QSIRecon#
Reconstructing a structural connectome#
Author: Monika Doerig
Date: 16 July 2026
License:
Note: If this notebook uses neuroimaging tools from Neurocontainers, those tools retain their original licenses. Please see Neurodesk citation guidelines for details.
✨ Use of AI ▽
This notebook was drafted with assistance from an LLM (GLM-5.2, via Neurodesk) and then revised by the author. The author reviewed the final content and takes responsibility for it.
Citation and Resources:#
Tools included in this workflow#
QSIRecon:
Cieslak, M., Cook, P. A., He, X., Yeh, F. C., Dhollander, T., Adebimpe, A., Aguirre, G. K., Bassett, D. S., Betzel, R. F., Bourque, J., Cabral, L. M., Davatzikos, C., Detre, J. A., Earl, E., Elliott, M. A., Fadnavis, S., Fair, D. A., Foran, W., Fotiadis, P., Garyfallidis, E., … Satterthwaite, T. D. (2021). QSIPrep: an integrative platform for preprocessing and reconstructing diffusion MRI data. Nature methods, 18(7), 775–778. https://doi.org/10.1038/s41592-021-01185-5
Workflows this work is based on#
Chains on the QSIPrep output produced by the companion QSIPrep notebook.
Dataset#
OpenNeuro:
Hannelore Aerts and Daniele Marinazzo (2018). BTC_preop. OpenNeuro Dataset ds001226
OSF Preprocessed data with QSIPrep :
Dörig, M. (2026, July 14). Diffusion MRI with QSIPrep & QSIRecon: Interactive NeurodeskEDU Examples. Retrieved from osf.io/q7v8c
Educational resources#
Load software tools and import python libraries#
# Load QSIRecon
import module
await module.load('qsirecon/1.1.0')
await module.list()
['qsirecon/1.1.0']
The base image already provides the common scientific Python packages (see the Neurodesktop Dockerfile). Only a few standard libraries are needed below.
# Import the necessary libraries
import os
import glob
import shutil
import numpy as np
import matplotlib.pyplot as plt
from pathlib import Path
from bs4 import BeautifulSoup
from IPython.display import HTML, display
import base64
import subprocess
FreeSurfer license#
# Request a freesurfer license from https://surfer.nmr.mgh.harvard.edu/registration.html
# and store it in your homedirectory
# This is just an exampe - please replace with your license id:
!echo "Steffen.Bollmann@cai.uq.edu.au" > ~/.license
!echo "21029" >> ~/.license
!echo "*Cqyn12sqTCxo" >> ~/.license
!echo "FSxgcvGkNR59Y" >> ~/.license
Introduction#
QSIRecon is the post-processing companion to QSIPrep (it does for diffusion MRI what XCP-D does for BOLD). Where QSIPrep stops at preprocessed data, QSIRecon builds the workflows that turn it into many of the biologically interesting derivatives you actually test hypotheses on: ODF/FOD reconstruction, model fits and parameter estimates, tractography, tractometry, regional connectivity, and tabular outputs.
Its aim is to make state-of-the-art methods from DIPY, MRtrix3, DSI Studio, PyAFQ and other packages straightforward to apply to preprocessed dMRI. Rather than one fixed pipeline, QSIRecon offers a set of curated reconstruction workflows, selected at runtime.
This notebook runs one of them: an MRtrix3 multi-shell pipeline using MSMT-CSD to estimate fibre orientation distributions, iFOD2 probabilistic tractography to generate streamlines, and SIFT2 to weight them — producing a structural connectome, which we inspect in the QSIRecon visual report.
Learning objectives#
This notebook assumes a basic understanding of diffusion MRI and familiarity with QSIPrep’s role in preprocessing (see the companion QSIPrep notebook). By the end you will be able to:
Describe what QSIRecon does and how it relates to QSIPrep
Select and run a QSIRecon reconstruction workflow on QSIPrep derivatives
Inspect the resulting FOD, tractography and connectome outputs in the QSIRecon visual report
Data Preparation#
QSIRecon consumes QSIPrep derivatives. We download a copy of the output from the QSIPrep notebook from OSF, so this notebook can be run on its own.
def fetch_if_missing(remote, local):
"""Fetch from OSF, downloading to a temp name so a partial file never
looks like a complete one on rerun."""
if os.path.exists(local):
print(f"Already exists, skipping download: {local}")
return
tmp = local + ".part"
subprocess.run(["osf", "-p", "q7v8c", "fetch", remote, tmp], check=True)
os.replace(tmp, local)
print(f"Downloaded: {local}")
fetch_if_missing("qsiprep/qsiprep-CON01.tar.gz", "qsiprep-CON01.tar.gz")
if os.path.exists("qsiprep-output/sub-CON01"):
print("Already extracted, skipping: qsiprep-output/sub-CON01")
else:
os.makedirs("qsiprep-output", exist_ok=True)
subprocess.run(["tar", "xzf", "qsiprep-CON01.tar.gz", "-C", "qsiprep-output"], check=True)
print("Extracted QSIPrep derivatives to qsiprep-output/")
if os.path.exists("qsiprep-CON01.tar.gz"):
os.remove("qsiprep-CON01.tar.gz")
print("Removed tarball to save disk")
Downloaded: qsiprep-CON01.tar.gz
Extracted QSIPrep derivatives to qsiprep-output/
Removed tarball to save disk
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Analysis#
We run QSIRecon on the QSIPrep derivatives using the mrtrix_multishell_msmt_noACT reconstruction spec — an MRtrix3 multishell pipeline using MSMT-CSD for FOD estimation, iFOD2 probabilistic tractography, SIFT2 streamline weighting, and tck2connectome to produce a structural connectome.
As the name suggests, this spec does not use anatomically constrained tractography (ACT). The alternative mrtrix_multishell_msmt_ACT-hsvs spec constrains tractography using a hybrid surface-volume segmentation, but that requires FreeSurfer derivatives passed via --fs-subjects-dir, which our QSIPrep 1.0.1 run from the companion notebook doesn’t produce — FreeSurfer would have to be run separately. The mrtrix_multishell_msmt_ACT-fast variant substitutes FSL FAST for the segmentation, but the QSIRecon documentation does not recommend it. So we use the non-ACT spec here.
Customising the spec#
Reconstruction workflows are defined in YAML files, and --recon-spec accepts either a
built-in name or a path to your own file. The built-in specs are a good starting point for
customisation — so rather than invoking mrtrix_multishell_msmt_noACT by name, we download it and reduce tckgen’s select parameter from 10 million streamlines to 200,000.
This is purely to keep the notebook runnable in reasonable time and disk: streamline count drives most of the cost of tractography. A research analysis would use the full count. Note the YAML is fetched at a pinned commit (af43da9), which is the commit the QSIRecon version in this container was built from — so the spec we edit matches the built-in one.
Long-running
Even at a reduced streamline count, tractography plus SIFT2 is compute-heavy — expect this cell to take a while depending on available resources.
Let’s look at the command-line arguments first and then run qsirecon:
!qsirecon --help
usage: qsirecon [-h]
[--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--session-id SESSION_ID [SESSION_ID ...]]
[-d PACKAGE=PATH [PACKAGE=PATH ...]] [--bids-filter-file FILE]
[--bids-database-dir PATH] [--nprocs NPROCS]
[--omp-nthreads OMP_NTHREADS] [--mem MEMORY_MB] [--low-mem]
[--use-plugin FILE] [--sloppy] [--boilerplate-only]
[--reports-only]
[--report-output-level {root,subject,session}] [--infant]
[--b0-threshold B0_THRESHOLD]
[--output-resolution OUTPUT_RESOLUTION]
[--fs-license-file PATH] [--recon-spec RECON_SPEC]
[--input-type {qsiprep,ukb,hcpya}] [--fs-subjects-dir PATH]
[--skip-odf-reports] [--atlases ATLAS [ATLAS ...]] [--version]
[-v] [-w WORK_DIR] [--resource-monitor] [--config-file FILE]
[--write-graph] [--stop-on-first-crash] [--notrack]
[--debug {pdb,all} [{pdb,all} ...]]
input_dir output_dir {participant}
QSIRecon v1.1.1.dev0+gaf43da9.d20250414: q-Space Image Reconstruction
Workflows
positional arguments:
input_dir The root folder of the input dataset (subject-level
folders should be found at the top level in this
folder). If the dataset is not BIDS-valid, then a
BIDS-compliant version will be created based on the
--input-type value.
output_dir The output path for the outcomes of postprocessing and
visual reports
{participant} Processing stage to be run, only "participant" in the
case of QSIRecon (for now).
options:
-h, --help show this help message and exit
Options for filtering input data:
--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
A space delimited list of participant identifiers or a
single identifier (the sub- prefix can be removed)
(default: None)
--session-id SESSION_ID [SESSION_ID ...]
A space delimited list of session identifiers or a
single identifier (the ses- prefix can be removed)
(default: None)
-d PACKAGE=PATH [PACKAGE=PATH ...], --datasets PACKAGE=PATH [PACKAGE=PATH ...]
Search PATH(s) for derivatives or atlas datasets.
These may be provided as named folders (e.g.,
``--datasets smriprep=/path/to/smriprep``). (default:
None)
--bids-filter-file FILE
A JSON file describing custom BIDS input filters using
PyBIDS. For further details, please check out https://
fmriprep.readthedocs.io/en/latest/faq.html#how-do-I-
select-only-certain-files-to-be-input-to-fMRIPrep
(default: None)
--bids-database-dir PATH
Path to a PyBIDS database folder, for faster indexing
(especially useful for large datasets). Will be
created if not present. (default: None)
Options to handle performance:
--nprocs NPROCS, --nthreads NPROCS, --n-cpus NPROCS
Maximum number of threads across all processes
(default: None)
--omp-nthreads OMP_NTHREADS
Maximum number of threads per-process (default: None)
--mem MEMORY_MB, --mem-mb MEMORY_MB
Upper bound memory limit for QSIRecon processes
(default: None)
--low-mem Attempt to reduce memory usage (will increase disk
usage in working directory) (default: False)
--use-plugin FILE, --nipype-plugin-file FILE
Nipype plugin configuration file (default: None)
--sloppy Use low-quality tools for speed - TESTING ONLY
(default: False)
Options for performing only a subset of the workflow:
--boilerplate-only, --boilerplate
Generate boilerplate only (default: False)
--reports-only Only generate reports, don't run workflows. This will
only rerun report aggregation, not reportlet
generation for specific nodes. (default: False)
--report-output-level {root,subject,session}
Where should the html reports be written? By default
root will write them to the --output-dir. Other
options will write them into their subject or session
directory. (default: root)
Workflow configuration:
--infant configure pipelines to process infant brains (default:
False)
--b0-threshold B0_THRESHOLD
any value in the .bval file less than this will be
considered a b=0 image. Current default threshold =
100; this threshold can be lowered or increased. Note,
setting this too high can result in inaccurate
results. (default: 100)
--output-resolution OUTPUT_RESOLUTION
the isotropic voxel size in mm the data will be
resampled to after preprocessing. If set to a lower
value than the original voxel size, your data will be
upsampled using BSpline interpolation. (default: None)
Specific options for FreeSurfer preprocessing:
--fs-license-file PATH
Path to FreeSurfer license key file. Get it (for free)
by registering at
https://surfer.nmr.mgh.harvard.edu/registration.html
(default: None)
Options for recon workflows:
--recon-spec RECON_SPEC
json file specifying a reconstruction pipeline to be
run after preprocessing (default: None)
--input-type {qsiprep,ukb,hcpya}
Specify which pipeline was used to create the data
specified as the input_dir.Not necessary to specify if
the data was processed by QSIPrep. Other options
include "ukb" for data processed with the UK BioBank
minimal preprocessing pipeline and "hcpya" for the HCP
young adult minimal preprocessing pipeline. (default:
qsiprep)
--fs-subjects-dir PATH
Directory containing Freesurfer outputs to be
integrated into recon. Freesurfer must already be run.
QSIRecon will not run Freesurfer. (default: None)
--skip-odf-reports run only reconstruction, assumes preprocessing has
already completed. (default: False)
Parcellation options:
--atlases ATLAS [ATLAS ...]
Selection of atlases to apply to the data. Built-in
atlases include: AAL116, AICHA384Ext,
Brainnetome246Ext, Gordon333Ext, and the 4S atlases.
(default: None)
Other options:
--version show program's version number and exit
-v, --verbose Increases log verbosity for each occurrence, debug
level is -vvv (default: 0)
-w WORK_DIR, --work-dir WORK_DIR
Path where intermediate results should be stored
(default: /home/jovyan/workspace/books/examples/diffus
ion_imaging/work)
--resource-monitor Enable Nipype's resource monitoring to keep track of
memory and CPU usage (default: False)
--config-file FILE Use pre-generated configuration file. Values in file
will be overridden by command-line arguments.
(default: None)
--write-graph Write workflow graph. (default: False)
--stop-on-first-crash
Force stopping on first crash, even if a work
directory was specified. (default: False)
--notrack Opt-out of sending tracking information of this run to
the QSIRecon developers. This information helps to
improve QSIRecon and provides an indicator of real
world usage crucial for obtaining funding. (default:
False)
--debug {pdb,all} [{pdb,all} ...]
Debug mode(s) to enable. 'all' is alias for all
available modes. (default: None)
Now we’ll customise the spec file and reduce the streamlines to 20000:
%%bash
set -e -u -o pipefail
curl -fsSL -o recon_spec_ci.yaml \
https://raw.githubusercontent.com/PennLINC/qsirecon/af43da9/qsirecon/data/pipelines/mrtrix_multishell_msmt_noACT.yaml
sed -i -E 's/^([[:space:]]*select:).*/\1 200000/' recon_spec_ci.yaml
grep -q 'select: 200000' recon_spec_ci.yaml || { echo "sed did not match — spec unchanged"; exit 1; }
cat recon_spec_ci.yaml
anatomical: []
name: mrtrix_multishell_msmt_noACT
nodes:
- action: csd
input: qsirecon
nam
e: msmt_csd
parameters:
fod:
algorithm: msmt_csd
max_sh:
- 8
- 8
- 8
mtnormalize: true
response:
alg
orithm: dhollander
qsirecon_suffix: MRtrix3_act-None
software: MRTrix3
- action: tractogra
phy
input: msmt_csd
name: track_ifod2
parameters:
sift2: {}
tckgen:
algorithm: iFOD2
max_length: 250
min_length: 30
power: 0
.33
quiet: true
select: 200000
use_5tt: false
use_sift2: tru
e
qsirecon_suffix: MRtrix3_act-None
software: MRTrix3
- action: connectivity
input: tr
ack_ifod2
name: mrtrix_conn
parameters:
tck2connectome:
- measure: sift_in
vnodevol_radius2_count
scale_invnodevol: true
search_radius: 2
s
tat_edge: sum
symmetric: true
use_sift_weights: true
zero_diagon
al: false
- length_scale: length
measure: radius2_meanlength
scale
_invnodevol: false
search_radius: 2
stat_edge: mean
symmetric: t
rue
use_sift_weights: false
zero_diagonal: false
- measure: radius
2_count
scale_invnodevol: false
search_radius: 2
stat_edge: sum
symmetric: true
use_sift_weights: false
zero_diagonal: false
- measure: sift_radius2_count
scale_invnodevol: false
search_radius:
2
stat_edge: sum
symmetric: true
use_sift_weights: true
zero_diagonal: false
qsirecon_suffix: MRtrix3_act-None
software: MRTrix3
space: T1w
%%bash
set -e -u -o pipefail
# ensure subjects dir exists at startup
export SUBJECTS_DIR="$HOME/qsiprep-freesurfer-dir"
export APPTAINERENV_SUBJECTS_DIR=$SUBJECTS_DIR
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
mkdir -p "$SUBJECTS_DIR"
N_CPUS=$(nproc); N_CPUS=$(( N_CPUS > 12 ? 12 : N_CPUS ))
MEM_MB=$(awk '/MemTotal/ {printf "%d", $2/1024}' /proc/meminfo)
QSIRECON_MEM=$(( MEM_MB * 75 / 100 ))
OMP_THREADS=$(( N_CPUS >= 8 ? 4 : 2 ))
qsirecon qsiprep-output qsirecon-output participant \
--participant-label CON01 \
--recon-spec recon_spec_ci.yaml \
--fs-license-file ~/.license \
--atlases AAL116 \
-w qsirecon-work \
--nthreads "${N_CPUS}" --omp-nthreads "${OMP_THREADS}" --mem-mb "${QSIRECON_MEM}" \
2>&1 | tee qsirecon.log
260728-23:48:42,988 nipype.workflow IMPORTANT:
Running QSIRecon version 1.1.1.dev0+gaf43da9.d20250
414
License NOTICE ##################################################
QSIRecon 1.
1.1.dev0+gaf43da9.d20250414
Copyright The PennLINC Developers.
This prod
uct includes software developed by
the NiPreps Community (https://nipreps.org/).
Portions of this software were developed at the Department of
Psychology at Stanfo
rd University, Stanford, CA, US.
This software is also distributed as a Docker co
ntainer image.
The bootstrapping file for the image ("Dockerfile") is licensed
und
er the MIT License.
This software may be distributed through an add-on package ca
lled
"Docker Wrapper" that is under the BSD 3-clause License.
####################
#############################################
260728-23:48:43,170 nipype.workflow IMPORTANT:
Building QSIRecon's workflow:
* BIDS dat
aset path: /home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output.
* Part
icipant list: ['CON01'].
* Run identifier: 20260728-234759_905ab0bb-d4d5-4aa3-a94f-121ce1
4992ba.
260728-23:49:35,627 nipype.utils INFO:
Collected anatomical data:
acpc_aparc: null
acpc_aseg: /hom
e/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_space-AC
PC_desc-aseg_dseg.nii.gz
acpc_brain_mask: /home/jovyan/workspace/books/examples/diffusion_imaging/qs
iprep-output/sub-CON01/anat/sub-CON01_space-ACPC_desc-brain_mask.nii.gz
acpc_csf_probseg: null
acpc_
gm_probseg: null
acpc_preproc: /home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-outpu
t/sub-CON01/anat/sub-CON01_space-ACPC_desc-preproc_T1w.nii.gz
acpc_seg: /home/jovyan/workspace/books
/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_space-ACPC_dseg.nii.gz
acpc_to_t
emplate_xfm: /home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/s
ub-CON01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5
acpc_wm_probseg: null
orig_to_acpc_xfm:
null
template_to_acpc_xfm: /home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/su
b-CON01/anat/sub-CON01_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5
260728-23:49:35,628 nipype.workflow INFO:
Anatomical data available for /home/jovyan/workspace/boo
ks/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_space-ACPC_desc-preproc_T1w.ni
i.gz:
acpc_aparc: null
acpc_aseg: /home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-ou
tput/sub-CON01/anat/sub-CON01_space-ACPC_desc-aseg_dseg.nii.gz
acpc_brain_mask: /home/jovyan/workspa
ce/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_space-ACPC_desc-brain_ma
sk.nii.gz
acpc_csf_probseg: null
acpc_gm_probseg: null
acpc_preproc: /home/jovyan/workspace/books/ex
amples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_space-ACPC_desc-preproc_T1w.nii.gz
acpc_seg: /home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-
CON01_space-ACPC_dseg.nii.gz
acpc_to_template_xfm: /home/jovyan/workspace/books/examples/diffusion_i
maging/qsiprep-output/sub-CON01/anat/sub-CON01_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5
ac
pc_wm_probseg: null
orig_to_acpc_xfm: null
template_to_acpc_xfm: /home/jovyan/workspace/books/exampl
es/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_from-MNI152NLin2009cAsym_to-ACPC_mode-i
mage_xfm.h5
260728-23:49:35,630 nipype.workflow INFO:
Found high-res anatomical data in preproces
sed inputs for CON01.
260728-23:49:35,631 nipype.workflow INFO:
acpc_aparc (<class 'str'>): None (
<class 'NoneType'>)
260728-23:49:35,631 nipype.workflow INFO:
acpc_seg (<class 'str'>): /home/jovy
an/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_space-ACPC_dse
g.nii.gz (<class 'str'>)
260728-23:49:35,631 nipype.workflow INFO:
acpc_aseg (<class 'str'>): /hom
e/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_space-AC
PC_desc-aseg_dseg.nii.gz (<class 'str'>)
260728-23:49:35,631 nipype.workflow INFO:
acpc_brain_mask
(<class 'str'>): /home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/a
nat/sub-CON01_space-ACPC_desc-brain_mask.nii.gz (<class 'str'>)
260728-23:49:35,631 nipype.workflow
INFO:
acpc_preproc (<class 'str'>): /home/jovyan/workspace/books/examples/diffusion_imaging/qsipre
p-output/sub-CON01/anat/sub-CON01_space-ACPC_desc-preproc_T1w.nii.gz (<class 'str'>)
260728-23:49:35
,631 nipype.workflow INFO:
acpc_csf_probseg (<class 'str'>): None (<class 'NoneType'>)
260728-23:4
9:35,631 nipype.workflow INFO:
acpc_gm_probseg (<class 'str'>): None (<class 'NoneType'>)
260728-2
3:49:35,631 nipype.workflow INFO:
acpc_wm_probseg (<class 'str'>): None (<class 'NoneType'>)
26072
8-23:49:35,631 nipype.workflow INFO:
orig_to_acpc_xfm (<class 'str'>): None (<class 'NoneType'>)
2
60728-23:49:35,631 nipype.workflow INFO:
template_to_acpc_xfm (<class 'str'>): /home/jovyan/worksp
ace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_from-MNI152NLin2009cAsy
m_to-ACPC_mode-image_xfm.h5 (<class 'str'>)
260728-23:49:35,632 nipype.workflow INFO:
acpc_to_template_xfm (<class 'str'>): /home/jovyan/works
pace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/anat/sub-CON01_from-ACPC_to-MNI152NLi
n2009cAsym_mode-image_xfm.h5 (<class 'str'>)
260728-23:49:35,899 nipype.workflow INFO:
Found 1 high-res anatomicals to process
260728-23:49:35,938 nipype.workflow INFO:
Found T1w-to-template transforms from QSIRecon
260728-23:49:35,939 nipype.workflow INFO:
Transforming ODF ROIs into DWI space for visual report.
260728-23:49:35,951 nipype.interface INFO:
Response configuration: {'algorithm': 'dhollander', 'nt
hreads': 4}
260728-23:49:35,951 nipype.interface INFO:
Using 4 threads in MRtrix3
260728-23:49:39,275 nipype.workflow INFO:
QSIRecon workflow graph with 65 nodes built successfully
.
260728-23:50:01,846 nipype.workflow IMPORTANT:
QSIRecon started!
260728-23:50:08,253 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.datasink_atlas_orig_AAL116_0" in "/home/jovyan/workspace/books/examples/diffusion_
imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/datasink_atlas_orig_AAL
116_0".
260728-23:50:08,254 nipype.workflow INFO:
[Node] Executing "datasink_atlas_orig_AAL116_0" <qsireco
n.interfaces.bids.CopyAtlas>
260728-23:50:08,262 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.datasink_atlas_labels_orig_AAL116_0" in "/home/jovyan/workspace/books/examples/dif
fusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/datasink_atlas_l
abels_orig_AAL116_0".
260728-23:50:08,264 nipype.workflow INFO:
[Node] Executing "datasink_atlas_labels_orig_AAL116_0" <
qsirecon.interfaces.bids.CopyAtlas>
260728-23:50:08,268 nipype.workflow INFO:
[Node] Finished "datasink_atlas_labels_orig_AAL116_0", e
lapsed time 0.00045s.
260728-23:50:08,327 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_ingressed_dwi_data" in "/home/j
ovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_mult
ishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_ingressed_dwi_data".
260728-23:50:08,328 nipype.workflow INFO:
[Node] Executing "sub_CON01_ses_preop_acq_AP_space_ACPC_
desc_preproc_ingressed_dwi_data" <qsirecon.interfaces.ingress.QSIPrepDWIIngress>
260728-23:50:08,333 nipype.workflow INFO:
[Node] Finished "sub_CON01_ses_preop_acq_AP_space_ACPC_d
esc_preproc_ingressed_dwi_data", elapsed time 0.002076s.
260728-23:50:08,383 nipype.workflow INFO:
[Node] Finished "datasink_atlas_orig_AAL116_0", elapsed
time 0.124573s.
260728-23:50:08,448 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.get_templa
te" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CO
N01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_ana
t_wf/get_template".
260728-23:50:08,449 nipype.workflow INFO:
[Node] Executing "get_template" <qsirecon.interfaces.ana
tomical.GetTemplate>
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_re
s-01_T1w.nii.gz
260728-23:50:08,947 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.odf_rois"
in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_
mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf
/odf_rois".
260728-23:50:08,947 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.resample_m
ask" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-C
ON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_an
at_wf/resample_mask".
260728-23:50:08,949 nipype.workflow INFO:
[Node] Executing "odf_rois" <nipyp
e.interfaces.ants.resampling.ApplyTransforms>
260728-23:50:08,951 nipype.workflow INFO:
[Node] Executing "resample_mask" <nipype.interfaces.ants
.resampling.ApplyTransforms>
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8%|▊ | 1.11M/13.7M [00:01<00:09, 1.34MB/s]
16%|█▋ | 2.23M/13.7M [00:01<00:04, 2.62MB/s]
33%|███▎ | 4.45M/13.7M [00:01<00:01, 5.14MB/s]
51%|█████ | 6.93M/13.7M [00:02<00:00, 7.19MB/s]
260728-23:50:11,424 nipype.workflow INFO:
[Node] Finished "resample_mask", elapsed time 0.606232s.
70%|██████▉ | 9.52M/13.7M [00:02<00:00, 8.82MB/s]
86%|████████▌ | 11.7M/13.7M [00:02<00:00, 9.35MB/s]
100%|██████████| 13.7M/13.7M [00:02<00:00, 5.45MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_re
s-01_desc-brain_mask.nii.gz
0%| | 0.00/160k [00:00<?, ?B/s]
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100%|██████████| 160k/160k [00:00<00:00, 194kB/s]
260728-23:50:13,217 nipype.workflow INFO:
[Node] Finished "get_template", elapsed time 4.764763s.
260728-23:50:17,276 nipype.workflow INFO:
[Node] Finished "odf_rois", elapsed time 6.50771s.
labelconvert: Image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_
1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi
_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg_to_dwi.nii.gz"
stored with floating-point type; need to check for non-integer or negative values
labelconvert: [ 10%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_
space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_
res-01_dseg_to_dwi.nii.gz"...?7h
labelconvert: [ 20%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_
space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_
res-01_dseg_to_dwi.nii.gz"...?7h
labelconvert: [ 30%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_
space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_
res-01_dseg_to_dwi.nii.gz"...?7h
labelconvert: [ 40%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_
space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_
res-01_dseg_to_dwi.nii.gz"...?7h
labelconvert: [ 50%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_
space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_
labelconvert: [ 60%] uncompressing image "/home/jovyan/w
orkspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_
msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/a
tlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg_to_dwi.nii.gz"...?7h
labelconvert: [ 70%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_
space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_
labelconvert: [ 80%] uncompressing image "/home/jovyan/w
orkspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_
msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/a
tlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg_to_dwi.nii.gz"...?7h
labelconvert: [ 90%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_
space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_
labelconvert: [100%] uncompressing image "/home/jovyan/w
orkspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_
msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/a
labelconvert: [100%] un
compressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_
1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_s
pecific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg_to_dwi.nii.gz"0
K
labelconvert: [ 1%] Veri
labelconvert: [ 2%] Verifying parcellation image...
?7h
labelconvert: [ 4%] Verify
labelconvert: [ 5%] Verifying parcellation image...?7
labelconvert: [ 7%] Verif
labelconvert: [ 8%] Verifying parcellation image...?
labelconvert: [ 10%] Veri
labelconvert: [ 11%] Verifying parcellation image...
labelconvert: [ 13%] Ver
labelconvert: [ 14%] Verifying parcellation image...
labelconvert: [ 16%] Ve
labelconvert: [ 17%] Verifying parcellation image...
labelconvert: [ 19%] V
labelconvert: [ 20%] Verifying parcellation image...0
labelconvert: [ 22%]
labelconvert: [ 23%] Verifying parcellation image...
labelconvert: [ 25%]
labelconvert: [ 26%] Verifying parcellation image...
labelconvert: [ 28%
labelconvert: [ 29%] Verifying parcellation image...
labelconvert: [ 31
%] Verifying parcellation image...?7h
labelconvert: [ 33%] Verify
labelconvert: [ 34%] Verifying parcellation image...?7
labelconvert: [ 36%] Verif
labelconvert: [ 37%] Verifying parcellation image...?
labelconvert: [ 39%] Veri
labelconvert: [ 40%] Verifying parcellation image...
labelconvert: [ 42%] Ver
labelconvert: [ 43%] Verifying parcellation image...
labelconvert: [ 45%] Ve
labelconvert: [ 46%] Verifying parcellation image...
labelconvert: [ 48%] V
labelconvert: [ 49%] Verifying parcellation image...0
labelconvert: [ 51%]
labelconvert: [ 52%] Verifying parcellation image...
labelconvert: [ 54%]
labelconvert: [ 55%] Verifying parcellation image...
labelconvert: [ 57%
labelconvert: [ 58%] Verifying parcellation image...
labelconvert: [ 60
labelconvert: [ 61%] Verifying parcellation image..
labelconvert: [ 6
labelconvert: [ 64%] Verifying parcellation image.
labelconvert: [
labelconvert: [ 67%] Verifying parcellation image
labelconvert: [
labelconvert: [ 70%] Verifying parcellation imag
labelconvert:
labelconvert: [ 73%] Verifying parcellation ima
labelconvert:
labelconvert: [ 76%] Verifying parcellation im
labelconvert
labelconvert: [ 79%] Verifying parcellation i
labelconver
labelconvert: [ 82%] Verifying parcellation
labelconve
labelconvert: [ 85%] Verifying parcellation
labelconv
labelconvert: [ 88%] Verifying parcellatio
labelconvert: [ 89%] Verifying parcellation image...?7h
labelconvert: [ 91%] Verify
labelconvert: [ 92%] Verifying parcellation image...?7
labelconvert: [ 94%] Verif
labelconvert: [ 95%] Verifying parcellation image...?
labelconvert: [ 97%] Veri
labelconvert: [ 98%] Verifying parcellation image...
labelconvert: [100%] Ver
labelconvert: [100%] Verifying parcellation image
la
belconvert: [ 10%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsir
econ-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_AC
PC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_res-01_d
labelconvert: [ 20%] uncompressing image "/home/jovyan/workspace
/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noA
CT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL
labelconvert: [ 30%] uncom
pressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_w
f/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_spec
ific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg_to_dwi.nii.gz"...0
labelconvert: [ 40%] uncompressing image "/home/jovyan/workspace/books/examples/diffusio
n_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_a
cq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009
labelconvert: [ 50%] uncompressing image "/home/jo
vyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multi
shell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atl
labelconvert
: [ 60%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/
qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_pr
eproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg_to_dwi
labelconvert: [ 70%] uncompressing image "/home/jovyan/workspace/books/exa
mples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON
01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-
labelconvert: [ 80%] uncompressing i
mage "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON0
1_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_
wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg_to_dwi.nii.gz"...?7h?7
labelconvert: [ 90%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/
qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_spac
e_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_res-
labelconvert: [100%] uncompressing image "/home/jovyan/works
pace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt
_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf/prepare_atlases/atlas
labelconvert: [100%] uncomp
ressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf
/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_speci
fic_anat_wf/prepare_atlases/atlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg_to_dwi.nii.gz"
260728-23:50:18,359 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.output_gri
d_wf.voxel_size_chooser" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/q
sirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_pre
proc_dwi_specific_anat_wf/output_grid_wf/voxel_size_chooser".
260728-23:50:18,363 nipype.workflow INFO:
[Node] Executing "voxel_size_chooser" <qsirecon.interfac
es.anatomical.VoxelSizeChooser>
260728-23:50:18,390 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.mask_templ
ate" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-C
ON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_an
at_wf/mask_template".
260728-23:50:18,391 nipype.workflow INFO:
[Node] Finished "voxel_size_chooser", elapsed time 0.027
264s.
260728-23:50:18,393 nipype.workflow INFO:
[Node] Executing "mask_template" <nipype.interfaces.afni
.utils.Calc>
260728-23:50:18,400 nipype.interface WARNING:
Changing /home/jovyan/workspace/books/examples/diffu
sion_imaging/qsirecon-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_seg-AAL11
6_dseg.nii.gz dtype from float64 to int16
260728-23:50:19,656 nipype.workflow INFO:
[Node] Finished "mask_template", elapsed time 1.261579s.
260728-23:50:20,380 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.reorient_t
o_lps" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub
-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_
anat_wf/reorient_to_lps".
260728-23:50:20,382 nipype.workflow INFO:
[Node] Executing "reorient_to_lps" <nipype.interfaces.af
ni.utils.Resample>
260728-23:50:20,965 nipype.workflow INFO:
[Node] Finished "reorient_to_lps", elapsed time 0.5821s.
260728-23:50:22,369 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.output_gri
d_wf.autobox_template" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsi
recon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_prepr
oc_dwi_specific_anat_wf/output_grid_wf/autobox_template".
260728-23:50:22,373 nipype.workflow INFO:
[Node] Executing "autobox_template" <nipype.interfaces.a
fni.utils.Autobox>
260728-23:50:23,83 nipype.workflow INFO:
[Node] Finished "autobox_template", elapsed time 0.709339
s.
260728-23:50:24,349 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.output_gri
d_wf.deoblique_autobox" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qs
irecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_prep
roc_dwi_specific_anat_wf/output_grid_wf/deoblique_autobox".
260728-23:50:24,352 nipype.workflow INFO:
[Node] Executing "deoblique_autobox" <nipype.interfaces.
afni.preprocess.Warp>
260728-23:50:25,261 nipype.workflow INFO:
[Node] Finished "deoblique_autobox", elapsed time 0.9081
66s.
260728-23:50:26,322 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_dwi_specific_anat_wf.output_gri
d_wf.resample_to_voxel_size" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-wo
rk/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc
_preproc_dwi_specific_anat_wf/output_grid_wf/resample_to_voxel_size".
260728-23:50:26,325 nipype.workflow INFO:
[Node] Executing "resample_to_voxel_size" <nipype.interf
aces.afni.utils.Resample>
260728-23:50:26,475 nipype.workflow INFO:
[Node] Finished "resample_to_voxel_size", elapsed time 0
.149539s.
260728-23:50:28,353 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_inputs" in "/home/jovyan/
workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_multishell
_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_inputs".
260728-23:50:29,191 nipype.workflow INFO:
[Node] Executing "sub_CON01_ses_preop_acq_AP_space_ACPC_
desc_preproc_recon_inputs" <qsirecon.interfaces.interchange.ReconWorkflowInputs>
260728-23:50:29,192 nipype.workflow INFO:
[Node] Finished "sub_CON01_ses_preop_acq_AP_space_ACPC_d
esc_preproc_recon_inputs", elapsed time 0.000381s.
260728-23:50:30,323 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.msmt_csd.create_mif" i
n "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_m
rtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/msmt_csd/cre
ate_mif".
260728-23:50:30,353 nipype.workflow INFO:
[Node] Executing "create_mif" <qsirecon.interfaces.mrtri
x.MRTrixIngress>
260728-23:50:31,934 nipype.interface INFO:
mrconvert: [ 0
%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-C
m
rconvert: [ 1%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsipre
p-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...
mrconvert: [ 2%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_
imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dw
mrconvert: [ 3%] uncompressing image "/home/jovyan/workspace/books/examp
les/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_d
mrconvert: [ 4%] uncompressing image "/home/jovyan/workspa
ce/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-A
mrconvert: [ 5%] uncompressing image "/home/
jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_s
mrconvert: [ 6%] uncompressing
image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/d
mrconvert: [ 7%]
uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON
mrc
onvert: [ 8%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-
output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...
mrconvert: [ 9%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_im
aging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.
mrconvert: [ 10%] uncompressing image "/home/jovyan/workspace/books/example
s/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_des
mrconvert: [ 11%] uncompressing image "/home/jovyan/workspace
/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_
mrconvert: [ 12%] uncompressing image "/home/jo
vyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses
mrconvert: [ 13%] uncompressing i
mage "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi
mrconvert: [ 14%] u
ncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01
mrcon
vert: [ 15%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-ou
tput/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...
mrconvert: [ 16%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.ni
mrconvert: [ 17%] uncompressing image "/home/jovyan/workspace/books/examples/
diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-
mrconvert: [ 18%] uncompressing image "/home/jovyan/workspace/b
ooks/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_sp
mrconvert: [ 19%] uncompressing image "/home/jovy
an/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-p
mrconvert: [ 20%] uncompressing ima
ge "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/s
mrconvert: [ 21%] unc
ompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/s
mrconve
rt: [ 22%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-outp
ut/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...?7
mrconvert: [ 23%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imagin
g/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.
mrconvert: [ 24%] uncompressing image "/home/jovyan/workspace/books/examples/di
ffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-pr
mrconvert: [ 25%] uncompressing image "/home/jovyan/workspace/boo
ks/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_spac
mrconvert: [ 26%] uncompressing image "/home/jovyan
/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-pre
mrconvert: [ 27%] uncompressing image
"/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub
mrconvert: [ 28%] uncom
pressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses
mrconvert
: [ 29%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output
/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...?7h
mrconvert: [ 30%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/
qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz
mrconvert: [ 31%] uncompressing image "/home/jovyan/workspace/books/examples/diff
usion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-prep
mrconvert: [ 32%] uncompressing image "/home/jovyan/workspace/books
/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-
mrconvert: [ 33%] uncompressing image "/home/jovyan/w
orkspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop
mrconvert: [ 34%] uncompressing image "
/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-C
mrconvert: [ 35%] uncompr
essing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-p
mrconvert:
[ 36%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/s
ub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...?7h?
mrconvert: [ 37%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qs
iprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz".
mrconvert: [ 38%] uncompressing image "/home/jovyan/workspace/books/examples/diffus
ion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-prepro
mrconvert: [ 39%] uncompressing image "/home/jovyan/workspace/books/e
xamples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-AC
mrconvert: [ 40%] uncompressing image "/home/jovyan/wor
kspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_a
mrconvert: [ 41%] uncompressing image "/h
ome/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON
mrconvert: [ 42%] uncompres
sing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-pre
mrconvert: [
43%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub
-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...?7h?7l
mrconvert: [ 44%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsip
rep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...
mrconvert: [ 45%] uncompressing image "/home/jovyan/workspace/books/examples/diffusio
n_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_
mrconvert: [ 46%] uncompressing image "/home/jovyan/workspace/books/exa
mples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC
mrconvert: [ 47%] uncompressing image "/home/jovyan/works
pace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq
mrconvert: [ 48%] uncompressing image "/hom
e/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01
mrconvert: [ 49%] uncompressi
ng image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop
mrconvert: [ 50
%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-C
m
rconvert: [ 51%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsipre
p-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...
mrconvert: [ 52%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_
imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dw
mrconvert: [ 53%] uncompressing image "/home/jovyan/workspace/books/examp
les/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_d
mrconvert: [ 54%] uncompressing image "/home/jovyan/workspa
ce/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-A
mrconvert: [ 55%] uncompressing image "/home/
jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_s
mrconvert: [ 56%] uncompressing
image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/d
mrconvert: [ 57%]
uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON
mrc
onvert: [ 58%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-
output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...
mrconvert: [ 59%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_im
aging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.
mrconvert: [ 60%] uncompressing image "/home/jovyan/workspace/books/example
s/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_des
mrconvert: [ 61%] uncompressing image "/home/jovyan/workspace
/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_
mrconvert: [ 62%] uncompressing image "/home/jo
vyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses
mrconvert: [ 63%] uncompressing i
mage "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi
mrconvert: [ 64%] u
ncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01
mrcon
vert: [ 65%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-ou
tput/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...
mrconvert: [ 66%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imag
ing/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.ni
mrconvert: [ 67%] uncompressing image "/home/jovyan/workspace/books/examples/
diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-
mrconvert: [ 68%] uncompressing image "/home/jovyan/workspace/b
ooks/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_sp
mrconvert: [ 69%] uncompressing image "/home/jovy
an/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-p
mrconvert: [ 70%] uncompressing ima
ge "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/s
mrconvert: [ 71%] unc
ompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/s
mrconve
rt: [ 72%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-outp
ut/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...?7
mrconvert: [ 73%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imagin
g/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.
mrconvert: [ 74%] uncompressing image "/home/jovyan/workspace/books/examples/di
ffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-pr
mrconvert: [ 75%] uncompressing image "/home/jovyan/workspace/boo
ks/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_spac
mrconvert: [ 76%] uncompressing image "/home/jovyan
/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-pre
mrconvert: [ 77%] uncompressing image
"/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub
mrconvert: [ 78%] uncom
pressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses
mrconvert
: [ 79%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output
/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...?7h
mrconvert: [ 80%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/
qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz
mrconvert: [ 81%] uncompressing image "/home/jovyan/workspace/books/examples/diff
usion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-prep
mrconvert: [ 82%] uncompressing image "/home/jovyan/workspace/books
/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-
mrconvert: [ 83%] uncompressing image "/home/jovyan/w
orkspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop
mrconvert: [ 84%] uncompressing image "
/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-C
mrconvert: [ 85%] uncompr
essing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-p
mrconvert:
[ 86%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/s
ub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...?7h?
mrconvert: [ 87%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qs
iprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz".
mrconvert: [ 88%] uncompressing image "/home/jovyan/workspace/books/examples/diffus
ion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-prepro
mrconvert: [ 89%] uncompressing image "/home/jovyan/workspace/books/e
xamples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-AC
mrconvert: [ 90%] uncompressing image "/home/jovyan/wor
kspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_a
mrconvert: [ 91%] uncompressing image "/h
ome/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON
mrconvert: [ 92%] uncompres
sing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-pre
mrconvert: [
93%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub
-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...?7h?7l
mrconvert: [ 94%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsip
rep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"...
mrconvert: [ 95%] uncompressing image "/home/jovyan/workspace/books/examples/diffusio
n_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_
mrconvert: [ 96%] uncompressing image "/home/jovyan/workspace/books/exa
mples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC
mrconvert: [ 97%] uncompressing image "/home/jovyan/works
pace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq
mrconvert: [ 98%] uncompressing image "/hom
e/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop/dwi/sub-CON01
mrconvert: [ 99%] uncompressi
ng image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-CON01/ses-preop
mrconvert: [100
%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-output/sub-C
mrconv
ert: [100%] uncompressing image "/home/jovyan/workspace/books/examples/diffusion_imaging/qsiprep-out
put/sub-CON01/ses-preop/dwi/sub-CON01_ses-preop_acq-AP_space-ACPC_desc-preproc_dwi.nii.gz"
260728-23:50:33,165 nipype.interface INFO:
mrconvert: [ 0
%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.
mrconvert: [ 1%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "
mrconvert: [ 2%] copying from "/home/jov
mrco
nvert: [ 3%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-p
mrconvert: [ 4%] copying from "/home/jovy...CPC_desc-preproc_dwi.n
mrconvert: [ 5%] copying from
"/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?7
mrconvert: [ 6%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-
mrconvert: [ 7%] copying from "/home/jovy...CPC_desc-pr
mrconvert: [ 8%] c
opying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"
mrconvert: [ 9%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/hom
mrconvert: [ 10%] copying from "/home/jovy...
mrconver
t: [ 11%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-prepr
mrconvert: [ 12%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.g
mrconvert: [ 13%] copying from "/h
ome/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?7h?
mrconvert: [ 14%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC
mrconvert: [ 15%] copying from "/home/jovy...CPC_desc-prepro
mrconvert: [ 16%] copyi
ng from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...
mrconvert: [ 17%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jo
mrconvert: [ 18%] copying from "/home/jovy...CPC_
mrconvert: [
19%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_d
mrconvert: [ 20%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" t
mrconvert: [ 21%] copying from "/home/
m
rconvert: [ 22%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_des
mrconvert: [ 23%] copying from "/home/jovy...CPC_desc-preproc_dw
mrconvert: [ 24%] copying f
rom "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...
mrconvert: [ 25%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy..
mrconvert: [ 26%] copying from "/home/jovy...CPC_desc
mrconvert: [ 27%
] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.m
mrconvert: [ 28%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/
mrconvert: [ 29%] copying from "/home/jovy
mrcon
vert: [ 30%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-pr
mrconvert: [ 31%] copying from "/home/jovy...CPC_desc-preproc_dwi.ni
mrconvert: [ 32%] copying from
"/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?7h
mrconvert: [ 33%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-A
mrconvert: [ 34%] copying from "/home/jovy...CPC_desc-pre
mrconvert: [ 35%] co
pying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif".
mrconvert: [ 36%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home
mrconvert: [ 37%] copying from "/home/jovy...C
mrconvert
: [ 38%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-prepro
mrconvert: [ 39%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz
mrconvert: [ 40%] copying from "/ho
me/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?7h?7
mrconvert: [ 41%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_
mrconvert: [ 42%] copying from "/home/jovy...CPC_desc-preproc
mrconvert: [ 43%] copyin
g from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...
mrconvert: [ 44%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jov
mrconvert: [ 45%] copying from "/home/jovy...CPC_d
mrconvert: [
46%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dw
mrconvert: [ 47%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to
mrconvert: [ 48%] copying from "/home/j
mr
convert: [ 49%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc
mrconvert: [ 50%] copying from "/home/jovy...CPC_desc-preproc_dwi
mrconvert: [ 51%] copying fr
om "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...
mrconvert: [ 52%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...
mrconvert: [ 53%] copying from "/home/jovy...CPC_desc-
mrconvert: [ 54%]
copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mi
mrconvert: [ 55%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/h
mrconvert: [ 56%] copying from "/home/jovy.
mrconv
ert: [ 57%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-pre
mrconvert: [ 58%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii
mrconvert: [ 59%] copying from "
/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?7h
mrconvert: [ 60%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-AC
mrconvert: [ 61%] copying from "/home/jovy...CPC_desc-prep
mrconvert: [ 62%] cop
ying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"..
mrconvert: [ 63%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/
mrconvert: [ 64%] copying from "/home/jovy...CP
mrconvert:
[ 65%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc
mrconvert: [ 66%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz"
mrconvert: [ 67%] copying from "/hom
e/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?7h?7l
mrconvert: [ 68%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_d
mrconvert: [ 69%] copying from "/home/jovy...CPC_desc-preproc_
mrconvert: [ 70%] copying
from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...0
mrconvert: [ 71%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy
mrconvert: [ 72%] copying from "/home/jovy...CPC_de
mrconvert: [ 7
3%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi
mrconvert: [ 74%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to
mrconvert: [ 75%] copying from "/home/jo
mrc
onvert: [ 76%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-
mrconvert: [ 77%] copying from "/home/jovy...CPC_desc-preproc_dwi.
mrconvert: [ 78%] copying fro
m "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?
mrconvert: [ 79%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e
mrconvert: [ 80%] copying from "/home/jovy...CPC_desc-p
mrconvert: [ 81%]
copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif
mrconvert: [ 82%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/ho
mrconvert: [ 83%] copying from "/home/jovy..
mrconve
rt: [ 84%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-prep
mrconvert: [ 85%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.
mrconvert: [ 86%] copying from "/
home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?7h
mrconvert: [ 87%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACP
mrconvert: [ 88%] copying from "/home/jovy...CPC_desc-prepr
mrconvert: [ 89%] copy
ing from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...
mrconvert: [ 90%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/j
mrconvert: [ 91%] copying from "/home/jovy...CPC
mrconvert:
[ 92%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_
mrconvert: [ 93%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz"
mrconvert: [ 94%] copying from "/home
/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...?7h?7l
mrconvert: [ 95%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_de
mrconvert: [ 96%] copying from "/home/jovy...CPC_desc-preproc_d
mrconvert: [ 97%] copying
from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.mif"...
mrconvert: [ 98%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy.
mrconvert: [ 99%] copying from "/home/jovy...CPC_des
mrconvert: [100
%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home/jovy...e-ACPC_desc-preproc_dwi.
mrconvert: [100%] copying from "/home/jovy...CPC_desc-preproc_dwi.nii.gz" to "/home
/jovy...e-ACPC_desc-preproc_dwi.mif"
260728-23:50:33,255 nipype.workflow INFO:
[Node] Finished "create_mif", elapsed time 2.900777s.
260728-23:50:34,334 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.msmt_csd.estimate_resp
onse" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-
CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/msmt_
csd/estimate_response".
260728-23:50:34,362 nipype.workflow INFO:
[Node] Executing "estimate_response" <qsirecon.interface
s.mrtrix.SS3TDwi2Response>
260728-23:50:46,442 nipype.workflow INFO:
[Node] Finished "estimate_response", elapsed time 11.993
562s.
260728-23:50:48,345 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.msmt_csd.estimate_fod"
in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01
_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/msmt_csd/e
stimate_fod".
260728-23:50:48,379 nipype.workflow INFO:
[Node] Executing "estimate_fod" <qsirecon.interfaces.mrt
rix.EstimateFOD>
260729-00:09:01,991 nipype.workflow INFO:
[Node] Finished "estimate_fod", elapsed time 1093.523404
s.
260729-00:09:03,469 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.msmt_csd.intensity_nor
m" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON
01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/msmt_csd
/intensity_norm".
260729-00:09:03,475 nipype.workflow INFO:
[Node] Executing "intensity_norm" <qsirecon.interfaces.m
rtrix.MTNormalize>
260729-00:09:06,686 nipype.workflow INFO:
[Node] Finished "intensity_norm", elapsed time 3.099986s
.
260729-00:09:08,235 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.msmt_csd.plot_peaks" i
n "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_m
rtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/msmt_csd/plo
t_peaks".
260729-00:09:08,238 nipype.workflow INFO:
[Node] Executing "plot_peaks" <qsirecon.interfaces.repor
ts.CLIReconPeaksReport>
260729-00:09:12,589 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.track_ifod2.tractograp
hy" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CO
N01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/track_i
fod2/tractography".
260729-00:09:12,593 nipype.workflow INFO:
[Node] Executing "tractography" <qsirecon.interfaces.mrt
rix.TckGen>
260729-00:09:53,375 nipype.workflow INFO:
[Node] Finished "plot_peaks", elapsed time 45.13644s.
260729-00:14:47,448 nipype.workflow INFO:
[Node] Finished "tractography", elapsed time 334.854991s
.
260729-00:14:48,931 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.track_ifod2.tck_sift2"
in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01
_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/track_ifod
2/tck_sift2".
260729-00:14:48,936 nipype.workflow INFO:
[Node] Executing "tck_sift2" <qsirecon.interfaces.mrtrix
.SIFT2>
260729-00:15:35,419 nipype.workflow INFO:
[Node] Finished "tck_sift2", elapsed time 46.4821s.
260729-00:15:37,147 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.mrtrix_conn.calc_conne
ctivity" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/s
ub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mr
trix_conn/calc_connectivity".
260729-00:15:37,153 nipype.workflow INFO:
[Node] Executing "calc_connectivity" <qsirecon.interface
s.mrtrix.MRTrixAtlasGraph>
260729-00:15:37,163 nipype.workflow INFO:
Workflow mrtrix_atlasgraph settings: ['check', 'executio
n', 'logging', 'monitoring']
260729-00:15:37,169 nipype.workflow INFO:
Running in parallel.
260729-00:15:37,171 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:39,174 nipype.workflow INFO:
[MultiProc] Running 1 tasks, and 3 jobs ready. Free memo
ry (GB): 56.31/56.51, Free processors: 0/4.
Currently running:
* mrtrix_atlasgraph.AAL116_sift_invnodevol_radius2_count
260729-00:15:42,257 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.AAL116_sift_invnode
vol_radius2_count" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsireco
n_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_r
econ_wf/mrtrix_conn/calc_connectivity/mrtrix_atlasgraph/AAL116_sift_invnodevol_radius2_count".
260729-00:15:42,259 nipype.workflow INFO:
[Node] Executing "AAL116_sift_invnodevol_radius2_count"
<qsirecon.interfaces.mrtrix.BuildConnectome>
260729-00:15:43,206 nipype.workflow INFO:
[Node] Finished "AAL116_sift_invnodevol_radius2_count",
elapsed time 0.833991s.
260729-00:15:45,180 nipype.workflow INFO:
[Job 0] Completed (mrtrix_atlasgraph.AAL116_sift_invnode
vol_radius2_count).
260729-00:15:45,181 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:45,251 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.AAL116_radius2_mean
length" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/su
b-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrt
rix_conn/calc_connectivity/mrtrix_atlasgraph/AAL116_radius2_meanlength".
260729-00:15:45,253 nipype.workflow INFO:
[Node] Executing "AAL116_radius2_meanlength" <qsirecon.i
nterfaces.mrtrix.BuildConnectome>
260729-00:15:46,115 nipype.workflow INFO:
[Node] Finished "AAL116_radius2_meanlength", elapsed tim
e 0.861181s.
260729-00:15:47,181 nipype.workflow INFO:
[Job 1] Completed (mrtrix_atlasgraph.AAL116_radius2_mean
length).
260729-00:15:47,183 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:47,250 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.AAL116_radius2_coun
t" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON
01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtrix_c
onn/calc_connectivity/mrtrix_atlasgraph/AAL116_radius2_count".
260729-00:15:47,252 nipype.workflow INFO:
[Node] Executing "AAL116_radius2_count" <qsirecon.interf
aces.mrtrix.BuildConnectome>
260729-00:15:47,732 nipype.workflow INFO:
[Node] Finished "AAL116_radius2_count", elapsed time 0.4
7921s.
260729-00:15:49,183 nipype.workflow INFO:
[Job 2] Completed (mrtrix_atlasgraph.AAL116_radius2_coun
t).
260729-00:15:49,184 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:49,259 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.AAL116_sift_radius2
_count" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/su
b-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrt
rix_conn/calc_connectivity/mrtrix_atlasgraph/AAL116_sift_radius2_count".
260729-00:15:49,261 nipype.workflow INFO:
[Node] Executing "AAL116_sift_radius2_count" <qsirecon.i
nterfaces.mrtrix.BuildConnectome>
260729-00:15:49,857 nipype.workflow INFO:
[Node] Finished "AAL116_sift_radius2_count", elapsed tim
e 0.595918s.
260729-00:15:51,185 nipype.workflow INFO:
[Job 3] Completed (mrtrix_atlasgraph.AAL116_sift_radius2
_count).
260729-00:15:51,187 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 6 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:51,260 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.AAL116_sift_invnode
vol_radius2_count_c2t" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsi
recon_1_1_wf/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_prepr
oc_recon_wf/mrtrix_conn/calc_connectivity/mrtrix_atlasgraph/AAL116_sift_invnodevol_radius2_count_c2t
".
260729-00:15:51,262 nipype.workflow INFO:
[Node] Executing "AAL116_sift_invnodevol_radius2_count_c
2t" <qsirecon.interfaces.mrtrix.Connectome2Tck>
260729-00:15:53,74 nipype.workflow INFO:
[Node] Finished "AAL116_sift_invnodevol_radius2_count_c2t
", elapsed time 1.811096s.
260729-00:15:53,188 nipype.workflow INFO:
[Job 4] Completed (mrtrix_atlasgraph.AAL116_sift_invnode
vol_radius2_count_c2t).
260729-00:15:53,189 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 5 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:53,263 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.AAL116_radius2_mean
length_c2t" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_w
f/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf
/mrtrix_conn/calc_connectivity/mrtrix_atlasgraph/AAL116_radius2_meanlength_c2t".
260729-00:15:53,265 nipype.workflow INFO:
[Node] Executing "AAL116_radius2_meanlength_c2t" <qsirec
on.interfaces.mrtrix.Connectome2Tck>
260729-00:15:54,873 nipype.workflow INFO:
[Node] Finished "AAL116_radius2_meanlength_c2t", elapsed
time 1.607249s.
260729-00:15:55,190 nipype.workflow INFO:
[Job 5] Completed (mrtrix_atlasgraph.AAL116_radius2_mean
length_c2t).
260729-00:15:55,191 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:55,261 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.AAL116_radius2_coun
t_c2t" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub
-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtr
ix_conn/calc_connectivity/mrtrix_atlasgraph/AAL116_radius2_count_c2t".
260729-00:15:55,264 nipype.workflow INFO:
[Node] Executing "AAL116_radius2_count_c2t" <qsirecon.in
terfaces.mrtrix.Connectome2Tck>
260729-00:15:56,923 nipype.workflow INFO:
[Node] Finished "AAL116_radius2_count_c2t", elapsed time
1.658312s.
260729-00:15:57,192 nipype.workflow INFO:
[Job 6] Completed (mrtrix_atlasgraph.AAL116_radius2_coun
t_c2t).
260729-00:15:57,193 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 3 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:57,262 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.AAL116_sift_radius2
_count_c2t" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_w
f/sub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf
/mrtrix_conn/calc_connectivity/mrtrix_atlasgraph/AAL116_sift_radius2_count_c2t".
260729-00:15:57,265 nipype.workflow INFO:
[Node] Executing "AAL116_sift_radius2_count_c2t" <qsirec
on.interfaces.mrtrix.Connectome2Tck>
260729-00:15:58,895 nipype.workflow INFO:
[Node] Finished "AAL116_sift_radius2_count_c2t", elapsed
time 1.629721s.
260729-00:15:59,194 nipype.workflow INFO:
[Job 7] Completed (mrtrix_atlasgraph.AAL116_sift_radius2
_count_c2t).
260729-00:15:59,195 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 4 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:15:59,270 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.merge_mats" in "/ho
me/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_
multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtrix_conn/calc_c
onnectivity/mrtrix_atlasgraph/merge_mats".
260729-00:15:59,274 nipype.workflow INFO:
[Node] Executing "merge_mats" <nipype.interfaces.utility
.base.Merge>
260729-00:15:59,275 nipype.workflow INFO:
[Node] Finished "merge_mats", elapsed time 0.000166s.
260729-00:15:59,277 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.merge_csvs" in "/ho
me/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_
multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtrix_conn/calc_c
onnectivity/mrtrix_atlasgraph/merge_csvs".
260729-00:15:59,280 nipype.workflow INFO:
[Node] Executing "merge_csvs" <nipype.interfaces.utility
.base.Merge>
260729-00:15:59,281 nipype.workflow INFO:
[Node] Finished "merge_csvs", elapsed time 0.000137s.
260729-00:15:59,283 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.merge_tcks" in "/ho
me/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtrix_
multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtrix_conn/calc_c
onnectivity/mrtrix_atlasgraph/merge_tcks".
260729-00:15:59,286 nipype.workflow INFO:
[Node] Executing "merge_tcks" <nipype.interfaces.utility
.base.Merge>
260729-00:15:59,287 nipype.workflow INFO:
[Node] Finished "merge_tcks", elapsed time 0.000141s.
260729-00:15:59,288 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.merge_weights" in "
/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mrtr
ix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtrix_conn/cal
c_connectivity/mrtrix_atlasgraph/merge_weights".
260729-00:15:59,291 nipype.workflow INFO:
[Node] Executing "merge_weights" <nipype.interfaces.util
ity.base.Merge>
260729-00:15:59,292 nipype.workflow INFO:
[Node] Finished "merge_weights", elapsed time 0.000129s.
260729-00:16:01,196 nipype.workflow INFO:
[Job 8] Completed (mrtrix_atlasgraph.merge_mats).
260729-00:16:01,197 nipype.workflow INFO:
[Job 9] Completed (mrtrix_atlasgraph.merge_csvs).
260729-00:16:01,198 nipype.workflow INFO:
[Job 10] Completed (mrtrix_atlasgraph.merge_tcks).
260729-00:16:01,199 nipype.workflow INFO:
[Job 11] Completed (mrtrix_atlasgraph.merge_weights).
260729-00:16:01,200 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:16:01,289 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.merge_exemplars" in
"/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01_mr
trix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtrix_conn/c
alc_connectivity/mrtrix_atlasgraph/merge_exemplars".
260729-00:16:01,292 nipype.workflow INFO:
[Node] Executing "merge_exemplars" <nipype.interfaces.ut
ility.base.Merge>
260729-00:16:01,293 nipype.workflow INFO:
[Node] Finished "merge_exemplars", elapsed time 0.000181
s.
260729-00:16:03,198 nipype.workflow INFO:
[Job 12] Completed (mrtrix_atlasgraph.merge_exemplars).
260729-00:16:03,199 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 1 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:16:03,268 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.compress_exemplars"
in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01
_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtrix_con
n/calc_connectivity/mrtrix_atlasgraph/compress_exemplars".
260729-00:16:03,271 nipype.workflow INFO:
[Node] Executing "compress_exemplars" <qsirecon.interfac
es.mrtrix.CompressConnectome2Tck>
260729-00:16:04,98 nipype.workflow INFO:
[Node] Finished "compress_exemplars", elapsed time 0.8260
01s.
260729-00:16:05,200 nipype.workflow INFO:
[Job 13] Completed (mrtrix_atlasgraph.compress_exemplars
).
260729-00:16:05,202 nipype.workflow INFO:
[MultiProc] Running 0 tasks, and 0 jobs ready. Free memo
ry (GB): 56.51/56.51, Free processors: 4/4.
260729-00:16:07,247 nipype.workflow INFO:
[Node] Setting-up "mrtrix_atlasgraph.compress_exemplars"
in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/sub-CON01
_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mrtrix_con
n/calc_connectivity/mrtrix_atlasgraph/compress_exemplars".
260729-00:16:07,249 nipype.workflow INFO:
[Node] Cached "mrtrix_atlasgraph.compress_exemplars" - c
ollecting precomputed outputs
260729-00:16:07,249 nipype.workflow INFO:
[Node] "mrtrix_atlasgraph.compress_exemplars" found cach
ed.
260729-00:16:07,250 nipype.workflow INFO:
[Node] Finished "calc_connectivity", elapsed time 30.096
713s.
260729-00:16:08,982 nipype.workflow INFO:
[Node] Setting-up "qsirecon_1_1_wf.sub-CON01_mrtrix_mult
ishell_msmt_noACT.sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf.mrtrix_conn.plot_conne
ctivity" in "/home/jovyan/workspace/books/examples/diffusion_imaging/qsirecon-work/qsirecon_1_1_wf/s
ub-CON01_mrtrix_multishell_msmt_noACT/sub_CON01_ses_preop_acq_AP_space_ACPC_desc_preproc_recon_wf/mr
trix_conn/plot_connectivity".
260729-00:16:08,986 nipype.workflow INFO:
[Node] Executing "plot_connectivity" <qsirecon.interface
s.reports.ConnectivityReport>
260729-00:16:09,181 nipype.workflow INFO:
[Node] Finished "plot_connectivity", elapsed time 0.1944
83s.
260729-00:16:12,899 nipype.workflow IMPORTANT:
QSIRecon finished successfully!
260729-00:16:12,904 nipype.workflow IMPORTANT:
Works derived from this QSIRecon execution should i
nclude the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
260729-00:16:12,936 nipype.utils WARNING:
DatasetType key not in /home/jovyan/workspace/books/exam
ples/diffusion_imaging/qsiprep-output/dataset_description.json. Assuming 'derivative'.
260729-00:16:14,23 nipype.utils WARNING:
DatasetType key not in /home/jovyan/workspace/books/examp
les/diffusion_imaging/qsiprep-output/dataset_description.json. Assuming 'derivative'.
#remove the working dir
shutil.rmtree("qsirecon-work", ignore_errors=True)
QSIRecon outputs#
The reconstruction results are nested under derivatives/qsirecon-MRtrix3_act-None/ rather than sitting at the top level. The directory name comes from the qsirecon_suffix declared in the recon spec — a single run can emit several such datasets, so each is written as its own self-contained BIDS derivatives dataset, with act-None recording that we used the non-ACT variant.
Inside, sub-CON01/ses-preop/dwi/ holds the reconstruction proper: per-tissue FODs from MSMT-CSD (model-msmtcsd_param-fod_label-{WM,GM,CSF}, with the matching response functions as .txt), the mtnormalise outputs, the iFOD2 streamlines (model-ifod2_streamlines.tck.gz), the SIFT2 weights and proportionality coefficient (model-sift2_streamlineweights.csv, model-sift2_mu.txt), and the connectome itself in connectivity.mat. The figures/ directory holds the panels shown in the visual report, and sub-CON01_ses-preop.html is that report.
At the top level, atlases/ contains the AAL116 atlas as passed to --atlases, while the top-level sub-CON01/ses-preop/dwi/ holds it resampled into the subject’s ACPC space — the parcellation actually used to build the connectome.
! tree qsirecon-output/
qsirecon-output/
├── atlases
│ ├── atlas-AAL116
│ │ ├── atlas-AAL116_dseg.tsv
│ │ ├── atlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg.json
│ │ └── atlas-AAL116_space-MNI152NLin2009cAsym_res-01_dseg.nii.gz
│ └── dataset_description.json
├── dataset_description.json
├── derivatives
│ └── qsirecon-MRtrix3_act-None
│ ├── dataset_description.json
│ ├── logs
│ │ ├── CITATION.bib
│ │ ├── CITATION.html
│ │ ├── CITATION.md
│ │ └── CITATION.tex
│ ├── sub-CON01
│ │ └── ses-preop
│ │ ├── dwi
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_connectivity.mat
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_exemplarbundles.zip
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-ifod2_streamlines.tck.gz
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-msmtcsd_param-fod_label-CSF_dwimap.mif.gz
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-msmtcsd_param-fod_label-CSF_dwimap.txt
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-msmtcsd_param-fod_label-GM_dwimap.mif.gz
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-msmtcsd_param-fod_label-GM_dwimap.txt
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-msmtcsd_param-fod_label-WM_dwimap.mif.gz
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-msmtcsd_param-fod_label-WM_dwimap.txt
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-mtnorm_param-inliermask_dwimap.nii.gz
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-mtnorm_param-norm_dwimap.nii.gz
│ │ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_model-sift2_mu.txt
│ │ │ └── sub-CON01_ses-preop_acq-AP_space-ACPC_model-sift2_streamlineweights.csv
│ │ └── figures
│ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_desc-MRtrix3Connectivity_matrices.svg
│ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_desc-wmFOD_odfs.png
│ │ ├── sub-CON01_ses-preop_acq-AP_space-ACPC_desc-wmFOD_peaks.png
│ │ ├── sub-CON01_ses-preop_desc-about_T1w.html
│ │ └── sub-CON01_ses-preop_desc-summary_T1w.html
│ └── sub-CON01_ses-preop.html
├── logs
│ ├── CITATION.bib
│ ├── CITATION.html
│ ├── CITATION.md
│ └── CITATION.tex
└── sub-CON01
├── log
│ └── 20260728-234759_905ab0bb-d4d5-4aa3-a94f-121ce14992ba
│ ├── qsirecon.toml
│ └── recon_spec.yaml
└── ses-preop
└── dwi
├── sub-CON01_ses-preop_acq-AP_space-ACPC_seg-AAL116_dseg.mif.gz
├── sub-CON01_ses-preop_acq-AP_space-ACPC_seg-AAL116_dseg.nii.gz
└── sub-CON01_ses-preop_acq-AP_space-ACPC_seg-AAL116_dseg.txt
16 directories, 38 files
3. Results#
We display the full QSIRecon visual report. It contains FOD peak/ODF visualisations and the connectome matrices figure, alongside run provenance and summary sections. The report references its figures as separate files, so we inline them (PNGs as base64, SVGs embedded directly) to make it render in the notebook.
# Display the QSIRecon HTML report with all images inlined.
# PNGs are base64-encoded; SVGs are embedded directly into the DOM.
def display_report(report_path):
report_dir = os.path.dirname(report_path)
with open(report_path) as f:
soup = BeautifulSoup(f, 'html.parser')
# Inline <img src=...> tags: PNG as base64, SVG embedded directly
for img in soup.find_all('img'):
src = img.get('src', '')
if not src:
continue
img_path = os.path.join(report_dir, src.lstrip('./'))
if os.path.exists(img_path):
if src.endswith('.svg'):
with open(img_path) as f:
svg_soup = BeautifulSoup(f.read(), 'html.parser')
svg_tag = svg_soup.find('svg')
if svg_tag:
img.replace_with(svg_tag)
elif src.endswith('.png'):
with open(img_path, 'rb') as f:
data = base64.b64encode(f.read()).decode()
img['src'] = f'data:image/png;base64,{data}'
# Also inline SVGs referenced in <a href> tags
for tag in soup.find_all(href=lambda h: h and h.endswith('.svg')):
svg_path = os.path.join(report_dir, tag['href'])
if os.path.exists(svg_path):
with open(svg_path) as f:
svg_soup = BeautifulSoup(f.read(), 'html.parser')
tag.replace_with(svg_soup)
# Remove nav/button clutter
for tag in soup(['button', 'nav', 'head']):
tag.decompose()
display(HTML(str(soup)))
display_report('./qsirecon-output/derivatives/qsirecon-MRtrix3_act-None/sub-CON01_ses-preop.html')
Summary
- Subject ID: CON01
- Structural images: 1 T1-weighted
- Diffusion-weighted series: 1
- Standard output spaces: MNI152NLin2009cAsym
- Non-standard output spaces:
- FreeSurfer reconstruction: Pre-existing directory
MRtrix3
Reports for: session preop, acquisition AP.
Constrained Spherical Deconvolution
Directionally color-coded FOD peaks overlaid on the b=0 reference image.