500, sse=283454.1, rms=1.784 (31.145%)
016: dt: 0.2500, sse=240859.3, rms=1.504 (15.660%)
017: dt: 0.2500, sse=236846.4, rms=1.414 (5.997%)
rms = 1.3663/1.4141, sse=231703.4/236846.4, time step reduction 2 of 3 to 0.125 0 0 1
018: dt: 0.25
00, sse=231703.4, rms=1.366 (3.385%)
019: dt: 0.1250, sse=228145.7, rms=1.279 (6.407%)
rms = 1.2753/1.2787, sse=229590.0/228145.7, time step reduction 3 of 3 to 0.062 0 1 1
020: dt: 0.12
50, sse=229590.0, rms=1.275 (0.267%)
maximum number of reductions reached, breaking from loop
positioning took 1.1 minutes
done positioning surface
Iteration 2 ================================
=========
n_averages=1, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000
;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low = 58.4975320;
outside_h
i = 118.5830610;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdiag
_no=-1
VMPeak = 1704160
vno start=0, stop=118059
#SI# sigma=0.5 had to be increased for 47 verti
ces, nripped=6972
mean border=87.9, 97 (22) missing vertices, mean dist -0.1 [0.1 (%83.4)->0.1 (%16.
6))]
%91 local maxima, % 3 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0569 min
Finding expansion regions
mean absolute distance = 0.13 +- 0.19
560 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=05768, nav=1, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=468429.7, rms=3.572
rms = 3.5722/3.5725, sse=482006.7/468429.7, time step reduction 1 of 3 to 0.250 0 1 1
021: dt: 0.50
00, sse=482006.7, rms=3.572 (0.008%)
022: dt: 0.2500, sse=267489.9, rms=1.843 (48.395%)
023: dt: 0.2500, sse=236505.7, rms=1.437 (22.056%)
rms = 1.3315/1.4368, sse=238588.2/236505.7, time step reduction 2 of 3 to 0.125 0 1 0
024: dt: 0.25
00, sse=238588.2, rms=1.331 (7.333%)
025: dt: 0.1250, sse=230716.4, rms=1.169 (12.186%)
rms = 1.1484/1.1692, sse=231099.8/230716.4, time step reduction 3 of 3 to 0.062 0 1 1
026: dt: 0.12
50, sse=231099.8, rms=1.148 (1.782%)
maximum number of reductions reached, breaking from loop
positioning took 0.6 minutes
done positioning surface
Iteration 3 ================================
=========
n_averages=0, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 120.0000000
;
border_hi = 118.5830610;
border_low = 69.0000000;
outside_low = 58.4975320;
outside_h
i = 118.5830610;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which =
1
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdia
g_no=-1
VMPeak = 1827980
vno start=0, stop=118059
#SI# sigma=0.25 had to be increased for 30 ver
tices, nripped=6972
mean border=88.3, 119 (19) missing vertices, mean dist -0.0 [0.1 (%55.5)->0.1 (%
44.5))]
%92 local maxima, % 2 large gradients and % 0 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0419 min
Finding expansion regions
mean absolute distance = 0.09 +- 0.12
1288 vertices more than 2 sigmas from mean.
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, sprin
g = 0, niters = 100 l_repulse = 5, l_surf_repulse = 0, checktol = 0
Positioning surface subiter 0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->che
ck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=05768, nav=0, nbrs=2, l_repulse=5.000, l_
tspring=0.300, l_nspring=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=232879.9, rms=1.207
rms = 1.7820/1.2070, sse=265827.2/232879.9, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
027: dt: 0.2500, sse=215893.8, rms=0.937 (22.328%)
rms = 0.9381/0.9375, sse=212828.7/215893.8, time step reduction 2 of 3 to 0.125 0 0 1
RMS increa
sed, rejecting step
rms = 0.9287/0.9375, sse=215100.1/215893.8, time step reduction 3 of 3 to 0.062
0 0 1
028: dt: 0.1250, sse=215100.1, rms=0.929 (0.935%)
maximum number of reductions reached, bre
aking from loop
positioning took 0.4 minutes
done positioning surface
Removing intersections
#ET# mris_place_surface 3.70 minutes
Writing output to ../surf/rh.white
#VMPC# mris_place_surface
s VmPeak 1861996
mris_place_surface done
8.0.0
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical
mris_place_surface --adgws-in ../surf/autodet.gw.stats.lh.dat --
seg aseg.presurf.mgz --threads 2 --wm wm.mgz --invol brain.mgz --lh --i ../surf/lh.white --o ../surf
/lh.pial --pial --nsmooth 0 --rip-label ../label/lh.cortex+hipamyg.label --pin-medial-wall ../label/
lh.cortex.label --aparc ../label/lh.aparc.annot --repulse-surf ../surf/lh.white --white-surf ../surf
/lh.white
Reading in input surface ../surf/lh.white
Not smoothing input surface
Area 239404 0.34494 0.148
11 0.003374 3.1249
Corner 718212 60.00000 14.98467 0.554486 178.2044
Edge 359106 0.90567 0.2
4094 0.034434 4.0483
Hinge 359106 9.97787 11.14216 0.000006 179.9589
Reading white surface coordinates from ../surf/lh.white
Reading repulsion surface coordinates from .
./surf/lh.white
Reading in aparc ../label/lh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentrie
s=36, num_entries_to_read=36
Reading in input volume brain.mgz
Reading in seg volume aseg.presurf.mg
z
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
MRIfindBrightNonWM():
0 bright non-wm voxels segmented.
Masking bright non-wm for pial surface mid_gray = 67.4548
MRImask
(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxel
s
Ripping vertices not in label ../label/lh.cortex+hipamyg.label
MRISripNotLabel() ripped 5553/11970
4 vertices (114151 unripped)
INFO: rip surface needed but not specified, so using input surface
Ripp
ing segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2
2 0.5 ripped 0
opt weights int=0.2 loc=0 rep=0 nspr=0.3 curv=1
vertex 59852: xyz = (-45.1455,1.5418
4,32.7016) oxyz = (-45.1455,1.54184,32.7016) wxzy = (-45.1455,1.54184,32.7016) pxyz = (-45.1455,1.54
184,32.7016)
CBVO Creating mask 119704
n_averages 16
Iteration 0 =========================================
n_aver
ages=16, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 97.4169390
;
border_hi = 58.4975320;
border_low = 37.4925920;
outside_low = 10.0000000;
outside_h
i = 53.2463000;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdiag_n
o=-1
VMPeak = 902992
vno start=0, stop=119704
#SI# sigma=2 had to be increased for 232 vertices,
nripped=5553
mean border=54.8, 337 (337) missing vertices, mean dist 2.0 [2.6 (%0.2)->2.5 (%99.8))]
%13 local maxima, %63 large gradients and %19 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomp
uteBorderValues_new() finished in 0.0887 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spr
ing = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface subiter
0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->c
heck_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=05768, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring
=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages
0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_r
ms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
f
lags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 0
randomSeed 0
000: dt: 0.0000, sse=26278708.0, rms=33.862
001: dt: 0.5000, sse=16391795.0, rms=26.689 (21.184%)
002: dt: 0.5000, sse=10181511.0, rms=20.963 (21.455%)
003: dt: 0.5000, sse=7010593.0, rms=17.323 (17.365%)
004: dt: 0.5000, sse=5335874.0, rms=15.047 (13.137%)
005: dt: 0.5000, sse=4271542.0, rms=13.400 (10.948%)
006: dt: 0.5000, sse=3416771.5, rms=11.911 (11.107%)
007: dt: 0.5000, sse=2779212.8, rms=10.666 (10.453%)
008: dt: 0.5000, sse=2229615.0, rms=9.462 (11.289%)
009: dt: 0.5000, sse=1796111.6, rms=8.391 (11.322%)
010: dt: 0.5000, sse=1433678.9, rms=7.375 (12.100%)
011: dt: 0.5000, sse=1234551.1, rms=6.752 (8.451%)
012: dt: 0.5000, sse=1087280.8, rms=6.250 (7.436%)
013: dt: 0.5000, sse=1026670.5, rms=6.030 (3.523%)
014: dt: 0.5000, sse=958412.6, rms=5.772 (4.272%)
015: dt: 0.5000, sse=938520.6, rms=5.694 (1.364%)
016: dt: 0.5000, sse=898618.8, rms=5.535 (2.787%)
rms = 5.5296/5.5349, sse=897744.3/898618.8, time step reduction 1 of 3 to 0.250 0 0 1
017: dt: 0.50
00, sse=897744.3, rms=5.530 (0.096%)
018: dt: 0.2500, sse=565329.4, rms=3.971 (28.185%)
019: dt: 0.2500, sse=495180.7, rms=3.560 (10.348%)
020: dt: 0.2500, sse=480693.9, rms=3.467 (2.621%)
021: dt: 0.2500, sse=464712.3, rms=3.364 (2.978%)
rms = 3.3289/3.3636, sse=459625.8/464712.3, time step reduction 2 of 3 to 0.125 0 0 1
022: dt: 0.25
00, sse=459625.8, rms=3.329 (1.032%)
023: dt: 0.1250, sse=407950.0, rms=2.964 (10.959%)
024: dt: 0.1250, sse=397295.0, rms=2.883 (2.722%)
rms = 2.8582/2.8834, sse=394040.2/397295.0, time step reduction 3 of 3 to 0.062 0 0 1
025: dt: 0.12
50, sse=394040.2, rms=2.858 (0.874%)
maximum number of reductions reached, breaking from loop
positioning took 2.3 minutes
done positioning surface
Iteration 1 ================================
=========
n_averages=8, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 97.4169390
;
border_hi = 58.4975320;
border_low = 37.4925920;
outside_low = 10.0000000;
outside_h
i = 53.2463000;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdiag_n
o=-1
VMPeak = 1200676
vno start=0, stop=119704
#SI# sigma=1 had to be increased for 1398 vertice
s, nripped=5553
mean border=52.0, 541 (218) missing vertices, mean dist 0.1 [0.1 (%44.6)->0.3 (%55.4
))]
%31 local maxima, %49 large gradients and %14 min vals, 0 gradients ignored
nFirstPeakD1 0
MRISc
omputeBorderValues_new() finished in 0.0365 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spr
ing = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface subiter
0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->c
heck_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=05768, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=
0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=730081.7, rms=4.629
rms = 5.6088/4.6285, sse=960679.8/730081.7, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
026: dt: 0.2500, sse=553014.0, rms=3.690 (20.280%)
027: dt: 0.2500, sse=494770.4, rms=3.320 (10.031%)
028: dt: 0.2500, sse=479625.4, rms=3.222 (2.941%)
rms = 3.2433/3.2221, sse=482851.0/479625.4, time step reduction 2 of 3 to 0.125 0 1 1
RMS increa
sed, rejecting step
029: dt: 0.1250, sse=460259.5, rms=3.086 (4.238%)
030: dt: 0.1250, sse=432450.3, rms=2.878 (6.729%)
031: dt: 0.1250, sse=424719.6, rms=2.818 (2.089%)
rms = 2.7999/2.8178, sse=422448.6/424719.6, time step reduction 3 of 3 to 0.062 0 0 1
032: dt: 0.12
50, sse=422448.6, rms=2.800 (0.636%)
maximum number of reductions reached, breaking from loop
positioning took 0.7 minutes
done positioning surface
Iteration 2 ================================
=========
n_averages=4, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 97.4169390
;
border_hi = 58.4975320;
border_low = 37.4925920;
outside_low = 10.0000000;
outside_h
i = 53.2463000;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdiag
_no=-1
VMPeak = 1227720
vno start=0, stop=119704
#SI# sigma=0.5 had to be increased for 1924 ver
tices, nripped=5553
mean border=49.3, 783 (194) missing vertices, mean dist 0.1 [0.1 (%37.6)->0.2 (%
62.4))]
%47 local maxima, %34 large gradients and %14 min vals, 0 gradients ignored
nFirstPeakD1 0
M
RIScomputeBorderValues_new() finished in 0.0119 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spr
ing = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface subiter
0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->c
heck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=05768, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=
0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=691667.6, rms=4.433
rms = 5.6350/4.4331, sse=969930.9/691667.6, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
033: dt: 0.2500, sse=508970.5, rms=3.405 (23.186%)
034: dt: 0.2500, sse=478839.9, rms=3.200 (6.023%)
rms = 3.1621/3.2001, sse=472398.1/478839.9, time step reduction 2 of 3 to 0.125 0 0 1
035: dt: 0.25
00, sse=472398.1, rms=3.162 (1.187%)
036: dt: 0.1250, sse=420817.0, rms=2.777 (12.176%)
037: dt: 0.1250, sse=412191.7, rms=2.708 (2.477%)
rms = 2.6920/2.7083, sse=410150.4/412191.6, time step reduction 3 of 3 to 0.062 0 0 1
038: dt: 0.12
50, sse=410150.3, rms=2.692 (0.603%)
maximum number of reductions reached, breaking from loop
positioning took 0.6 minutes
done positioning surface
Iteration 3 ================================
=========
n_averages=2, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 97.4169390
;
border_hi = 58.4975320;
border_low = 37.4925920;
outside_low = 10.0000000;
outside_h
i = 53.2463000;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which =
2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=119704
Gdia
g_no=-1
VMPeak = 1250464
vno start=0, stop=119704
#SI# sigma=0.25 had to be increased for 1981 v
ertices, nripped=5553
mean border=48.4, 1186 (187) missing vertices, mean dist 0.0 [0.1 (%46.7)->0.2
(%53.3))]
%50 local maxima, %30 large gradients and %14 min vals, 0 gradients ignored
nFirstPeakD1
0
MRIScomputeBorderValues_new() finished in 0.0138 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spr
ing = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface subiter
0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->c
heck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=05768, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=
0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=445884.2, rms=2.975
rms = 4.5813/2.9753, sse=722735.5/445884.2, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
039: dt: 0.2500, sse=409050.0, rms=2.687 (9.705%)
rms = 2.7091/2.6866, sse=411431.1/409050.0, time step reduction 2 of 3 to 0.125 0 1 1
RMS increa
sed, rejecting step
rms = 2.6594/2.6866, sse=405761.4/409050.0, time step reduction 3 of 3 to 0.062
0 0 1
040: dt: 0.1250, sse=405761.4, rms=2.659 (1.009%)
maximum number of reductions reached, bre
aking from loop
positioning took 0.3 minutes
done positioning surface
Pinning medial wall to white surface
Removing intersections
removing intersecting faces
000: 49 intersecting
001: 22 intersecting
002: 5 intersecting
terminatin
g search with 0 intersecting
#ET# mris_place_surface 4.33 minutes
Writing output to ../surf/lh.pi
al
#VMPC# mris_place_surfaces VmPeak 1261136
mris_place_surface done
8.0.0
8.0.0
cd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical/TestSubject/mri
setenv SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical
mris_place_surface --adgws-in ../surf/autodet.gw.stats.rh.dat --
seg aseg.presurf.mgz --threads 2 --wm wm.mgz --invol brain.mgz --rh --i ../surf/rh.white --o ../surf
/rh.pial --pial --nsmooth 0 --rip-label ../label/rh.cortex+hipamyg.label --pin-medial-wall ../label/
rh.cortex.label --aparc ../label/rh.aparc.annot --repulse-surf ../surf/rh.white --white-surf ../surf
/rh.white
Reading in input surface ../surf/rh.white
Not smoothing input surface
Area 236114 0.34583 0.144
30 0.001450 3.6360
Corner 708342 60.00000 15.07878 0.243055 178.7098
Edge 354171 0.90686 0.2
3335 0.014164 4.0827
Hinge 354171 9.93449 10.67662 0.000058 179.8010
Reading white surface coordinates from ../surf/rh.white
Reading repulsion surface coordinates from .
./surf/rh.white
Reading in aparc ../label/rh.aparc.annot
[DEBUG] CTABreadFromBinaryV2(): ct->nentrie
s=36, num_entries_to_read=36
Reading in input volume brain.mgz
Reading in seg volume aseg.presurf.mg
z
Reading in wm volume wm.mgz
MRIclipBrightWM(): nthresh=0, wmmin=5, clip=110
MRIfindBrightNonWM():
0 bright non-wm voxels segmented.
Masking bright non-wm for pial surface mid_gray = 67.4548
MRImask
(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
MRImask(): AllowDiffGeom = 1
Ripping frozen voxel
s
Ripping vertices not in label ../label/rh.cortex+hipamyg.label
MRISripNotLabel() ripped 5409/11805
9 vertices (112650 unripped)
INFO: rip surface needed but not specified, so using input surface
Ripp
ing segs (eg, WMSA, BG, frozen)
Starting MRISripSegs() d = (-2 2 0.5) segnos: 247
MRISripSegs(): -2
2 0.5 ripped 0
opt weights int=0.2 loc=0 rep=0 nspr=0.3 curv=1
vertex 59030: xyz = (47.3122,4.28568
,45.8064) oxyz = (47.3122,4.28568,45.8064) wxzy = (47.3122,4.28568,45.8064) pxyz = (47.3122,4.28568,
45.8064)
CBVO Creating mask 118059
n_averages 16
Iteration 0 =========================================
n_aver
ages=16, current_sigma=2
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 97.4169390
;
border_hi = 58.4975320;
border_low = 37.4925920;
outside_low = 10.0000000;
outside_h
i = 53.2463000;
sigma = 2;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdiag_n
o=-1
VMPeak = 899540
vno start=0, stop=118059
#SI# sigma=2 had to be increased for 241 vertices,
nripped=5409
mean border=54.7, 395 (395) missing vertices, mean dist 2.0 [2.9 (%0.2)->2.6 (%99.8))]
%13 local maxima, %62 large gradients and %20 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0987 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spr
ing = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface subiter
0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->c
heck_tol = 0, niterations = 100
tol=1.0e-04, sigma=2.0, host=05768, nav=16, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring
=0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
complete_dist_mat 0
rms 0
smooth_averages
0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_r
ms_height 0.000000
momentum 0.000000
nbhd_size 0
max_nbrs 0
niterations 100
nsurfaces 0
SURFACES 3
f
lags 0 (0)
use curv 0
no sulc 0
no rigid align 0
mris->nsize 2
mris->hemisphere 1
randomSeed 0
000: dt: 0.0000, sse=25855234.0, rms=33.820
001: dt: 0.5000, sse=16189026.0, rms=26.707 (21.033%)
002: dt: 0.5000, sse=10140388.0, rms=21.067 (21.119%)
003: dt: 0.5000, sse=7081276.5, rms=17.535 (16.764%)
004: dt: 0.5000, sse=5466231.5, rms=15.345 (12.492%)
005: dt: 0.5000, sse=4445588.5, rms=13.780 (10.196%)
006: dt: 0.5000, sse=3638118.0, rms=12.402 (10.001%)
007: dt: 0.5000, sse=2998190.2, rms=11.189 (9.782%)
008: dt: 0.5000, sse=2443271.0, rms=10.019 (10.459%)
009: dt: 0.5000, sse=1960047.2, rms=8.874 (11.421%)
010: dt: 0.5000, sse=1545000.4, rms=7.757 (12.586%)
011: dt: 0.5000, sse=1280185.2, rms=6.951 (10.393%)
012: dt: 0.5000, sse=1108926.9, rms=6.374 (8.297%)
013: dt: 0.5000, sse=1025942.7, rms=6.074 (4.710%)
014: dt: 0.5000, sse=967847.8, rms=5.854 (3.624%)
015: dt: 0.5000, sse=950644.7, rms=5.786 (1.165%)
016: dt: 0.5000, sse=924723.3, rms=5.683 (1.780%)
rms = 5.6600/5.6830, sse=919300.3/924723.3, time step reduction 1 of 3 to 0.250 0 0 1
017: dt: 0.50
00, sse=919300.3, rms=5.660 (0.405%)
018: dt: 0.2500, sse=605863.4, rms=4.227 (25.321%)
019: dt: 0.2500, sse=538162.7, rms=3.852 (8.878%)
020: dt: 0.2500, sse=523578.7, rms=3.764 (2.285%)
021: dt: 0.2500, sse=509425.5, rms=3.679 (2.260%)
rms = 3.6540/3.6785, sse=505550.1/509425.5, time step reduction 2 of 3 to 0.125 0 0 1
022: dt: 0.25
00, sse=505550.1, rms=3.654 (0.668%)
023: dt: 0.1250, sse=457230.9, rms=3.343 (8.517%)
024: dt: 0.1250, sse=448026.9, rms=3.280 (1.869%)
rms = 3.2636/3.2803, sse=445614.3/448026.9, time step reduction 3 of 3 to 0.062 0 0 1
025: dt: 0.12
50, sse=445614.2, rms=3.264 (0.508%)
maximum number of reductions reached, breaking from loop
positioning took 2.3 minutes
done positioning surface
Iteration 1 ================================
=========
n_averages=8, current_sigma=1
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 97.4169390
;
border_hi = 58.4975320;
border_low = 37.4925920;
outside_low = 10.0000000;
outside_h
i = 53.2463000;
sigma = 1;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdiag_n
o=-1
VMPeak = 1196276
vno start=0, stop=118059
#SI# sigma=1 had to be increased for 1555 vertice
s, nripped=5409
mean border=52.0, 824 (280) missing vertices, mean dist 0.1 [0.1 (%44.9)->0.3 (%55.1
))]
%31 local maxima, %49 large gradients and %15 min vals, 0 gradients ignored
nFirstPeakD1 0
MRISc
omputeBorderValues_new() finished in 0.0295 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spr
ing = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface subiter
0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->c
heck_tol = 0, niterations = 100
tol=1.0e-04, sigma=1.0, host=05768, nav=8, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=
0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=762362.9, rms=4.814
rms = 5.8162/4.8142, sse=1003646.5/762362.9, time step reduction 1 of 3 to 0.250 0 1 1
RMS incre
ased, rejecting step
026: dt: 0.2500, sse=598782.3, rms=3.982 (17.277%)
027: dt: 0.2500, sse=546988.5, rms=3.677 (7.673%)
028: dt: 0.2500, sse=532333.2, rms=3.591 (2.346%)
rms = 3.6090/3.5907, sse=535343.7/532333.2, time step reduction 2 of 3 to 0.125 0 1 1
RMS increa
sed, rejecting step
029: dt: 0.1250, sse=514012.4, rms=3.474 (3.259%)
030: dt: 0.1250, sse=487517.7, rms=3.297 (5.087%)
031: dt: 0.1250, sse=479729.6, rms=3.243 (1.626%)
rms = 3.2250/3.2433, sse=477070.4/479729.6, time step reduction 3 of 3 to 0.062 0 0 1
032: dt: 0.12
50, sse=477070.4, rms=3.225 (0.566%)
maximum number of reductions reached, breaking from loop
positioning took 0.7 minutes
done positioning surface
Iteration 2 ================================
=========
n_averages=4, current_sigma=0.5
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 97.4169390
;
border_hi = 58.4975320;
border_low = 37.4925920;
outside_low = 10.0000000;
outside_h
i = 53.2463000;
sigma = 0.5;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which = 2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdiag
_no=-1
VMPeak = 1223224
vno start=0, stop=118059
#SI# sigma=0.5 had to be increased for 2089 ver
tices, nripped=5409
mean border=49.5, 1080 (268) missing vertices, mean dist 0.1 [0.1 (%38.0)->0.2 (
%62.0))]
%47 local maxima, %33 large gradients and %14 min vals, 0 gradients ignored
nFirstPeakD1 0
MRIScomputeBorderValues_new() finished in 0.0202 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spr
ing = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface subiter
0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->c
heck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.5, host=05768, nav=4, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=
0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=719141.6, rms=4.600
rms = 5.7825/4.6000, sse=997306.5/719141.6, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
033: dt: 0.2500, sse=552572.2, rms=3.703 (19.506%)
034: dt: 0.2500, sse=528306.0, rms=3.550 (4.127%)
rms = 3.5174/3.5499, sse=522220.8/528306.0, time step reduction 2 of 3 to 0.125 0 0 1
035: dt: 0.25
00, sse=522220.8, rms=3.517 (0.916%)
036: dt: 0.1250, sse=474292.5, rms=3.196 (9.127%)
037: dt: 0.1250, sse=463460.2, rms=3.120 (2.382%)
rms = 3.1061/3.1202, sse=461444.1/463460.1, time step reduction 3 of 3 to 0.062 0 0 1
038: dt: 0.12
50, sse=461444.1, rms=3.106 (0.454%)
maximum number of reductions reached, breaking from loop
positioning took 0.6 minutes
done positioning surface
Iteration 3 ================================
=========
n_averages=2, current_sigma=0.25
Computing target border values
Entering MRIScomputeBorderValues_new():
inside_hi = 97.4169390
;
border_hi = 58.4975320;
border_low = 37.4925920;
outside_low = 10.0000000;
outside_h
i = 53.2463000;
sigma = 0.25;
max_thickness = 10;
step_size=0.5;
STEP_SIZE=0.1;
which =
2
thresh = 0.5
flags = 0
CBVfindFirstPeakD1=0
CBVfindFirstPeakD2=0
nvertices=118059
Gdia
g_no=-1
VMPeak = 1246060
vno start=0, stop=118059
#SI# sigma=0.25 had to be increased for 1999 v
ertices, nripped=5409
mean border=48.6, 1543 (260) missing vertices, mean dist 0.0 [0.1 (%46.4)->0.2
(%53.6))]
%50 local maxima, %30 large gradients and %15 min vals, 0 gradients ignored
nFirstPeakD1
0
MRIScomputeBorderValues_new() finished in 0.0138 min
Averaging target values for 5 iterations...
Positioning Surface: tspring = 0.3, nspring = 0.3, spr
ing = 0, niters = 100 l_repulse = 0, l_surf_repulse = 5, checktol = 0
Positioning surface subiter
0
Entering MRISpositionSurface()
max_mm = 0.3
MAX_REDUCTIONS = 2, REDUCTION_PCT = 0.5
parms->c
heck_tol = 0, niterations = 100
tol=1.0e-04, sigma=0.2, host=05768, nav=2, nbrs=2, l_surf_repulse=5.000, l_tspring=0.300, l_nspring=
0.300, l_intensity=0.200, l_curv=1.000
mom=0.00, dt=0.50
000: dt: 0.0000, sse=495084.9, rms=3.342
rms = 4.7327/3.3422, sse=747695.1/495084.9, time step reduction 1 of 3 to 0.250 0 1 1
RMS increa
sed, rejecting step
039: dt: 0.2500, sse=461330.8, rms=3.106 (7.058%)
rms = 3.1133/3.1063, sse=461917.4/461330.8, time step reduction 2 of 3 to 0.125 0 1 1
RMS increa
sed, rejecting step
rms = 3.0823/3.1063, sse=458021.6/461330.8, time step reduction 3 of 3 to 0.062
0 0 1
040: dt: 0.1250, sse=458021.6, rms=3.082 (0.770%)
maximum number of reductions reached, bre
aking from loop
positioning took 0.3 minutes
done positioning surface
Pinning medial wall to white surface
Removing intersections
removing intersecting faces
000: 38 intersecting
step 1 with no progress (num=39, old_num=38)
001: 3
9 intersecting
step 2 with no progress (num=45, old_num=39)
002: 45 intersecting
003: 15 intersectin
g
step 1 with no progress (num=17, old_num=15)
004: 17 intersecting
005: 9 intersecting
terminating
search with 0 intersecting
#ET# mris_place_surface 4.37 minutes
Writing output to ../surf/rh.pial
#VMPC# mris_place_surfaces VmPeak 1256204
mris_place_surface done
insurf ../surf/lh.white, nbrs 2, curvature_avgs 10
writing curvature file ../surf/lh.curv type -1
writing curvature file ../surf/lh.area type -1
insurf ../surf/lh.pial, nbrs 2, curvature_avgs 10
writing curvature file ../surf/lh.curv.pial type -1
writing curvature file ../surf/lh.area.pial type -1
0 of 119704 vertices processed
25000 of 119704 vertices processed
50000 of 119704 vertices processed
75000 of 119704 vertices processed
100000 of 119704 vertices processed
0 of 119704 vertices process
ed
25000 of 119704 vertices processed
50000 of 119704 vertices processed
75000 of 119704 vertices pr
ocessed
100000 of 119704 vertices processed
thickness calculation complete, 180:423 truncations.
596
66 vertices at 0 distance
108561 vertices at 1 distance
49068 vertices at 2 distance
14713 vertices
at 3 distance
4522 vertices at 4 distance
1740 vertices at 5 distance
671 vertices at 6 distance
274
vertices at 7 distance
113 vertices at 8 distance
32 vertices at 9 distance
11 vertices at 10 dista
nce
14 vertices at 11 distance
4 vertices at 12 distance
8 vertices at 13 distance
3 vertices at 14
distance
2 vertices at 15 distance
4 vertices at 16 distance
1 vertices at 17 distance
1 vertices at
18 distance
0 vertices at 19 distance
0 vertices at 20 distance
writing curvature file ../surf/lh.thickness type -1
0 of 119704 vertices processed
25000 of 119704 vertices processed
50000 of 119704 vertices processed
75000 of 119704 vertices processed
100000 of 119704 vertices processed
0 of 119704 vertices process
ed
25000 of 119704 vertices processed
50000 of 119704 vertices processed
75000 of 119704 vertices pr
ocessed
100000 of 119704 vertices processed
thickness calculation complete, 180:423 truncations.
596
66 vertices at 0 distance
108561 vertices at 1 distance
49068 vertices at 2 distance
14713 vertices
at 3 distance
4522 vertices at 4 distance
1740 vertices at 5 distance
671 vertices at 6 distance
274
vertices at 7 distance
113 vertices at 8 distance
32 vertices at 9 distance
11 vertices at 10 dista
nce
14 vertices at 11 distance
4 vertices at 12 distance
8 vertices at 13 distance
3 vertices at 14
distance
2 vertices at 15 distance
4 vertices at 16 distance
1 vertices at 17 distance
1 vertices at
18 distance
0 vertices at 19 distance
0 vertices at 20 distance
writing curvature file ../surf/lh.thickness type -1
insurf ../surf/rh.white, nbrs 2, curvature_avgs 10
writing curvature file ../surf/rh.curv type -1
writing curvature file ../surf/rh.area type -1
insurf ../surf/rh.pial, nbrs 2, curvature_avgs 10
writing curvature file ../surf/rh.curv.pial type -1
writing curvature file ../surf/rh.area.pial type -1
0 of 118059 vertices processed
25000 of 118059 vertices processed
50000 of 118059 vertices processed
75000 of 118059 vertices processed
100000 of 118059 vertices processed
0 of 118059 vertices process
ed
25000 of 118059 vertices processed
50000 of 118059 vertices processed
75000 of 118059 vertices pr
ocessed
100000 of 118059 vertices processed
thickness calculation complete, 85:200 truncations.
5509
5 vertices at 0 distance
105566 vertices at 1 distance
51192 vertices at 2 distance
15973 vertices a
t 3 distance
5133 vertices at 4 distance
1911 vertices at 5 distance
717 vertices at 6 distance
284
vertices at 7 distance
109 vertices at 8 distance
43 vertices at 9 distance
21 vertices at 10 distan
ce
21 vertices at 11 distance
12 vertices at 12 distance
15 vertices at 13 distance
3 vertices at 14
distance
5 vertices at 15 distance
5 vertices at 16 distance
1 vertices at 17 distance
0 vertices a
t 18 distance
2 vertices at 19 distance
10 vertices at 20 distance
writing curvature file ../surf/rh.thickness type -1
0 of 118059 vertices processed
25000 of 118059 vertices processed
50000 of 118059 vertices processed
75000 of 118059 vertices processed
100000 of 118059 vertices processed
0 of 118059 vertices process
ed
25000 of 118059 vertices processed
50000 of 118059 vertices processed
75000 of 118059 vertices pr
ocessed
100000 of 118059 vertices processed
thickness calculation complete, 85:200 truncations.
5509
5 vertices at 0 distance
105566 vertices at 1 distance
51192 vertices at 2 distance
15973 vertices a
t 3 distance
5133 vertices at 4 distance
1911 vertices at 5 distance
717 vertices at 6 distance
284
vertices at 7 distance
109 vertices at 8 distance
43 vertices at 9 distance
21 vertices at 10 distan
ce
21 vertices at 11 distance
12 vertices at 12 distance
15 vertices at 13 distance
3 vertices at 14
distance
5 vertices at 15 distance
5 vertices at 16 distance
1 vertices at 17 distance
0 vertices a
t 18 distance
2 vertices at 19 distance
10 vertices at 20 distance
writing curvature file ../surf/rh.thickness type -1
Toggling save flag on curvature files [ ok ]
Out
putting results using filestem [ ../stats/lh.curv.stats ]
Toggling save flag on curva
ture files [ ok ]
Setting surface [ TestSu
bject/lh.smoothwm ]
Reading surface...
[ ok ]
Setting texture [ curv ]
Reading texture...
[ ok ]
Setting texture [ sulc ]
Reading texture...
Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vno faces... [
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#] [ ok ]
Determining KH curvatures... [
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#] [ ok ]
Determining k1k2 curvatures... [#
######
#####
###
###
##] [ ok ]
deltaViolations [ 231 ]
Gb_filter = 0
Toggling save flag on curvature files [ ok ]
Out
putting results using filestem [ ../stats/rh.curv.stats ]
Toggling save flag on curva
ture files [ ok ]
Setting surface [ TestSu
bject/rh.smoothwm ]
Reading surface...
[ ok ]
Setting texture [ curv ]
Reading texture...
[ ok ]
Setting texture [ sulc ]
Reading texture...Gb_filter = 0
[ ok ]
Calculating Discrete Principal Curvatures...
Determining geometric order for vno faces... [
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#] [ ok ]
Determining KH curvatures... [
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
#
] [ ok ]
Determining k1k2 curvatures... [#######
########
#####] [ ok ]
deltaViolations [ 218 ]
Gb_filter = 0
WARN: S lookup min: -0.130228
WARN: S explicit min:
0.000000 vertex = 213
SUBJECTS_DIR is /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
loading input data...
Loading /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical/TestSubject/surf/lh.white
Loading /home/jovyan/workspace/books/examples/struct
ural_imaging/data/structural/recon-all-clinical/TestSubject/surf/lh.pial
Loading /home/jovyan/worksp
ace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf/rh.white
L
oading /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/T
estSubject/surf/rh.pial
Loading /home/jovyan/workspace/books/examples/structural_imaging/data/struct
ural/recon-all-clinical/TestSubject/mri/aseg.presurf.mgz
Running hemis serially
Processing left hemi
computing distance to left white surface
computing distance to left pial surface
Processing right
hemi
computing distance to right white surface
computing distance to right pial surface
hemi masks ove
rlap voxels = 9
writing volume /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-cl
inical/TestSubject/mri/ribbon.mgz
mris_volmask took 4.31 minutes
writing ribbon files
/opt/freesurfer-8.0.0/python/scripts/refine_synthSR.py:8: DeprecationWarning: Please use `distance_t
ransform_edt` from the `scipy.ndimage` namespace, the `scipy.ndimage.morphology` namespace is deprec
ated.
from scipy.ndimage.morphology import distance_transform_edt
/opt/freesurfer-8.0.0/python
Rea
ding inputs
Processing
Writing to disk
Done!
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clin
ical
outvol aseg.mgz
32 avail.processors, using 1
Loading aseg.presurf.mgz
Loading ./ribbon.mgz
Load
ing ../surf/lh.white
Loading ../surf/lh.pial
Loading ../label/lh.cortex.label
Loading ../surf/rh.whi
te
Loading ../surf/rh.pial
Loading ../label/rh.cortex.label
Done loading
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nrelabeled = 0
ndotcheck = 0
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak 762
736
mri_surf2volseg done
setting seed for random number generator to 1234
using ./aseg.presurf.mgz aseg volume to correct mid
line
8.0.0
8.0.0
reading atlas from /opt/freesurfer-8.0.0/average/lh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs.
..
reading color table from GCSA file....
average std = 3.0 using min determinant for regularizati
on = 0.088
0 singular and 0 ill-conditioned covariance matrices regularized
reading surface from /ho
me/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject
/surf/lh.smoothwm...
set_atable_from_ctable(): 76 entries
GCSA::load_default_data(): ninputs=1 sulc
_only=0 which_norm=0
labeling surface...
59 labels changed using aseg
relabeling using gibbs priors...
000: 8146 changed, 119704 examined..
.
001: 1802 changed, 31692 examined...
002: 503 changed, 9717 examined...
003: 211 changed,
2962 examined...
004: 98 changed, 1222 examined...
005: 50 changed, 567 examined...
006:
24 changed, 297 examined...
007: 10 changed, 137 examined...
008: 5 changed, 69 examined..
.
009: 5 changed, 27 examined...
010: 4 changed, 24 examined...
011: 1 changed, 21 ex
amined...
012: 0 changed, 7 examined...
29 labels changed using aseg
000: 203 total segments, 1
21 labels (1561 vertices) changed
001: 99 total segments, 17 labels (68 vertices) changed
002: 82 to
tal segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested, 20 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wall label...
relabeling unkn
own label...
1112 vertices marked for relabeling...
1112 labels changed in reclassification.
writing output to ../label/lh.aparc.a2009s.annot...
classif
ication took 0 minutes and 13 seconds.
setting seed for random number generator to 1234
using ./aseg.presurf.mgz aseg volume to correct mid
line
8.0.0
8.0.0
reading atlas from /opt/freesurfer-8.0.0/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs.
..
reading color table from GCSA file....
average std = 1.4 using min determinant for regularizati
on = 0.021
0 singular and 0 ill-conditioned covariance matrices regularized
reading surface from /ho
me/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject
/surf/rh.smoothwm...
set_atable_from_ctable(): 76 entries
GCSA::load_default_data(): ninputs=1 sulc
_only=0 which_norm=0
labeling surface...
86 labels changed using aseg
relabeling using gibbs priors...
000: 8240 changed, 118059 examined..
.
001: 1869 changed, 32187 examined...
002: 508 changed, 10023 examined...
003: 215 changed,
2923 examined...
004: 108 changed, 1230 examined...
005: 59 changed, 600 examined...
006:
33 changed, 351 examined...
007: 15 changed, 181 examined...
008: 3 changed, 85 examined.
..
009: 1 changed, 20 examined...
010: 0 changed, 8 examined...
78 labels changed using as
eg
000: 209 total segments, 120 labels (1639 vertices) changed
001: 92 total segments, 3 labels (7 v
ertices) changed
002: 89 total segments, 0 labels (0 vertices) changed
10 filter iterations complete
(10 requested, 31 changed)
rationalizing unknown annotations with cortex label
relabeling Medial_wa
ll label...
relabeling unknown label...
1083 vertices marked for relabeling...
1083 labels changed in reclassification.
writing output to ../label/rh.aparc.a2009s.annot...
classif
ication took 0 minutes and 15 seconds.
setting seed for random number generator to 1234
using ./aseg.presurf.mgz aseg volume to correct mid
line
8.0.0
8.0.0
reading atlas from /opt/freesurfer-8.0.0/average/lh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
...
reading color table from GCSA file....
average std = 1.4 using min determinant for regularizat
ion = 0.020
0 singular and 383 ill-conditioned covariance matrices regularized
reading surface from
/home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubj
ect/surf/lh.smoothwm...
set_atable_from_ctable(): 36 entries
GCSA::load_default_data(): ninputs=1 s
ulc_only=0 which_norm=0
labeling surface...
1934 labels changed using aseg
relabeling using gibbs priors...
000: 1823 changed, 119704 examined
...
001: 428 changed, 8495 examined...
002: 104 changed, 2420 examined...
003: 44 changed,
637 examined...
004: 29 changed, 268 examined...
005: 20 changed, 163 examined...
006:
17 changed, 112 examined...
007: 13 changed, 93 examined...
008: 8 changed, 74 examined...
009: 9 changed, 50 examined...
010: 7 changed, 49 examined...
011: 8 changed, 38 exam
ined...
012: 10 changed, 47 examined...
013: 7 changed, 51 examined...
014: 2 changed,
42 examined...
015: 0 changed, 15 examined...
329 labels changed using aseg
000: 60 total segm
ents, 27 labels (141 vertices) changed
001: 33 total segments, 0 labels (0 vertices) changed
10 filt
er iterations complete (10 requested, 3 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeling corpuscallosum label...
886 vertices marked for relabeling..
.
886 labels changed in reclassification.
writing output to ../label/lh.aparc.DKTatlas.annot...
classi
fication took 0 minutes and 11 seconds.
setting seed for random number generator to 1234
using ./aseg.presurf.mgz aseg volume to correct mid
line
8.0.0
8.0.0
reading atlas from /opt/freesurfer-8.0.0/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs
...
reading color table from GCSA file....
average std = 0.9 using min determinant for regularizat
ion = 0.009
0 singular and 325 ill-conditioned covariance matrices regularized
reading surface from
/home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubj
ect/surf/rh.smoothwm...
set_atable_from_ctable(): 36 entries
GCSA::load_default_data(): ninputs=1 s
ulc_only=0 which_norm=0
labeling surface...
1993 labels changed using aseg
relabeling using gibbs priors...
000: 1792 changed, 118059 examined
...
001: 456 changed, 8342 examined...
002: 150 changed, 2513 examined...
003: 78 changed,
856 examined...
004: 53 changed, 432 examined...
005: 37 changed, 284 examined...
006:
24 changed, 204 examined...
007: 15 changed, 126 examined...
008: 11 changed, 90 examined...
009: 6 changed, 68 examined...
010: 4 changed, 43 examined...
011: 1 changed, 24 exa
mined...
012: 1 changed, 7 examined...
013: 2 changed, 6 examined...
014: 0 changed,
11 examined...
486 labels changed using aseg
000: 55 total segments, 22 labels (255 vertices) change
d
001: 33 total segments, 0 labels (0 vertices) changed
10 filter iterations complete (10 requested,
3 changed)
rationalizing unknown annotations with cortex label
relabeling unknown label...
relabeli
ng corpuscallosum label...
841 vertices marked for relabeling...
841 labels changed in reclassification.
writing output to ../label/rh.aparc.DKTatlas.annot...
classi
fication took 0 minutes and 10 seconds.
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clin
ical
outvol aparc+aseg.mgz
32 avail.processors, using 2
Loading aseg.mgz
Loading ../surf/lh.white
Lo
ading ../surf/lh.pial
Loading ../label/lh.cortex.label
Ripping lh vertices labeled not in lh.cortex.
label
ripped 6447 vertices from lh hemi
Loading ../label/lh.aparc.annot
Loading ../surf/rh.white
L
oading ../surf/rh.pial
Loading ../label/rh.cortex.label
Ripping rh vertices labeled not in rh.cortex
.label
ripped 6430 vertices from rh hemi
Loading ../label/rh.aparc.annot
Done loading
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nrelabeled = 0
ndotcheck = 10375
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak 790704
mri_surf2volseg done
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clin
ical
outvol aparc.a2009s+aseg.mgz
32 avail.processors, using 2
Loading aseg.mgz
Loading ../surf/lh.w
hite
Loading ../surf/lh.pial
Loading ../label/lh.cortex.label
Ripping lh vertices labeled not in lh.
cortex.label
ripped 6447 vertices from lh hemi
Loading ../label/lh.aparc.a2009s.annot
Loading ../s
urf/rh.white
Loading ../surf/rh.pial
Loading ../label/rh.cortex.label
Ripping rh vertices labeled no
t in rh.cortex.label
ripped 6430 vertices from rh hemi
Loading ../label/rh.aparc.a2009s.annot
Done
loading
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nrelabeled = 0
ndotcheck = 10375
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak 790780
mri_surf2volseg done
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clin
ical
outvol aparc.DKTatlas+aseg.mgz
32 avail.processors, using 2
Loading aseg.mgz
Loading ../surf/lh
.white
Loading ../surf/lh.pial
Loading ../label/lh.cortex.label
Ripping lh vertices labeled not in l
h.cortex.label
ripped 6447 vertices from lh hemi
Loading ../label/lh.aparc.DKTatlas.annot
Loading
../surf/rh.white
Loading ../surf/rh.pial
Loading ../label/rh.cortex.label
Ripping rh vertices labele
d not in rh.cortex.label
ripped 6430 vertices from rh hemi
Loading ../label/rh.aparc.DKTatlas.anno
t
Done loading
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nrelabeled = 0
ndotcheck = 10375
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak 790704
mri_surf2volseg done
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clin
ical
outvol wmparc.mgz
32 avail.processors, using 2
Loading aparc+aseg.mgz
Loading ../surf/lh.white
Loading ../surf/lh.pial
Loading ../label/lh.cortex.label
Ripping lh vertices labeled not in lh.corte
x.label
ripped 6447 vertices from lh hemi
Loading ../label/lh.aparc.annot
Loading ../surf/rh.white
Loading ../surf/rh.pial
Loading ../label/rh.cortex.label
Ripping rh vertices labeled not in rh.cort
ex.label
ripped 6430 vertices from rh hemi
Loading ../label/rh.aparc.annot
Done loading
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nrelabeled = 0
ndotcheck = 3461
Starting Surf2VolSeg free
free done
#VMPC# mri_surf2volseg VmPeak 790716
mri_surf2volseg done
computing statistics for each annotation in ../label/lh.aparc.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/lh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/lh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.la
bel as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total f
ace volume 213820
Total vertex volume 213649 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- st
andard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curv
ature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1439845
mm^3 (det: 1.352997 )
1733 1120 2756 2.581 0.353 0.086 0.015 8 1.0 ban
kssts
842 625 1718 2.605 0.651 0.160 0.032 19 1.1 caudalanteriorcingulate
2813 1823 5157 2.663 0.379 0.098 0.016 18 2.0 caudalmiddlefrontal
1550
1278 2782 2.115 0.426 0.175 0.047 24 3.6 cuneus
388 236 826 3.063 0.5
46 0.103 0.021 3 0.3 entorhinal
3311 2505 6977 2.660 0.428 0.126 0
.024 39 3.4 fusiform
6195 3924 10448 2.463 0.371 0.102 0.019 54 4.
9 inferiorparietal
4271 3189 10219 2.839 0.507 0.136 0.027 54 5.0 inferiort
emporal
1124 784 1984 2.421 0.644 0.117 0.025 11 1.1 isthmuscingulate
662
5 4680 9879 2.057 0.393 0.146 0.033 84 10.3 lateraloccipital
3471 2434 6
956 2.734 0.526 0.121 0.022 33 3.3 lateralorbitofrontal
3250 2755 6064 2.1
61 0.527 0.170 0.037 53 5.8 lingual
2478 1878 4699 2.373 0.660 0.116
0.022 32 2.5 medialorbitofrontal
4421 3259 12045 2.947 0.663 0.126 0.023
54 4.6 middletemporal
1142 699 1936 2.411 0.552 0.067 0.011 5 0.
4 parahippocampal
1859 1178 2864 2.288 0.464 0.095 0.013 11 1.1 paracentra
l
2149 1423 4023 2.644 0.380 0.104 0.017 15 1.5 parsopercularis
924 66
2 2159 2.659 0.473 0.132 0.026 11 1.0 parsorbitalis
1989 1264 3375 2.524
0.340 0.096 0.015 16 1.2 parstriangularis
1055 1262 2314 1.925 0.519 0
.239 0.066 20 3.3 pericalcarine
5916 3886 8514 2.008 0.556 0.105 0.018
50 4.6 postcentral
1542 1045 2612 2.435 0.537 0.120 0.023 17 1.5
posteriorcingulate
7289 4621 12398 2.489 0.433 0.095 0.015 47 4.6 precentra
l
4736 3233 8227 2.365 0.458 0.112 0.018 44 3.9 precuneus
1034 745 25
20 3.042 0.679 0.140 0.027 15 1.2 rostralanteriorcingulate
7540 5661 15487
2.481 0.404 0.137 0.027 98 9.5 rostralmiddlefrontal
10160 6788 20574 2.733 0.
473 0.111 0.019 82 8.3 superiorfrontal
7676 4884 11440 2.158 0.418 0.107
0.020 64 7.1 superiorparietal
5551 3781 12110 2.792 0.671 0.108 0.019
52 4.8 superiortemporal
5792 3883 11011 2.625 0.494 0.118 0.021 55
5.0 supramarginal
349 291 930 2.581 0.471 0.162 0.032 6 0.5 frontalpol
e
409 308 1403 3.487 0.545 0.130 0.027 4 0.5 temporalpole
676 392
1020 2.359 0.255 0.093 0.013 5 0.3 transversetemporal
2997 2093 6221 3.0
03 0.860 0.110 0.024 29 2.8 insula
mris_anatomical_stats done
computing statistics for each annotation in ../label/lh.aparc.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/lh.pial...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/lh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.la
bel as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total f
ace volume 213820
Total vertex volume 213649 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- st
andard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curv
ature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1439845
mm^3 (det: 1.352997 )
1733 1012 2756 2.581 0.353 0.090 0.023 22 1.4 ban
kssts
842 725 1718 2.605 0.651 0.141 0.035 45 0.8 caudalanteriorcingulate
2813 1996 5157 2.663 0.379 0.107 0.020 27 2.4 caudalmiddlefrontal
1550
1492 2782 2.115 0.426 0.167 0.035 25 2.2 cuneus
388 314 826 3.063 0.5
46 0.166 0.064 7 0.8 entorhinal
3311 2845 6977 2.660 0.428 0.139 0
.031 224 4.0 fusiform
6195 4528 10448 2.463 0.371 0.115 0.022 61 5.
7 inferiorparietal
4271 3895 10219 2.839 0.507 0.151 0.033 385 6.0 inferiort
emporal
1124 847 1984 2.421 0.644 0.125 0.030 38 1.2 isthmuscingulate
662
5 5166 9879 2.057 0.393 0.132 0.029 84 8.0 lateraloccipital
3471 2688 6
956 2.734 0.526 0.133 0.028 62 4.1 lateralorbitofrontal
3250 3044 6064 2.1
61 0.527 0.161 0.036 67 4.8 lingual
2478 2183 4699 2.373 0.660 0.123
0.025 30 2.4 medialorbitofrontal
4421 4706 12045 2.947 0.663 0.158 0.030
56 5.6 middletemporal
1142 942 1936 2.411 0.552 0.114 0.025 8 1.
3 parahippocampal
1859 1337 2864 2.288 0.464 0.106 0.018 18 1.4 paracentra
l
2149 1590 4023 2.644 0.380 0.121 0.022 26 2.0 parsopercularis
924 97
4 2159 2.659 0.473 0.157 0.031 10 1.2 parsorbitalis
1989 1404 3375 2.524
0.340 0.112 0.021 23 1.6 parstriangularis
1055 1267 2314 1.925 0.519 0
.217 0.048 23 2.1 pericalcarine
5916 4650 8514 2.008 0.556 0.117 0.022
59 5.1 postcentral
1542 1102 2612 2.435 0.537 0.116 0.029 37 1.5
posteriorcingulate
7289 5214 12398 2.489 0.433 0.102 0.019 65 5.6 precentra
l
4736 3677 8227 2.365 0.458 0.128 0.024 65 4.6 precuneus
1034 924 25
20 3.042 0.679 0.159 0.043 132 1.3 rostralanteriorcingulate
7540 6885 15487
2.481 0.404 0.154 0.031 120 10.1 rostralmiddlefrontal
10160 8143 20574 2.733 0.
473 0.127 0.026 129 10.5 superiorfrontal
7676 5704 11440 2.158 0.418 0.122
0.023 780 7.0 superiorparietal
5551 4685 12110 2.792 0.671 0.129 0.026
106 5.8 superiortemporal
5792 4391 11011 2.625 0.494 0.127 0.027 87
6.2 supramarginal
349 442 930 2.581 0.471 0.207 0.037 4 0.5 frontalpol
e
409 513 1403 3.487 0.545 0.177 0.032 7 0.6 temporalpole
676 490
1020 2.359 0.255 0.094 0.016 4 0.4 transversetemporal
2997 1932 6221 3.0
03 0.860 0.116 0.027 53 3.4 insula
mris_anatomical_stats done
computing statistics for each annotation in ../label/rh.aparc.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/rh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/rh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.la
bel as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total f
ace volume 216652
Total vertex volume 216510 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- st
andard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curv
ature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1439845
mm^3 (det: 1.352997 )
1197 796 2110 2.761 0.371 0.097 0.017 6 0.9 ban
kssts
971 713 2069 2.609 0.672 0.146 0.025 13 1.1 caudalanteriorcingulate
2932 1861 5465 2.676 0.380 0.104 0.018 22 2.2 caudalmiddlefrontal
1730
1443 2767 1.896 0.348 0.172 0.035 25 3.2 cuneus
366 236 799 3.110 0.4
53 0.078 0.014 2 0.1 entorhinal
3401 2605 7105 2.722 0.476 0.138 0
.025 42 4.0 fusiform
6857 4554 12663 2.562 0.447 0.115 0.021 67 6.
1 inferiorparietal
4228 2884 9546 2.925 0.593 0.126 0.025 48 4.5 inferiort
emporal
1001 710 1875 2.515 0.632 0.125 0.024 10 1.0 isthmuscingulate
681
4 4915 12100 2.253 0.480 0.143 0.029 83 8.9 lateraloccipital
3327 2370 6
664 2.714 0.541 0.122 0.023 38 3.2 lateralorbitofrontal
2967 2610 6112 2.2
85 0.493 0.174 0.040 47 5.6 lingual
2470 1894 4815 2.453 0.578 0.122
0.022 31 2.5 medialorbitofrontal
4988 3403 12052 3.042 0.517 0.119 0.022
55 5.0 middletemporal
1061 650 1748 2.452 0.532 0.075 0.009 5 0.
4 parahippocampal
2022 1306 3226 2.334 0.469 0.090 0.013 10 1.1 paracentra
l
1678 1140 3495 2.834 0.340 0.104 0.016 12 1.2 parsopercularis
1079 75
7 2499 2.694 0.440 0.122 0.024 12 1.0 parsorbitalis
1934 1327 3736 2.652
0.426 0.112 0.019 17 1.4 parstriangularis
1304 1197 1986 1.781 0.413 0
.164 0.035 16 2.1 pericalcarine
5401 3645 8292 2.069 0.543 0.108 0.021
47 4.8 postcentral
1611 1117 2817 2.355 0.679 0.130 0.021 19 1.6
posteriorcingulate
6478 4122 11922 2.676 0.460 0.093 0.014 38 3.9 precentra
l
4728 3208 8233 2.385 0.475 0.109 0.020 45 3.9 precuneus
654 465 14
80 2.901 0.558 0.148 0.027 10 0.8 rostralanteriorcingulate
8545 6163 17034
2.494 0.447 0.130 0.026 102 10.0 rostralmiddlefrontal
9827 6710 20944 2.776 0.
456 0.119 0.024 94 9.6 superiorfrontal
7179 4737 11239 2.186 0.432 0.113
0.020 63 6.2 superiorparietal
5341 3610 11361 2.814 0.507 0.100 0.017
43 4.0 superiortemporal
5054 3390 9923 2.650 0.485 0.116 0.022 51
4.9 supramarginal
379 348 1237 2.641 0.523 0.174 0.036 8 0.6 frontalpol
e
442 365 1889 3.583 0.557 0.137 0.026 5 0.5 temporalpole
538 326
1021 2.724 0.345 0.099 0.013 4 0.3 transversetemporal
3125 2194 6282 2.9
40 0.827 0.104 0.021 32 2.3 insula
mris_anatomical_stats done
computing statistics for each annotation in ../label/rh.aparc.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/rh.pial...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/rh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.la
bel as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total f
ace volume 216652
Total vertex volume 216510 (mask=0)
Saving annotation colortable ../label/aparc.annot.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- st
andard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curv
ature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1439845
mm^3 (det: 1.352997 )
1197 726 2110 2.761 0.371 0.109 0.027 16 1.5 ban
kssts
971 842 2069 2.609 0.672 0.143 0.035 29 1.2 caudalanteriorcingulate
2932 2141 5465 2.676 0.380 0.117 0.022 37 2.8 caudalmiddlefrontal
1730
1671 2767 1.896 0.348 0.153 0.031 22 2.5 cuneus
366 279 799 3.110 0.4
53 0.116 0.030 7 0.3 entorhinal
3401 2776 7105 2.722 0.476 0.144 0
.036 82 4.6 fusiform
6857 5269 12663 2.562 0.447 0.129 0.028 99 7.
3 inferiorparietal
4228 3655 9546 2.925 0.593 0.138 0.031 81 5.3 inferiort
emporal
1001 774 1875 2.515 0.632 0.128 0.037 20 1.4 isthmuscingulate
681
4 5912 12100 2.253 0.480 0.145 0.031 103 9.0 lateraloccipital
3327 2589 6
664 2.714 0.541 0.138 0.029 113 4.1 lateralorbitofrontal
2967 2919 6112 2.2
85 0.493 0.176 0.040 63 5.6 lingual
2470 2125 4815 2.453 0.578 0.124
0.024 56 2.2 medialorbitofrontal
4988 4512 12052 3.042 0.517 0.138 0.029
73 6.2 middletemporal
1061 810 1748 2.452 0.532 0.116 0.024 11 1.
2 parahippocampal
2022 1441 3226 2.334 0.469 0.093 0.016 14 1.3 paracentra
l
1678 1306 3495 2.834 0.340 0.125 0.025 21 1.8 parsopercularis
1079 109
0 2499 2.694 0.440 0.156 0.025 14 1.2 parsorbitalis
1934 1463 3736 2.652
0.426 0.134 0.023 29 1.8 parstriangularis
1304 1165 1986 1.781 0.413 0
.159 0.043 27 2.1 pericalcarine
5401 4464 8292 2.069 0.543 0.129 0.027
86 5.5 postcentral
1611 1254 2817 2.355 0.679 0.131 0.030 37 1.8
posteriorcingulate
6478 4656 11922 2.676 0.460 0.100 0.018 76 4.5 precentra
l
4728 3660 8233 2.385 0.475 0.128 0.026 55 5.1 precuneus
654 544 14
80 2.901 0.558 0.152 0.036 14 0.7 rostralanteriorcingulate
8545 7493 17034
2.494 0.447 0.153 0.032 171 11.3 rostralmiddlefrontal
9827 8299 20944 2.776 0.
456 0.134 0.028 117 11.4 superiorfrontal
7179 5541 11239 2.186 0.432 0.128
0.026 90 7.5 superiorparietal
5341 4402 11361 2.814 0.507 0.120 0.025
98 5.4 superiortemporal
5054 4017 9923 2.650 0.485 0.129 0.026 56
5.2 supramarginal
379 589 1237 2.641 0.523 0.220 0.037 5 0.6 frontalpol
e
442 680 1889 3.583 0.557 0.243 0.063 12 1.4 temporalpole
538 432
1021 2.724 0.345 0.096 0.018 2 0.4 transversetemporal
3125 2006 6282 2.9
40 0.827 0.117 0.026 72 3.0 insula
mris_anatomical_stats done
computing statistics for each annotation in ../label/lh.aparc.a2009s.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/lh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/lh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.la
bel as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total f
ace volume 213820
Total vertex volume 213649 (mask=0)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab
table columns are:
number of vert
ices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thicknes
s +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussi
an curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) =
1439845 mm^3 (det: 1.352997 )
1292 1024 2531 2.435 0.421 0.148 0.032 25 2
.0 G_and_S_frontomargin
1310 919 2202 2.237 0.406 0.136 0.026 15 1.5 G_an
d_S_occipital_inf
1452 928 2277 2.140 0.451 0.107 0.018 13 1.2 G_and_S_par
acentral
1460 1011 3095 2.732 0.373 0.128 0.023 14 1.5 G_and_S_subcentral
681 578 1774 2.476 0.389 0.162 0.029 13 0.8 G_and_S_transv_frontopol
2010
1449 4456 2.977 0.523 0.121 0.022 20 2.0 G_and_S_cingul-Ant
1066 746
1968 2.698 0.436 0.123 0.020 9 1.1 G_and_S_cingul-Mid-Ant
1218 823 2037
2.476 0.355 0.108 0.020 8 1.0 G_and_S_cingul-Mid-Post
534 370 1229 2.911
0.360 0.129 0.029 6 0.6 G_cingul-Post-dorsal
283 199 621 2.588 0.556
0.106 0.019 2 0.2 G_cingul-Post-ventral
1413 1303 2980 2.107 0.454 0.21
0 0.062 28 4.6 G_cuneus
1250 835 3130 2.831 0.364 0.115 0.018 13
1.1 G_front_inf-Opercular
431 282 996 2.620 0.336 0.128 0.023 6 0.
4 G_front_inf-Orbital
1089 692 2343 2.628 0.383 0.106 0.018 12 0.8 G_fron
t_inf-Triangul
3321 2350 7974 2.636 0.428 0.128 0.027 42 4.1 G_front_middle
6958 4566 15687 2.839 0.466 0.117 0.020 64 6.0 G_front_sup
431 377 1
246 3.499 0.868 0.146 0.035 6 0.5 G_Ins_lg_and_S_cent_ins
662 419 2009
3.423 0.845 0.113 0.027 10 0.7 G_insular_short
2134 1242 3539 2.291 0.384
0.128 0.028 29 2.4 G_occipital_middle
1133 792 1768 2.003 0.365 0.153
0.042 16 2.3 G_occipital_sup
1420 1121 3536 2.663 0.408 0.146 0.028
25 1.8 G_oc-temp_lat-fusifor
2147 2010 4728 2.140 0.515 0.206 0.050 47
5.2 G_oc-temp_med-Lingual
1175 698 2118 2.576 0.613 0.074 0.014 5 0.6
G_oc-temp_med-Parahip
1969 1530 5300 2.746 0.552 0.141 0.027 28 2.3 G_orbit
al
2518 1584 5446 2.653 0.391 0.123 0.026 36 2.6 G_pariet_inf-Angular
2782
1836 6374 2.853 0.455 0.125 0.023 32 2.6 G_pariet_inf-Supramar
2873 1830
5391 2.357 0.424 0.118 0.026 33 3.4 G_parietal_sup
2271 1415 3392 2.000
0.413 0.114 0.020 25 2.0 G_postcentral
2486 1538 5430 2.723 0.363 0.10
4 0.017 23 1.8 G_precentral
2475 1687 5109 2.447 0.492 0.119 0.022
30 2.4 G_precuneus
1032 814 2447 2.473 0.517 0.135 0.025 24 1.2 G_r
ectus
644 435 815 1.910 1.009 0.111 0.037 8 1.1 G_subcallosal
513
290 902 2.435 0.278 0.091 0.014 4 0.2 G_temp_sup-G_T_transv
1796 1360 5
842 2.988 0.650 0.150 0.029 29 2.5 G_temp_sup-Lateral
615 403 1608 3.546
0.869 0.063 0.009 1 0.2 G_temp_sup-Plan_polar
1155 715 2009 2.520 0.420
0.079 0.013 6 0.6 G_temp_sup-Plan_tempo
2265 1736 6632 2.934 0.547 0.1
51 0.035 40 3.3 G_temporal_inf
2484 1924 8592 3.133 0.673 0.143 0.027
43 3.0 G_temporal_middle
335 220 402 2.309 0.271 0.087 0.010 1
0.1 Lat_Fis-ant-Horizont
409 258 516 2.481 0.312 0.076 0.010 1 0.1 La
t_Fis-ant-Vertical
1068 686 1355 2.466 0.289 0.096 0.015 5 0.7 Lat_Fi
s-post
1821 1246 2373 1.832 0.326 0.146 0.036 25 3.1 Pole_occipital
1108
862 3698 3.280 0.548 0.137 0.023 13 1.3 Pole_temporal
1454 1418 2505 1
.992 0.556 0.168 0.039 18 2.3 S_calcarine
3012 1996 3350 1.897 0.514 0.
087 0.013 12 1.6 S_central
1005 689 1205 1.979 0.270 0.081 0.009
4 0.4 S_cingul-Marginalis
516 360 933 3.093 0.421 0.098 0.018 2 0
.4 S_circular_insula_ant
1214 794 1916 2.839 0.914 0.077 0.010 4 0.5 S_c
ircular_insula_inf
1647 1101 2289 2.624 0.312 0.096 0.016 7 1.2 S_circular
_insula_sup
575 412 1138 3.036 0.413 0.123 0.025 6 0.5 S_collat_transv_a
nt
330 266 488 2.309 0.334 0.173 0.038 3 0.6 S_collat_transv_post
2298
1595 3833 2.465 0.355 0.115 0.021 18 2.1 S_front_inf
1528 1147 2536 2
.348 0.334 0.131 0.023 14 1.6 S_front_middle
2925 1977 5063 2.503 0.405
0.095 0.015 16 2.0 S_front_sup
450 312 736 2.569 0.380 0.118 0.018
3 0.4 S_interm_prim-Jensen
3019 1930 3800 2.187 0.367 0.085 0.011 12
1.6 S_intrapariet_and_P_trans
866 826 1264 1.903 0.326 0.177 0.041 10
1.9 S_oc_middle_and_Lunatus
1279 915 1571 1.974 0.371 0.115 0.021 8 1.3
S_oc_sup_and_transversal
693 470 895 2.250 0.312 0.085 0.011 3 0.4 S_
occipital_ant
866 635 1517 2.563 0.392 0.109 0.020 6 0.6 S_oc-temp_lat
1770 1201 2651 2.479 0.416 0.096 0.015 10 1.0 S_oc-temp_med_and_Lingual
35
8 251 500 2.357 0.360 0.131 0.025 2 0.4 S_orbital_lateral
690 450
815 2.313 0.451 0.096 0.012 4 0.4 S_orbital_med-olfact
1262 843 2213 2.
785 0.443 0.114 0.023 10 1.3 S_orbital-H_Shaped
1835 1184 2404 2.213 0.357
0.105 0.015 11 1.2 S_parieto_occipital
927 633 835 1.888 0.566 0.156
0.036 24 1.1 S_pericallosal
2968 1888 3462 2.005 0.354 0.099 0.017
21 2.1 S_postcentral
1694 1086 2437 2.538 0.350 0.088 0.012 7 0.9
S_precentral-inf-part
1315 844 1556 2.300 0.292 0.080 0.011 4 0.7 S_prece
ntral-sup-part
563 416 808 2.505 0.409 0.121 0.018 4 0.5 S_suborbital
732 510 1150 2.461 0.350 0.111 0.019 5 0.6 S_subparietal
1598 1138 2
447 2.645 0.431 0.118 0.019 11 1.4 S_temporal_inf
6025 3971 9053 2.531 0.3
77 0.096 0.017 35 4.3 S_temporal_sup
354 228 404 2.420 0.244 0.100
0.010 2 0.2 S_temporal_transverse
mris_anatomical_stats done
computing statistics for each annotation in ../label/rh.aparc.a2009s.annot.
reading input surface /h
ome/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubjec
t/surf/rh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/rh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.la
bel as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total f
ace volume 216652
Total vertex volume 216510 (mask=0)
Saving annotation colortable ../label/aparc.annot.a2009s.ctab
table columns are:
number of vert
ices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thicknes
s +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussi
an curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) =
1439845 mm^3 (det: 1.352997 )
979 775 2185 2.519 0.424 0.153 0.032 17 1
.4 G_and_S_frontomargin
1308 971 2858 2.616 0.403 0.149 0.031 18 1.8 G_an
d_S_occipital_inf
1269 831 2239 2.305 0.442 0.103 0.017 10 0.9 G_and_S_par
acentral
1366 950 2818 2.707 0.300 0.119 0.024 12 1.4 G_and_S_subcentral
910 827 2753 2.654 0.530 0.185 0.040 18 1.6 G_and_S_transv_frontopol
2554
1843 5169 2.752 0.490 0.125 0.023 27 2.6 G_and_S_cingul-Ant
1477 1033
2789 2.675 0.390 0.109 0.019 9 1.2 G_and_S_cingul-Mid-Ant
1189 846 2186
2.470 0.525 0.120 0.021 10 1.1 G_and_S_cingul-Mid-Post
492 351 1208 2.984
0.416 0.141 0.026 7 0.6 G_cingul-Post-dorsal
250 168 594 2.601 0.668
0.117 0.020 3 0.2 G_cingul-Post-ventral
1557 1358 2684 1.897 0.345 0.17
7 0.036 25 2.9 G_cuneus
1180 824 3206 2.931 0.333 0.113 0.019 12
1.0 G_front_inf-Opercular
398 270 998 2.747 0.273 0.129 0.027 5 0.
5 G_front_inf-Orbital
763 522 1949 2.887 0.417 0.123 0.023 9 0.7 G_fron
t_inf-Triangul
3988 2660 8899 2.624 0.503 0.129 0.026 54 5.0 G_front_middle
6772 4496 15739 2.857 0.448 0.124 0.025 78 7.2 G_front_sup
465 370 1
229 3.478 0.809 0.115 0.032 5 0.4 G_Ins_lg_and_S_cent_ins
568 417 1835
3.395 0.713 0.120 0.024 8 0.6 G_insular_short
2233 1478 4909 2.591 0.425
0.137 0.027 31 2.8 G_occipital_middle
1621 1009 2515 2.075 0.432 0.119
0.023 17 1.6 G_occipital_sup
1514 1148 3552 2.729 0.420 0.142 0.025
24 1.7 G_oc-temp_lat-fusifor
1779 1630 4214 2.321 0.501 0.192 0.046 34
4.0 G_oc-temp_med-Lingual
1078 653 2066 2.744 0.580 0.075 0.011 5 0.4
G_oc-temp_med-Parahip
2488 1817 6071 2.649 0.683 0.128 0.028 44 2.6 G_orbit
al
2916 1906 7027 2.740 0.474 0.129 0.026 41 3.3 G_pariet_inf-Angular
2335
1566 5371 2.824 0.478 0.120 0.024 27 2.4 G_pariet_inf-Supramar
2251 1476
4204 2.290 0.486 0.116 0.020 24 2.0 G_parietal_sup
2052 1435 3519 2.041
0.483 0.131 0.027 26 2.6 G_postcentral
2305 1396 5607 2.938 0.366 0.10
4 0.016 20 1.5 G_precentral
2067 1409 4299 2.426 0.486 0.111 0.019
25 1.7 G_precuneus
700 615 1804 2.404 0.507 0.142 0.026 12 0.9 G_r
ectus
344 216 582 2.558 1.002 0.069 0.019 1 0.1 G_subcallosal
360
213 772 2.819 0.354 0.108 0.015 3 0.2 G_temp_sup-G_T_transv
1725 1217 4
912 2.989 0.474 0.127 0.022 24 1.7 G_temp_sup-Lateral
663 441 1395 2.968
0.556 0.065 0.011 2 0.3 G_temp_sup-Plan_polar
915 622 1748 2.573 0.392
0.095 0.016 7 0.7 G_temp_sup-Plan_tempo
2517 1665 6522 2.998 0.632 0.1
32 0.027 34 3.1 G_temporal_inf
2844 1970 8252 3.146 0.485 0.127 0.024
42 3.1 G_temporal_middle
343 229 452 2.396 0.310 0.085 0.009 1
0.1 Lat_Fis-ant-Horizont
296 194 391 2.574 0.308 0.087 0.013 1 0.1 La
t_Fis-ant-Vertical
1364 923 1871 2.516 0.386 0.095 0.015 6 0.9 Lat_Fi
s-post
2989 2397 5019 1.938 0.443 0.172 0.040 47 5.6 Pole_occipital
1195
978 4469 3.327 0.617 0.161 0.030 19 1.6 Pole_temporal
1522 1240 2288 2
.096 0.536 0.139 0.027 14 1.9 S_calcarine
2674 1765 3140 2.037 0.556 0.
080 0.012 9 1.4 S_central
1264 864 1662 2.052 0.409 0.093 0.014
7 0.7 S_cingul-Marginalis
518 357 855 2.998 0.387 0.084 0.012 1 0
.3 S_circular_insula_ant
1092 711 1664 2.724 0.711 0.070 0.009 3 0.4 S_c
ircular_insula_inf
1296 882 1928 2.742 0.365 0.092 0.015 5 0.9 S_circular
_insula_sup
723 499 1408 3.096 0.529 0.112 0.019 6 0.6 S_collat_transv_a
nt
335 281 498 2.170 0.264 0.160 0.037 3 0.5 S_collat_transv_post
1888
1296 3363 2.568 0.384 0.116 0.020 15 1.6 S_front_inf
2475 1736 4200 2
.442 0.382 0.115 0.022 20 2.2 S_front_middle
2355 1617 3608 2.473 0.346
0.102 0.018 13 1.8 S_front_sup
217 157 334 2.526 0.336 0.125 0.030
2 0.2 S_interm_prim-Jensen
2889 1953 3937 2.195 0.374 0.106 0.017 18
2.1 S_intrapariet_and_P_trans
883 635 1204 2.321 0.396 0.119 0.023 5
0.8 S_oc_middle_and_Lunatus
1158 781 1445 2.070 0.366 0.094 0.013 6 0.6
S_oc_sup_and_transversal
545 418 869 2.499 0.381 0.149 0.030 7 0.8 S_
occipital_ant
802 605 1363 2.675 0.437 0.128 0.026 7 0.7 S_oc-temp_lat
1588 1122 2266 2.401 0.425 0.101 0.017 9 1.1 S_oc-temp_med_and_Lingual
38
4 295 610 2.365 0.399 0.123 0.020 3 0.3 S_orbital_lateral
679 482
885 2.172 0.586 0.104 0.016 4 0.5 S_orbital_med-olfact
1279 875 2267 2.
704 0.405 0.121 0.022 12 1.2 S_orbital-H_Shaped
1907 1250 2506 2.177 0.370
0.104 0.017 12 1.4 S_parieto_occipital
1008 687 903 1.924 0.673 0.154
0.026 17 1.0 S_pericallosal
2146 1361 2544 2.092 0.381 0.103 0.016
15 1.5 S_postcentral
1522 953 2087 2.673 0.417 0.078 0.010 5 0.7
S_precentral-inf-part
1212 786 1600 2.434 0.383 0.084 0.011 5 0.6 S_prece
ntral-sup-part
293 236 487 2.427 0.331 0.144 0.017 3 0.3 S_suborbital
886 627 1623 2.604 0.454 0.118 0.024 8 0.8 S_subparietal
1275 882 1
849 2.756 0.446 0.111 0.017 7 1.0 S_temporal_inf
6097 4072 9754 2.711 0.4
23 0.100 0.018 34 4.7 S_temporal_sup
338 230 482 2.605 0.404 0.102
0.014 2 0.3 S_temporal_transverse
mris_anatomical_stats done
computing statistics for each annotation in ../label/lh.aparc.DKTatlas.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/lh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/lh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/lh.cortex.la
bel as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total f
ace volume 213820
Total vertex volume 213649 (mask=0)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab
table columns are:
number of ve
rtices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickn
ess +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaus
sian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV)
= 1439845 mm^3 (det: 1.352997 )
1401 994 2585 2.647 0.587 0.142 0.027 24
1.6 caudalanteriorcingulate
3009 1947 5489 2.655 0.379 0.098 0.016 20 2.1
caudalmiddlefrontal
2242 1735 3774 2.120 0.399 0.159 0.042 31 4.6 cuneus
420 234 806 2.978 0.520 0.089 0.021 3 0.3 entorhinal
3085 2329 6345
2.629 0.413 0.126 0.025 36 3.1 fusiform
6386 4074 10916 2.458 0.383 0.
104 0.019 57 5.1 inferiorparietal
4087 3088 10322 2.869 0.514 0.140 0.02
9 55 5.1 inferiortemporal
1140 791 1994 2.409 0.650 0.118 0.025 11
1.1 isthmuscingulate
6596 4679 9716 2.043 0.401 0.148 0.033 83 10.5 late
raloccipital
3809 2729 7731 2.652 0.592 0.130 0.026 53 4.7 lateralorbitofro
ntal
3335 2806 6220 2.162 0.518 0.169 0.037 55 5.9 lingual
2119 1570 4
083 2.377 0.647 0.111 0.020 29 1.9 medialorbitofrontal
6056 4343 14551 2.84
5 0.619 0.118 0.021 64 5.6 middletemporal
1089 682 1861 2.407 0.545 0.
065 0.010 4 0.4 parahippocampal
2179 1378 3413 2.333 0.465 0.096 0.014
13 1.3 paracentral
2003 1323 3765 2.674 0.363 0.104 0.018 14 1.4
parsopercularis
986 685 1986 2.596 0.352 0.110 0.017 8 0.8 parsorbital
is
2392 1540 4195 2.531 0.356 0.103 0.017 21 1.8 parstriangularis
1050 1
255 2258 1.901 0.500 0.233 0.063 18 3.1 pericalcarine
6762 4438 9633 2.0
40 0.553 0.107 0.019 56 5.4 postcentral
1659 1120 2765 2.452 0.510 0.11
9 0.024 18 1.6 posteriorcingulate
7192 4562 12219 2.496 0.429 0.096 0.01
4 46 4.6 precentral
4684 3201 8386 2.375 0.462 0.113 0.018 45 3.9
precuneus
1420 1040 3193 2.940 0.721 0.139 0.028 19 1.8 rostralanteriorci
ngulate
5380 3989 10995 2.507 0.411 0.135 0.028 60 6.6 rostralmiddlefrontal
11092 7706 23317 2.677 0.489 0.117 0.021 101 9.9 superiorfrontal
6182 3875
9197 2.167 0.421 0.104 0.020 51 5.3 superiorparietal
7136 4851 15451 2.81
2 0.657 0.106 0.019 61 6.1 superiortemporal
5147 3455 9829 2.639 0.486
0.117 0.021 49 4.4 supramarginal
677 394 1022 2.360 0.258 0.094 0.013
5 0.3 transversetemporal
2542 1777 5633 3.129 0.810 0.105 0.021 22
2.0 insula
mris_anatomical_stats done
computing statistics for each annotation in ../label/rh.aparc.DKTatlas.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/rh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/rh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
INFO: using ../label/rh.cortex.la
bel as mask to calc cortex NumVert, SurfArea and MeanThickness.
Using TH3 vertex volume calc
Total f
ace volume 216652
Total vertex volume 216510 (mask=0)
Saving annotation colortable ../label/aparc.annot.DKTatlas.ctab
table columns are:
number of ve
rtices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickn
ess +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaus
sian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV)
= 1439845 mm^3 (det: 1.352997 )
1023 749 2122 2.579 0.667 0.145 0.024 14
1.1 caudalanteriorcingulate
3029 1916 5540 2.668 0.381 0.107 0.018 24 2.4
caudalmiddlefrontal
2167 1722 3277 1.894 0.342 0.153 0.029 27 3.2 cuneus
397 245 830 3.091 0.438 0.076 0.013 2 0.2 entorhinal
3054 2321 6215
2.732 0.468 0.138 0.025 37 3.5 fusiform
6809 4538 12566 2.554 0.446 0.
116 0.021 67 6.1 inferiorparietal
4518 3163 10605 2.906 0.604 0.128 0.02
5 53 4.9 inferiortemporal
1021 719 1857 2.483 0.623 0.122 0.024 10
1.0 isthmuscingulate
7056 5026 12326 2.241 0.479 0.142 0.030 85 9.3 late
raloccipital
3852 2838 8248 2.628 0.619 0.129 0.026 58 4.2 lateralorbitofro
ntal
2889 2535 5961 2.288 0.495 0.172 0.039 44 5.2 lingual
1887 1490 4
021 2.449 0.658 0.120 0.022 23 1.9 medialorbitofrontal
5836 3978 13445 3.00
8 0.504 0.117 0.021 61 5.7 middletemporal
1024 635 1668 2.436 0.507 0.
073 0.009 4 0.4 parahippocampal
2114 1355 3390 2.354 0.467 0.087 0.013
11 1.2 paracentral
1938 1310 3884 2.804 0.351 0.104 0.016 14 1.3
parsopercularis
873 614 1947 2.689 0.397 0.110 0.019 8 0.7 parsorbital
is
1926 1332 3707 2.626 0.435 0.119 0.020 18 1.7 parstriangularis
1324 1
244 2080 1.777 0.401 0.177 0.040 19 2.6 pericalcarine
5931 4009 9107 2.0
79 0.539 0.110 0.021 53 5.4 postcentral
1684 1165 2985 2.381 0.676 0.12
9 0.022 20 1.7 posteriorcingulate
6300 4009 11782 2.689 0.461 0.092 0.01
4 37 3.8 precentral
4944 3351 8736 2.391 0.470 0.111 0.020 48 4.2
precuneus
946 666 1970 2.796 0.604 0.137 0.024 13 1.0 rostralanteriorci
ngulate
6318 4430 12614 2.512 0.461 0.126 0.026 74 7.2 rostralmiddlefrontal
12412 8649 25672 2.704 0.464 0.123 0.024 126 12.6 superiorfrontal
5717 3784
9157 2.216 0.437 0.114 0.020 51 4.9 superiorparietal
6580 4501 14527 2.85
6 0.537 0.103 0.018 53 5.1 superiortemporal
4907 3278 9596 2.652 0.487
0.113 0.021 47 4.5 supramarginal
511 309 991 2.720 0.349 0.098 0.013
4 0.3 transversetemporal
2642 1892 5686 3.098 0.695 0.100 0.018 20
1.8 insula
mris_anatomical_stats done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = .
/lh.BA1_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg =
sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SU
BJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-cli
nical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 4129 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 4129 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 73
Checking for and removing dup
licates
Writing label file ./lh.BA1_exvivo.label 4202
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = .
/lh.BA2_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg =
sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SU
BJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-cli
nical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 7909 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 7909 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 223
Checking for and removing du
plicates
Writing label file ./lh.BA2_exvivo.label 8132
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.BA3a_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 4077 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 4077 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 52
Checking for and removing dup
licates
Writing label file ./lh.BA3a_exvivo.label 4129
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.BA3b_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 5983 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 5983 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 87
Checking for and removing dup
licates
Writing label file ./lh.BA3b_exvivo.label 6070
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.BA4a_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 5784 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 5784 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 68
Checking for and removing dup
licates
Writing label file ./lh.BA4a_exvivo.label 5852
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.BA4p_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 4070 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 4070 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 54
Checking for and removing dup
licates
Writing label file ./lh.BA4p_exvivo.label 4124
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = .
/lh.BA6_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg =
sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SU
BJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-cli
nical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 13589 points in source label
.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 13589 nlabel points
Performing mapping from tar
get back to the source label 119704
Number of reverse mapping hits = 431
Checking for and removing d
uplicates
Writing label file ./lh.BA6_exvivo.label 14020
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.BA44_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 4181 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 4181 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 87
Checking for and removing dup
licates
Writing label file ./lh.BA44_exvivo.label 4268
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.BA45_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3422 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3422 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 354
Checking for and removing du
plicates
Writing label file ./lh.BA45_exvivo.label 3776
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = ./
lh.V1_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sp
here.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJ
ECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 4641 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 4641 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 390
Checking for and removing du
plicates
Writing label file ./lh.V1_exvivo.label 5031
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = ./
lh.V2_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sp
here.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJ
ECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 8114 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 8114 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 919
Checking for and removing du
plicates
Writing label file ./lh.V2_exvivo.label 9033
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = ./
lh.MT_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sp
here.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJ
ECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 2018 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 2018 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 145
Checking for and removing du
plicates
Writing label file ./lh.MT_exvivo.label 2163
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./lh.entorhinal_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1290 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1290 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 1
Checking for and removing dupl
icates
Writing label file ./lh.entorhinal_exvivo.label 1291
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./lh.perirhinal_exvivo.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1199 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1199 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 2
Checking for and removing dupl
icates
Writing label file ./lh.perirhinal_exvivo.label 1201
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.FG1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.FG1.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfre
g = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 414 points in source lab
el.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 414 nlabel points
Performing mapping from targe
t back to the source label 119704
Number of reverse mapping hits = 59
Checking for and removing dupl
icates
Writing label file ./lh.FG1.mpm.vpnl.label 473
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.FG2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.FG2.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfre
g = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 703 points in source lab
el.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 703 nlabel points
Performing mapping from targe
t back to the source label 119704
Number of reverse mapping hits = 89
Checking for and removing dupl
icates
Writing label file ./lh.FG2.mpm.vpnl.label 792
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.FG3.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.FG3.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfre
g = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1873 points in source la
bel.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1873 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 47
Checking for and removing dup
licates
Writing label file ./lh.FG3.mpm.vpnl.label 1920
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.FG4.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./lh.FG4.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfre
g = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 2101 points in source la
bel.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 2101 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 170
Checking for and removing du
plicates
Writing label file ./lh.FG4.mpm.vpnl.label 2271
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.hOc1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel
= ./lh.hOc1.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurf
reg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint
0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-a
ll-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3877 points in source
label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3877 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 220
Checking for and removing du
plicates
Writing label file ./lh.hOc1.mpm.vpnl.label 4097
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.hOc2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel
= ./lh.hOc2.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurf
reg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint
0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-a
ll-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 2919 points in source
label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 2919 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 449
Checking for and removing du
plicates
Writing label file ./lh.hOc2.mpm.vpnl.label 3368
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.hOc3v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel
= ./lh.hOc3v.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsu
rfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPai
nt 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1286 points in sourc
e label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1286 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 166
Checking for and removing du
plicates
Writing label file ./lh.hOc3v.mpm.vpnl.label 1452
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.hOc4v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel
= ./lh.hOc4v.mpm.vpnl.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsu
rfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPai
nt 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1006 points in sourc
e label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1006 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 152
Checking for and removing du
plicates
Writing label file ./lh.hOc4v.mpm.vpnl.label 1158
mri_label2label: Done
Reading ctab /opt/freesurfer-8.0.0/average/colortable_vpnl.txt
Number of ctab entries 9
8.0.0
cwd /
home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubje
ct/label
cmdline mris_label2annot --s TestSubject --ctab /opt/freesurfer-8.0.0/average/colortable_vp
nl.txt --hemi lh --a mpm.vpnl --maxstatwinner --noverbose --l lh.FG1.mpm.vpnl.label --l lh.FG2.mpm.v
pnl.label --l lh.FG3.mpm.vpnl.label --l lh.FG4.mpm.vpnl.label --l lh.hOc1.mpm.vpnl.label --l lh.hOc2
.mpm.vpnl.label --l lh.hOc3v.mpm.vpnl.label --l lh.hOc4v.mpm.vpnl.label
sysname Linux
hostname 057
6828a704f
machine x86_64
user jovyan
subject TestSubject
hemi lh
SUBJECTS_DIR /home/jovyan/
workspace/books/examples/structural_imaging/data/structural/recon-all-clinical
ColorTable /opt/frees
urfer-8.0.0/average/colortable_vpnl.txt
AnnotName mpm.vpnl
nlables 8
LabelThresh 0 0.000000
ERROR:
/home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubj
ect/label/lh.mpm.vpnl.annot already exists
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./lh.BA1_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1014 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1014 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 8
Checking for and removing dupl
icates
Writing label file ./lh.BA1_exvivo.thresh.label 1022
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./lh.BA2_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 2092 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 2092 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 71
Checking for and removing dup
licates
Writing label file ./lh.BA2_exvivo.thresh.label 2163
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./lh.BA3a_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1504 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1504 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 13
Checking for and removing dup
licates
Writing label file ./lh.BA3a_exvivo.thresh.label 1517
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./lh.BA3b_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1996 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1996 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 22
Checking for and removing dup
licates
Writing label file ./lh.BA3b_exvivo.thresh.label 2018
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./lh.BA4a_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 2319 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 2319 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 29
Checking for and removing dup
licates
Writing label file ./lh.BA4a_exvivo.thresh.label 2348
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./lh.BA4p_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1549 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1549 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 9
Checking for and removing dupl
icates
Writing label file ./lh.BA4p_exvivo.thresh.label 1558
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./lh.BA6_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 7035 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 7035 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 122
Checking for and removing du
plicates
Writing label file ./lh.BA6_exvivo.thresh.label 7157
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./lh.BA44_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1912 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1912 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 43
Checking for and removing dup
licates
Writing label file ./lh.BA44_exvivo.thresh.label 1955
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./lh.BA45_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1151 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1151 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 142
Checking for and removing du
plicates
Writing label file ./lh.BA45_exvivo.thresh.label 1293
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trglab
el = ./lh.V1_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
s
rcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
D
oPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/r
econ-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3405 points in s
ource label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3405 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 198
Checking for and removing du
plicates
Writing label file ./lh.V1_exvivo.thresh.label 3603
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trglab
el = ./lh.V2_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
s
rcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
D
oPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/r
econ-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3334 points in s
ource label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3334 nlabel points
Performing mapping from targ
et back to the source label 119704
Number of reverse mapping hits = 406
Checking for and removing du
plicates
Writing label file ./lh.V2_exvivo.thresh.label 3740
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trglab
el = ./lh.MT_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgsurface = white
s
rcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
D
oPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/r
econ-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 513 points in so
urce label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 513 nlabel points
Performing mapping from targe
t back to the source label 119704
Number of reverse mapping hits = 35
Checking for and removing dupl
icates
Writing label file ./lh.MT_exvivo.thresh.label 548
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.entorhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubjec
t
trglabel = ./lh.entorhinal_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgs
urface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use P
rojFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/d
ata/structural/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found
470 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 470 nlabel points
Performing mapping from targe
t back to the source label 119704
Number of reverse mapping hits = 0
Checking for and removing dupli
cates
Writing label file ./lh.entorhinal_exvivo.thresh.label 470
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/lh.perirhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubjec
t
trglabel = ./lh.perirhinal_exvivo.thresh.label
regmethod = surface
srchemi = lh
trghemi = lh
trgs
urface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use P
rojFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/d
ata/structural/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found
450 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/lh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/lh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/lh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 450 nlabel points
Performing mapping from targe
t back to the source label 119704
Number of reverse mapping hits = 0
Checking for and removing dupli
cates
Writing label file ./lh.perirhinal_exvivo.thresh.label 450
mri_label2label: Done
Reading ctab /opt/freesurfer-8.0.0/average/colortable_BA.txt
Number of ctab entries 15
8.0.0
cwd /h
ome/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubjec
t/label
cmdline mris_label2annot --s TestSubject --hemi lh --ctab /opt/freesurfer-8.0.0/average/colo
rtable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_e
xvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_ex
vivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.l
abel --l lh.perirhinal_exvivo.label --l lh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --n
overbose
sysname Linux
hostname 0576828a704f
machine x86_64
user jovyan
subject TestSubject
hemi lh
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/rec
on-all-clinical
ColorTable /opt/freesurfer-8.0.0/average/colortable_BA.txt
AnnotName BA_exvivo
nlab
les 14
LabelThresh 0 0.000000
ERROR: /home/jovyan/workspace/books/examples/structural_imaging/data/s
tructural/recon-all-clinical/TestSubject/label/lh.BA_exvivo.annot already exists
Reading ctab /opt/freesurfer-8.0.0/average/colortable_BA_thresh.txt
Number of ctab entries 15
8.0.0
cwd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/Tes
tSubject/label
cmdline mris_label2annot --s TestSubject --hemi lh --ctab /opt/freesurfer-8.0.0/avera
ge/colortable_BA_thresh.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3
a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_ex
vivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.
thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.lab
el --l lh.perirhinal_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh
--maxstatwinner --noverbose
sysname Linux
hostname 0576828a704f
machine x86_64
user jovyan
s
ubject TestSubject
hemi lh
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/
data/structural/recon-all-clinical
ColorTable /opt/freesurfer-8.0.0/average/colortable_BA_thresh.txt
AnnotName BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
ERROR: /home/jovyan/workspace/books/e
xamples/structural_imaging/data/structural/recon-all-clinical/TestSubject/label/lh.BA_exvivo.thresh.
annot already exists
computing statistics for each annotation in ./lh.BA_exvivo.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/lh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/lh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Tota
l face volume 213820
Total vertex volume 213649 (mask=0)
Saving annotation colortable ./BA_exvivo.ctab
table columns are:
number of vertices
total s
urface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard de
viation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1439845 mm^3
(det: 1.352997 )
1027 654 1661 2.069 0.435 0.133 0.025 13 1.1 BA1_exvivo
3885 2438 5374 2.114 0.445 0.102 0.018 32 2.9 BA2_exvivo
1065 721 999
1.760 0.370 0.127 0.022 9 1.0 BA3a_exvivo
2237 1527 2972 1.842 0.531
0.099 0.016 17 1.6 BA3b_exvivo
1480 858 2543 2.595 0.358 0.087 0.012
8 0.7 BA4a_exvivo
1266 822 1996 2.465 0.412 0.079 0.011 5 0.6
BA4p_exvivo
8806 5493 17364 2.695 0.437 0.102 0.017 67 6.4 BA6_exvivo
2270
1479 4161 2.646 0.357 0.095 0.015 14 1.6 BA44_exvivo
2786 1865 5245 2
.533 0.370 0.111 0.020 27 2.2 BA45_exvivo
2115 2251 4348 1.884 0.514 0.
225 0.065 45 6.6 V1_exvivo
6171 4880 10336 2.041 0.430 0.168 0.041
93 11.8 V2_exvivo
1735 1151 2857 2.293 0.380 0.120 0.020 18 1.7 MT_exv
ivo
415 268 759 2.731 0.619 0.093 0.016 3 0.3 perirhinal_exvivo
304
184 620 2.896 0.530 0.063 0.012 1 0.1 entorhinal_exvivo
mris_anatomical_st
ats done
computing statistics for each annotation in ./lh.BA_exvivo.thresh.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/lh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/lh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/lh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Tota
l face volume 213820
Total vertex volume 213649 (mask=0)
Saving annotation colortable ./BA_exvivo.thresh.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- stan
dard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvat
ure
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1439845 m
m^3 (det: 1.352997 )
617 378 958 2.027 0.309 0.140 0.029 9 0.7 BA1_e
xvivo.thresh
1566 999 2009 1.967 0.402 0.096 0.015 11 1.1 BA2_exvivo.thres
h
886 602 771 1.728 0.347 0.130 0.023 7 0.9 BA3a_exvivo.thresh
1375
889 1459 1.551 0.339 0.073 0.010 6 0.7 BA3b_exvivo.thresh
1444 841 248
5 2.613 0.364 0.080 0.011 7 0.6 BA4a_exvivo.thresh
1002 667 1535 2.354 0
.409 0.078 0.010 4 0.5 BA4p_exvivo.thresh
4741 2983 9260 2.652 0.437 0
.104 0.017 34 3.5 BA6_exvivo.thresh
1403 904 2642 2.625 0.352 0.095 0.
015 10 1.0 BA44_exvivo.thresh
1128 740 2312 2.549 0.379 0.110 0.018
12 0.9 BA45_exvivo.thresh
2249 2370 4610 1.877 0.518 0.223 0.065 49 7.2
V1_exvivo.thresh
2995 2483 5103 2.002 0.424 0.180 0.046 50 6.5 V2_exvivo.
thresh
455 300 647 2.156 0.296 0.113 0.016 4 0.3 MT_exvivo.thresh
163
97 253 2.664 0.543 0.081 0.015 1 0.1 perirhinal_exvivo.thresh
193
120 363 2.810 0.455 0.050 0.008 0 0.1 entorhinal_exvivo.thresh
mris_anatomic
al_stats done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA1_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = .
/rh.BA1_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg =
sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SU
BJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-cli
nical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3962 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3962 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 50
Checking for and removing dup
licates
Writing label file ./rh.BA1_exvivo.label 4012
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA2_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = .
/rh.BA2_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg =
sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SU
BJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-cli
nical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 6687 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 6687 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 62
Checking for and removing dup
licates
Writing label file ./rh.BA2_exvivo.label 6749
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA3a_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.BA3a_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3980 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3980 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 18
Checking for and removing dup
licates
Writing label file ./rh.BA3a_exvivo.label 3998
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA3b_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.BA3b_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 4522 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 4522 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 40
Checking for and removing dup
licates
Writing label file ./rh.BA3b_exvivo.label 4562
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA4a_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.BA4a_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 5747 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 5747 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 30
Checking for and removing dup
licates
Writing label file ./rh.BA4a_exvivo.label 5777
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA4p_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.BA4p_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 4473 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 4473 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 24
Checking for and removing dup
licates
Writing label file ./rh.BA4p_exvivo.label 4497
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA6_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = .
/rh.BA6_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg =
sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SU
BJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-cli
nical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 12256 points in source label
.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 12256 nlabel points
Performing mapping from tar
get back to the source label 118059
Number of reverse mapping hits = 202
Checking for and removing d
uplicates
Writing label file ./rh.BA6_exvivo.label 12458
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA44_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.BA44_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 6912 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 6912 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 138
Checking for and removing du
plicates
Writing label file ./rh.BA44_exvivo.label 7050
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA45_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.BA45_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg
= sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-c
linical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 5355 points in source labe
l.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 5355 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 288
Checking for and removing du
plicates
Writing label file ./rh.BA45_exvivo.label 5643
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.V1_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = ./
rh.V1_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sp
here.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJ
ECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 4727 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 4727 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 403
Checking for and removing du
plicates
Writing label file ./rh.V1_exvivo.label 5130
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.V2_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = ./
rh.V2_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sp
here.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJ
ECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 8016 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 8016 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 1124
Checking for and removing d
uplicates
Writing label file ./rh.V2_exvivo.label 9140
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.MT_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel = ./
rh.MT_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sp
here.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJ
ECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1932 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1932 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 200
Checking for and removing du
plicates
Writing label file ./rh.MT_exvivo.label 2132
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.entorhinal_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./rh.entorhinal_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1038 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1038 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 0
Checking for and removing dupl
icates
Writing label file ./rh.entorhinal_exvivo.label 1038
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.perirhinal_exvivo.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./rh.perirhinal_exvivo.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 752 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 752 nlabel points
Performing mapping from targe
t back to the source label 118059
Number of reverse mapping hits = 0
Checking for and removing dupli
cates
Writing label file ./rh.perirhinal_exvivo.label 752
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.FG1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.FG1.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfre
g = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 541 points in source lab
el.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 541 nlabel points
Performing mapping from targe
t back to the source label 118059
Number of reverse mapping hits = 81
Checking for and removing dupl
icates
Writing label file ./rh.FG1.mpm.vpnl.label 622
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.FG2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.FG2.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfre
g = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 721 points in source lab
el.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 721 nlabel points
Performing mapping from targe
t back to the source label 118059
Number of reverse mapping hits = 146
Checking for and removing dup
licates
Writing label file ./rh.FG2.mpm.vpnl.label 867
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.FG3.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.FG3.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfre
g = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1523 points in source la
bel.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1523 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 49
Checking for and removing dup
licates
Writing label file ./rh.FG3.mpm.vpnl.label 1572
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.FG4.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel =
./rh.FG4.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfre
g = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all
-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1586 points in source la
bel.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1586 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 195
Checking for and removing du
plicates
Writing label file ./rh.FG4.mpm.vpnl.label 1781
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.hOc1.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel
= ./rh.hOc1.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurf
reg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint
0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-a
ll-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3667 points in source
label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3667 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 213
Checking for and removing du
plicates
Writing label file ./rh.hOc1.mpm.vpnl.label 3880
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.hOc2.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel
= ./rh.hOc2.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurf
reg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint
0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-a
ll-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 2719 points in source
label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 2719 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 379
Checking for and removing du
plicates
Writing label file ./rh.hOc2.mpm.vpnl.label 3098
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.hOc3v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel
= ./rh.hOc3v.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsu
rfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPai
nt 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1228 points in sourc
e label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1228 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 272
Checking for and removing du
plicates
Writing label file ./rh.hOc3v.mpm.vpnl.label 1500
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.hOc4v.mpm.vpnl.label
srcsubject = fsaverage
trgsubject = TestSubject
trglabel
= ./rh.hOc4v.mpm.vpnl.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsu
rfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPai
nt 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1025 points in sourc
e label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1025 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 290
Checking for and removing du
plicates
Writing label file ./rh.hOc4v.mpm.vpnl.label 1315
mri_label2label: Done
Reading ctab /opt/freesurfer-8.0.0/average/colortable_vpnl.txt
Number of ctab entries 9
8.0.0
cwd /
home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubje
ct/label
cmdline mris_label2annot --s TestSubject --ctab /opt/freesurfer-8.0.0/average/colortable_vp
nl.txt --hemi rh --a mpm.vpnl --maxstatwinner --noverbose --l rh.FG1.mpm.vpnl.label --l rh.FG2.mpm.v
pnl.label --l rh.FG3.mpm.vpnl.label --l rh.FG4.mpm.vpnl.label --l rh.hOc1.mpm.vpnl.label --l rh.hOc2
.mpm.vpnl.label --l rh.hOc3v.mpm.vpnl.label --l rh.hOc4v.mpm.vpnl.label
sysname Linux
hostname 057
6828a704f
machine x86_64
user jovyan
subject TestSubject
hemi rh
SUBJECTS_DIR /home/jovyan/
workspace/books/examples/structural_imaging/data/structural/recon-all-clinical
ColorTable /opt/frees
urfer-8.0.0/average/colortable_vpnl.txt
AnnotName mpm.vpnl
nlables 8
LabelThresh 0 0.000000
ERROR:
/home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubj
ect/label/rh.mpm.vpnl.annot already exists
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./rh.BA1_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 876 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 876 nlabel points
Performing mapping from targe
t back to the source label 118059
Number of reverse mapping hits = 17
Checking for and removing dupl
icates
Writing label file ./rh.BA1_exvivo.thresh.label 893
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./rh.BA2_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 2688 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 2688 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 22
Checking for and removing dup
licates
Writing label file ./rh.BA2_exvivo.thresh.label 2710
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA3a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./rh.BA3a_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1698 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1698 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 5
Checking for and removing dupl
icates
Writing label file ./rh.BA3a_exvivo.thresh.label 1703
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA3b_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./rh.BA3b_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 2183 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 2183 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 12
Checking for and removing dup
licates
Writing label file ./rh.BA3b_exvivo.thresh.label 2195
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA4a_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./rh.BA4a_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1388 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1388 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 5
Checking for and removing dupl
icates
Writing label file ./rh.BA4a_exvivo.thresh.label 1393
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA4p_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./rh.BA4p_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1489 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1489 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 9
Checking for and removing dupl
icates
Writing label file ./rh.BA4p_exvivo.thresh.label 1498
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA6_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgla
bel = ./rh.BA6_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 6959 points in
source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 6959 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 52
Checking for and removing dup
licates
Writing label file ./rh.BA6_exvivo.thresh.label 7011
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA44_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./rh.BA44_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1012 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1012 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 22
Checking for and removing dup
licates
Writing label file ./rh.BA44_exvivo.thresh.label 1034
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.BA45_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trgl
abel = ./rh.BA45_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = whi
te
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0,
0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structur
al/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 1178 points
in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 1178 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 22
Checking for and removing dup
licates
Writing label file ./rh.BA45_exvivo.thresh.label 1200
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.V1_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trglab
el = ./rh.V1_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
s
rcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
D
oPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/r
econ-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3232 points in s
ource label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3232 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 195
Checking for and removing du
plicates
Writing label file ./rh.V1_exvivo.thresh.label 3427
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.V2_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trglab
el = ./rh.V2_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
s
rcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
D
oPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/r
econ-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 3437 points in s
ource label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 3437 nlabel points
Performing mapping from targ
et back to the source label 118059
Number of reverse mapping hits = 456
Checking for and removing du
plicates
Writing label file ./rh.V2_exvivo.thresh.label 3893
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.MT_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubject
trglab
el = ./rh.MT_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgsurface = white
s
rcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use ProjFrac = 0, 0
D
oPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/r
econ-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found 268 points in so
urce label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 268 nlabel points
Performing mapping from targe
t back to the source label 118059
Number of reverse mapping hits = 38
Checking for and removing dupl
icates
Writing label file ./rh.MT_exvivo.thresh.label 306
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.entorhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubjec
t
trglabel = ./rh.entorhinal_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgs
urface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use P
rojFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/d
ata/structural/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found
694 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 694 nlabel points
Performing mapping from targe
t back to the source label 118059
Number of reverse mapping hits = 0
Checking for and removing dupli
cates
Writing label file ./rh.entorhinal_exvivo.thresh.label 694
mri_label2label: Done
srclabel = /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clini
cal/fsaverage/label/rh.perirhinal_exvivo.thresh.label
srcsubject = fsaverage
trgsubject = TestSubjec
t
trglabel = ./rh.perirhinal_exvivo.thresh.label
regmethod = surface
srchemi = rh
trghemi = rh
trgs
urface = white
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
usehash = 1
Use ProjAbs = 0, 0
Use P
rojFrac = 0, 0
DoPaint 0
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/d
ata/structural/recon-all-clinical
FREESURFER_HOME /opt/freesurfer-8.0.0
Loading source label.
Found
291 points in source label.
Starting surface-based mapping
Reading source registration
/home/jovyan/workspace/books/examples/s
tructural_imaging/data/structural/recon-all-clinical/fsaverage/surf/rh.sphere.reg
Rescaling ... ori
ginal radius = 100
Reading target surface
/home/jovyan/workspace/books/examples/structural_imaging
/data/structural/recon-all-clinical/TestSubject/surf/rh.white
Reading target registration
/home/jo
vyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubject/surf
/rh.sphere.reg
Rescaling ... original radius = 100
Building target registration hash (res=16).
Buil
ding source registration hash (res=16).
INFO: found 291 nlabel points
Performing mapping from targe
t back to the source label 118059
Number of reverse mapping hits = 0
Checking for and removing dupli
cates
Writing label file ./rh.perirhinal_exvivo.thresh.label 291
mri_label2label: Done
Reading ctab /opt/freesurfer-8.0.0/average/colortable_BA.txt
Number of ctab entries 15
8.0.0
cwd /h
ome/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/TestSubjec
t/label
cmdline mris_label2annot --s TestSubject --hemi rh --ctab /opt/freesurfer-8.0.0/average/colo
rtable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_e
xvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_ex
vivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.l
abel --l rh.perirhinal_exvivo.label --l rh.entorhinal_exvivo.label --a BA_exvivo --maxstatwinner --n
overbose
sysname Linux
hostname 0576828a704f
machine x86_64
user jovyan
subject TestSubject
hemi rh
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/data/structural/rec
on-all-clinical
ColorTable /opt/freesurfer-8.0.0/average/colortable_BA.txt
AnnotName BA_exvivo
nlab
les 14
LabelThresh 0 0.000000
ERROR: /home/jovyan/workspace/books/examples/structural_imaging/data/s
tructural/recon-all-clinical/TestSubject/label/rh.BA_exvivo.annot already exists
Reading ctab /opt/freesurfer-8.0.0/average/colortable_BA_thresh.txt
Number of ctab entries 15
8.0.0
cwd /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon-all-clinical/Tes
tSubject/label
cmdline mris_label2annot --s TestSubject --hemi rh --ctab /opt/freesurfer-8.0.0/avera
ge/colortable_BA_thresh.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3
a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_ex
vivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.
thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.lab
el --l rh.perirhinal_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --a BA_exvivo.thresh
--maxstatwinner --noverbose
sysname Linux
hostname 0576828a704f
machine x86_64
user jovyan
s
ubject TestSubject
hemi rh
SUBJECTS_DIR /home/jovyan/workspace/books/examples/structural_imaging/
data/structural/recon-all-clinical
ColorTable /opt/freesurfer-8.0.0/average/colortable_BA_thresh.txt
AnnotName BA_exvivo.thresh
nlables 14
LabelThresh 0 0.000000
ERROR: /home/jovyan/workspace/books/e
xamples/structural_imaging/data/structural/recon-all-clinical/TestSubject/label/rh.BA_exvivo.thresh.
annot already exists
computing statistics for each annotation in ./rh.BA_exvivo.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/rh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/rh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Tota
l face volume 216652
Total vertex volume 216510 (mask=0)
Saving annotation colortable ./BA_exvivo.ctab
table columns are:
number of vertices
total s
urface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard de
viation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1439845 mm^3
(det: 1.352997 )
803 571 1517 2.111 0.480 0.159 0.037 14 1.4 BA1_exvivo
2822 1842 4118 2.144 0.434 0.103 0.018 23 2.0 BA2_exvivo
958 675 1005
1.903 0.443 0.128 0.025 7 0.8 BA3a_exvivo
1718 1168 2327 1.772 0.466
0.089 0.014 10 1.3 BA3b_exvivo
1319 817 2644 2.739 0.330 0.082 0.012
6 0.7 BA4a_exvivo
1161 738 1903 2.584 0.370 0.069 0.009 4 0.5
BA4p_exvivo
7197 4540 14756 2.783 0.446 0.099 0.016 51 4.8 BA6_exvivo
3181
2083 6273 2.820 0.372 0.096 0.015 21 2.1 BA44_exvivo
3552 2490 7605 2
.659 0.419 0.125 0.023 38 3.4 BA45_exvivo
2498 2450 4679 1.842 0.475 0.
194 0.045 44 5.6 V1_exvivo
6215 4747 10580 2.106 0.434 0.157 0.034
85 9.9 V2_exvivo
1735 1251 3195 2.578 0.385 0.127 0.025 16 1.9 MT_exv
ivo
211 153 458 2.813 0.602 0.091 0.010 1 0.1 perirhinal_exvivo
283
188 682 3.074 0.489 0.079 0.013 2 0.1 entorhinal_exvivo
mris_anatomical_st
ats done
computing statistics for each annotation in ./rh.BA_exvivo.thresh.annot.
reading input surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/recon
-all-clinical/TestSubject/surf/rh.white...
reading input pial surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural/
recon-all-clinical/TestSubject/surf/rh.pial...
reading input white surface /home/jovyan/workspace/books/examples/structural_imaging/data/structural
/recon-all-clinical/TestSubject/surf/rh.white...
INFO: using TH3 volume calc
INFO: assuming MGZ format for volumes.
Using TH3 vertex volume calc
Tota
l face volume 216652
Total vertex volume 216510 (mask=0)
Saving annotation colortable ./BA_exvivo.thresh.ctab
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- stan
dard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvat
ure
folding index
intrinsic curvature index
structure name
atlas_icv (eTIV) = 1439845 m
m^3 (det: 1.352997 )
532 371 878 1.960 0.504 0.181 0.048 11 1.3 BA1_e
xvivo.thresh
1604 1050 2473 2.149 0.433 0.097 0.016 12 1.0 BA2_exvivo.thres
h
855 608 820 1.858 0.386 0.129 0.022 6 0.8 BA3a_exvivo.thresh
1349
901 1546 1.633 0.371 0.075 0.012 6 0.7 BA3b_exvivo.thresh
798 501 163
6 2.715 0.277 0.087 0.013 4 0.5 BA4a_exvivo.thresh
956 618 1586 2.630 0
.375 0.063 0.008 2 0.3 BA4p_exvivo.thresh
4416 2788 9020 2.771 0.448 0
.100 0.016 32 2.8 BA6_exvivo.thresh
789 532 1714 2.821 0.314 0.100 0.
016 6 0.5 BA44_exvivo.thresh
821 584 2073 2.860 0.421 0.122 0.023
8 0.8 BA45_exvivo.thresh
2363 2271 4241 1.823 0.472 0.191 0.045 40 5.3
V1_exvivo.thresh
3079 2541 5684 2.079 0.447 0.174 0.039 51 5.7 V2_exvivo.
thresh
278 205 748 2.744 0.467 0.153 0.029 3 0.4 MT_exvivo.thresh
15
9 25 2.796 0.170 0.049 0.004 0 0.0 perirhinal_exvivo.thresh
291
185 595 2.980 0.392 0.074 0.009 1 0.1 entorhinal_exvivo.thresh
mris_anatomic
al_stats done
All done!
If you have used results from this software for a publication, please cite:
K Gopina
th, DN Greeve, S Das, S Arnold, C Magdamo, JE Iglesias:
Cortical analysis of heterogeneous clinical
brain MRI scans for large-scale neuroimaging studies
https://arxiv.org/abs/2305.01827
B Billot, DN
Greve, O Puonti, A Thielscher, K Van Leemput, B Fischl, AV Dalca, JE Iglesias:
SynthSeg: Segmentati
on of brain MRI scans of any contrast and resolution without retraining
Medical Image Analysis, 83,
102789 (2023)
B Billot, C Magdamo, SE Arnold, S Das, JE Iglesias:
Robust machine learning segmenta
tion for large-scale analysis of heterogeneous clinical brain MRI datasets
PNAS, 120(9), e2216399120
(2023)
SynthSR: a public AI tool to turn heterogeneous clinical brain scans into high-resolution
T1-weighted images for 3D morphometry
JE Iglesias, B Billot, Y Balbastre, C Magdamo, S Arnold, S Das
, B Edlow, D Alexander, P Golland, B Fischl
Science Advances, 9(5), eadd3607 (2023)
----- recon-all-clinical.sh completed -----
Results saved to: ./data/structural/recon-all-clinical/T
estSubject
🎨 Viewing aseg.mgz
Now we will open the aseg.mgz file. This is FreeSurfer’s automatic brain segmentation, where different brain structures are given unique numbers and colors.
- 📂
aseg.mgz= FreeSurfer’s anatomical segmentation file - 🎨 Each color = a different brain structure (e.g., hippocampus, ventricles, cortex)
- 🧩 Helps us check if FreeSurfer labelled the brain correctly
- ➕ Crosshairs line up the same spot across all views
➡️ Click the cell below, then press Command + Enter (Mac) or Control + Enter (Windows/Linux).
This will open aseg.mgz in the viewer with FreeSurfer colors.
# Display aseg.mgz in FreeSurfer colors, labels 0–100
import tempfile, os
from pathlib import Path
ASEG_PATH = "./data/structural/recon-all-clinical/TestSubject/mri/aseg.mgz"
assert Path(ASEG_PATH).exists(), f"Missing aseg: {ASEG_PATH}"
aseg_img = nib.load(ASEG_PATH)
aseg = np.rint(aseg_img.get_fdata()).astype(np.int32)
# Keep only labels 0–100, everything else to 0
aseg = np.where((aseg >= 0) & (aseg <= 100), aseg, 0)
# Save temporary integer NIfTI
tmp_path = os.path.join(tempfile.gettempdir(), "aseg_fs_0to100.nii.gz")
nib.save(nib.Nifti1Image(aseg, aseg_img.affine, aseg_img.header), tmp_path)
# Viewer
nv = NiiVue(
height=600,
multiplanar_layout="GRID",
multiplanar_show_render=True,
is_colorbar=True,
is_orient_cube=True,
is_radiological_convention=True,
back_color=(0.1, 0.1, 0.1, 1.0),
)
# Use FreeSurfer colormap
nv.add_volume({
"path": tmp_path,
"name": "aseg",
"opacity": 1.0,
"colormap": "freesurfer",
})
nv.set_crosshair_color([0,0,0,1])
display(nv)
Viewing the Pial Surfaces
Now we will look at the pial surfaces. These are '3D' models of the outer surface of the brain (the grey matter boundary). FreeSurfer creates one for each hemisphere.
- 📂
lh.pial= left hemisphere surface - 📂
rh.pial= right hemisphere surface - 🔴 Left hemisphere is shown in red
- 🔵 Right hemisphere is shown in blue
- Displayed in a fully interactive 3D view (you can rotate and zoom)
➡️ Click the cell below, then press Command + Enter (Mac) or Control + Enter (Windows/Linux).
You’ll see a 3D model of the brain surface – red for left, blue for right.
# Pial surfaces with explicit per-mesh color + shader (ipyniivue)
from ipyniivue import Mesh
SUBJECTS_DIR = "./data/structural/recon-all-clinical"
SUBJECT = "TestSubject"
surf_dir = Path(SUBJECTS_DIR) / SUBJECT / "surf"
lh = surf_dir / "lh.pial"
rh = surf_dir / "rh.pial"
assert lh.exists() and rh.exists(), "Missing pial surfaces"
nv = NiiVue(
height=600,
is_colorbar=False,
is_orient_cube=True,
is_radiological_convention=True,
back_color=(0.05, 0.05, 0.05, 1.0),
)
# Use rgba255 (0..255 ints) — more reliable across builds than 0..1 floats
nv.add_mesh(Mesh(path=str(lh), name="lh.pial", rgba255=[255, 90, 90, 255], opacity=1.0))
nv.add_mesh(Mesh(path=str(rh), name="rh.pial", rgba255=[90, 90, 255, 255], opacity=1.0))
display(nv)
[HF-patcher] lh.pial: path → url
[HF-patcher] rh.pial: path → url
⚪ Viewing the White Matter Surfaces
Now we will open the white matter surfaces. These are 3D models of the inner boundary of the cortex, where the grey matter meets the white matter. They are used by FreeSurfer to measure cortical thickness.
- 📂
lh.white= left hemisphere white surface - 📂
rh.white= right hemisphere white surface - 🟠 Left hemisphere is shown in orange
- 🔵 Right hemisphere is shown in light blue
- 🌐 Fully interactive 3D display – rotate and zoom to explore
➡️ Click the cell below, then press Command + Enter (Mac) or Control + Enter (Windows/Linux).
You’ll see the white matter surfaces in 3D (orange = left, blue = right).
# White surfaces (lh/rh) with solid colors
lh = surf_dir/"lh.white"; rh = surf_dir/"rh.white"
assert lh.exists() and rh.exists(), "Missing white surfaces"
nv = NiiVue(height=600,is_colorbar=False, is_orient_cube=True,
is_radiological_convention=True, back_color=(0.05,0.05,0.05,1.0))
nv.add_mesh(Mesh(path=str(lh), name="lh.white", rgba255=[255,200,90,255], opacity=1.0))
nv.add_mesh(Mesh(path=str(rh), name="rh.white", rgba255=[90,200,255,255], opacity=1.0))
display(nv)
[HF-patcher] lh.white: path → url
[HF-patcher] rh.white: path → url
🌐 Viewing the Inflated Surface
Now we will look at the inflated brain surface. This is a special 3D model where the folds (sulci and gyri) are “smoothed out” so the entire cortex can be seen more clearly. It is very useful for visualising activity maps or large-scale anatomy without folds hiding important areas.
- 📂
lh.inflated= inflated left hemisphere surface - 🔴 Left hemisphere is shown here in light red
- 👁️ The sulci (valleys) are expanded so you can see regions that are normally hidden inside folds
- 🌐 Fully interactive 3D view – rotate and zoom to explore the cortical sheet
➡️ Click the cell below, then press Command + Enter (Mac) or Control + Enter (Windows/Linux).
You’ll see the inflated left hemisphere in 3D.
# Inflated surfaces (lh/rh) with solid colors
lh = surf_dir/"lh.inflated"; rh = surf_dir/"rh.inflated"
assert lh.exists() and rh.exists(), "Missing inflated surfaces"
nv = NiiVue(height=600, is_colorbar=False, is_orient_cube=True,
is_radiological_convention=True, back_color=(0.05,0.05,0.05,1.0))
nv.add_mesh(Mesh(path=str(lh), name="lh.inflated", rgba255=[255,140,140,255], opacity=1.0))
#nv.add_mesh(Mesh(path=str(rh), name="rh.inflated", rgba255=[140,140,255,255], opacity=1.0))
display(nv)
[HF-patcher] lh.inflated: path → url
🗂️ Inspecting the Subject Folder & Logs
This step shows the top-level contents of the subject’s FreeSurfer folder and the run logs. Use it to confirm that key outputs exist and to find logs if something went wrong.
SUBJECTS_DIR = ./data/structural/recon-all-clinical
SUBJECT = TestSubject
Path = ./data/structural/recon-all-clinical/TestSubject
📁 What the main folders mean
| Folder | Purpose |
|---|---|
mri/ |
All volumetric outputs (.mgz), e.g. native.mgz, aseg.mgz |
surf/ |
Cortical meshes (.white, .pial, .inflated) and annotations (.annot) |
label/ |
Region labels and color tables (.ctab) |
stats/ |
Per-region thickness/surface area stats (for group analysis) |
scripts/ |
Run logs, IsRunning flags, and command histories |
Tip: If a run crashes or stalls, check
scripts/ for recent log files and any IsRunning* flags.
➡️ Click the cell below, then press Command + Enter (Mac) or Control + Enter (Windows/Linux) to list the directory tree and show log files.
# Show directory layout and recon logs
import os, subprocess, textwrap
SUBJECTS_DIR = "./data/structural/recon-all-clinical"
SUBJECT = "TestSubject"
base = f"{SUBJECTS_DIR}/{SUBJECT}"
print("=== Subject directory tree (top) ===")
subprocess.run(["bash","-lc", f'ls -lh {base}'])
print("\n=== Logs/scripts ===")
scripts = f"{base}/scripts"
subprocess.run(["bash","-lc", f'ls -lh {scripts} 2>/dev/null || true'])
notes = [
("mri/", "All volumetric outputs (.mgz)."),
("surf/", "Cortical meshes and annotation files (.white, .pial, .inflated, .annot)."),
("label/", "Labels, annotation tables (.ctab), region lists."),
("stats/", "Cortex thickness/surface area stats per region (for group analysis)."),
("scripts/", "Run logs, IsRunning flags, and command histories."),
]
for d, t in notes:
print(f"{d:12s} {t}")
=== Subject directory tree (top) ===
total 32K
drwxrwxr-x 2 jovyan jovyan 4.0K Mar 3 11:09 label
drwxrwxr-x 3 jovyan jovyan 4.0K Mar 3 11:19 mri
drwxrwxr-x 2 jovyan jovyan 4.0K Mar 3 12:54 scripts
drwxrwxr-x 2 jovyan jovyan 4.0K Mar 3 11:09 stats
drwxrwxr-x 2 jovyan jovyan 4.0K Mar 3 12:17 surf
drwxrwxr-x 2 jovyan jovyan 4.0K Mar 3 09:23 tmp
drwxrwxr-x 2 jovyan jovyan 4.0K Mar 3 09:23 touch
drwxrwxr-x 2 jovyan jovyan 4.0K Mar 3 09:23 trash
=== Logs/scripts ===
total 348K
-rw-rw-r-- 1 jovyan jovyan 341K Mar 3 12:54 recon-all-clinical.log
mri/ All volumetric outputs (.mgz).
surf/ Cortical meshes and annotation files (.white, .pial, .inflated, .annot).
label/ Labels, annotation tables (.ctab), region lists.
stats/ Cortex thickness/surface area stats per region (for group analysis).
scripts/ Run logs, IsRunning flags, and command histories.
Dependencies in Jupyter/Python#
Using the package watermark to document system environment and software versions used in this notebook
%load_ext watermark
%watermark
%watermark --iversions
Last updated: 2026-03-03T12:54:31.936901+00:00
Python implementation: CPython
Python version : 3.13.11
IPython version : 9.9.0
Compiler : GCC 14.3.0
OS : Linux
Release : 5.15.0-170-generic
Machine : x86_64
Processor : x86_64
CPU cores : 32
Architecture: 64bit
IPython : 9.9.0
ipyniivue: 2.4.4
json : 2.0.9
nibabel : 5.3.3
numpy : 2.4.2