Scripted First-Level Analyses in FSL using fMRIPrep data#
This notebook walks through a simple, novice-friendly workflow in Neurodesk EDU:
install one OpenNeuro dataset and get one subject
run fMRIPrep for one task/run from that subject and extract FEAT-ready confounds
convert BIDS
events.tsvfiles to FSL 3-column EV filesrender and run a first-level FEAT model from a trust-game FEAT template
make a first pass at viewing the result in NiiVue
Author:
Date: April 2, 2026
License:
Provenance: This notebook adapts course materials and selected logic from the Fareri trust-game workflow code, but rewrites the steps so they can be followed directly in notebook cells. Full workflow repository: tubric/fareri-2022-neuroimage.
Acknowledgments: This notebook was generated with assistance from ChatGPT-5 across several iterations and then revised by the instructor. The instructor reviewed the final content and takes responsibility for it.
Citation and Resources#
Study-specific references#
Fareri et al. (2022): Fareri, D. S., Hackett, K., Tepfer, L. J., Kelly, V., Henninger, N., Reeck, C., Giovannetti, T., & Smith, D. V. (2022). Age-related differences in ventral striatal and default mode network function during reciprocated trust. NeuroImage, 256, 119267. https://doi.org/10.1016/j.neuroimage.2022.119267
Smith et al. (2024): Smith, D. V., Ludwig, R. M., Dennison, J. B., Reeck, C., & Fareri, D. S. (2024). An fMRI Dataset on Social Reward Processing and Decision Making in Younger and Older Adults. Scientific Data, 11(1), 158. https://doi.org/10.1038/s41597-024-02931-y
Full workflow repository#
Fareri trust-game workflow repo: tubric/fareri-2022-neuroimage
Tools included in this workflow#
fMRIPrep: Esteban, O., Markiewicz, C. J., Blair, R. W., et al. (2019). fMRIPrep: a robust preprocessing pipeline for functional MRI. Nature Methods, 16, 111–116.
FSL / FEAT: Jenkinson, M., Beckmann, C. F., Behrens, T. E. J., Woolrich, M. W., & Smith, S. M. (2012). FSL. NeuroImage, 62, 782–790.
DataLad: Halchenko, Y. O., Meyer, K., Poldrack, B., et al. (2021). DataLad: distributed system for joint management of code, data, and their relationship. Journal of Open Source Software, 6, 3262.
bidsutils / BIDSto3col.sh: Tom Nichols and contributors.
bids-standard/bidsutils.NiiVue / ipyniivue for interactive image viewing in Jupyter.
Dataset#
OpenNeuro ds003745 (trust game dataset used in class materials and labs)
Educational resources#
Course labs on Neurodesk, fMRIPrep, FEAT, and 3-column event files.
Table of content#
1. Load software tools and import python libraries
2. Data preparation
3. Run fMRIPrep for one selected run
4. Make a FEAT confounds file
5. Convert events.tsv to 3-column files
6. Render the FEAT template
7. Run first-level FEAT
8. Fix FEAT registration for fMRIPrep-preprocessed data
9. Results
10. Dependencies in Jupyter/Python
1. Load software tools and import python libraries#
import module
await module.load('fmriprep/25.2.5')
await module.load('fsl/6.0.7.22')
await module.list()
['fmriprep/25.2.5', 'fsl/6.0.7.22']
%%capture
!pip install pandas
from pathlib import Path
import os
import glob
import pandas as pd
from IPython.display import display, Markdown, Image
base_dir = Path.home() / "trust_example"
print(base_dir)
/home/jovyan/trust_example
2. Data preparation#
We will keep everything for this example in one folder directly under the home directory:
~/trust_example
That makes the paths easy to read, and it also makes it easier to rerun or delete the whole example later if you want a clean start.
Inside that folder, we will make a few subdirectories:
templates/for the FEAT templatebids/for the OpenNeuro datasetderivatives/for fMRIPrep output, confounds, EV files, and FEAT outputscratch/for temporary working filesbidsutils/for Tom Nichols’BIDSto3col.sh
%%bash
set -e
EXAMPLE_DIR="$HOME/trust_example"
mkdir -p "$EXAMPLE_DIR"
cd "$EXAMPLE_DIR"
# Keep the example organized in one project folder.
mkdir -p templates bids derivatives scratch
# Copy the one FEAT template we need.
curl -L \
https://raw.githubusercontent.com/tubric/fareri-2022-neuroimage/main/templates/L1_task-trust_model-01_type-act.fsf \
-o templates/L1_task-trust_model-01_type-act.fsf
# Install bidsutils separately so we can use BIDSto3col.sh.
if [ ! -d bidsutils ]; then
git clone --depth 1 https://github.com/bids-standard/bidsutils.git
fi
# Install the OpenNeuro dataset skeleton and get the full subject recursively.
cd bids
if [ ! -d ds003745 ]; then
datalad install https://github.com/OpenNeuroDatasets/ds003745.git
fi
cd ds003745
datalad get -r sub-104
install(ok): /home/jovyan/trust_example/bids/ds003745 (dataset)
get(ok): sub-104/anat/sub-104_T1w.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-104/anat/sub-104_T2w.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-104/fmap/sub-104_ma
gnitude1.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-104/fmap/sub-104_magnitude2.nii.gz (file) [f
rom s3-PUBLIC...]
get(ok): sub-104/fmap/sub-104_phasediff.nii.gz (file) [from s3-PUBLIC...]
get(ok):
sub-104/func/sub-104_task-sharedreward_run-01_bold.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-1
04/func/sub-104_task-sharedreward_run-02_bold.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-104/func/sub-104_task-trust_run-01_bold.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-
104/func/sub-104_task-trust_run-02_bold.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-104/func/sub-
104_task-trust_run-03_bold.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-104/func/sub-104_task-trus
t_run-04_bold.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-104/func/sub-104_task-trust_run-05_bold
.nii.gz (file) [from s3-PUBLIC...]
get(ok): sub-104/func/sub-104_task-ultimatum_run-01_bold.nii.gz (
file) [from s3-PUBLIC...]
get(ok): sub-104/func/sub-104_task-ultimatum_run-02_bold.nii.gz (file) [fr
om s3-PUBLIC...]
get(ok): sub-104 (directory)
action summary:
get (ok: 15)
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload T
otal Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-
- 0
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 73223 100 73223 0 0 230k 0 --:--:-- --:--:-- --:--:-- 229k
Cloning into 'bidsutils'...
[INFO] Attempting a clone into /home/jovyan/trust_example/bids/ds003745
[INFO] Attempting to clone
from https://github.com/OpenNeuroDatasets/ds003745.git to /home/jovyan/trust_example/bids/ds003745
[INFO] Start enumerating objects
[INFO] Start counting objects
[INFO] Start compressing objects
[INFO] Start receiving objects
[INFO] Start resolving deltas
[INFO] Completed clone attempts for Dataset(/home/jovyan/trust_example/bids/ds003745)
[INFO] Remote origin not usable by git-annex; setting annex-ignore
[INFO] https://github.com/OpenNeuroDatasets/ds003745.git/config download failed: Not Found
[INFO] Remote origin not usable by git-annex; setting annex-ignore
[INFO] https://github.com/OpenNeuroDatasets/ds003745.git/config download failed: Not Found
[INFO] access to 1 dataset sibling s3-PRIVATE not auto-enabled, enable with:
| datalad siblings -d
"/home/jovyan/trust_example/bids/ds003745" enable -s s3-PRIVATE
[INFO] Ensuring presence of Dataset(/home/jovyan/trust_example/bids/ds003745) to get /home/jovyan/tr
ust_example/bids/ds003745/sub-104
!tree -L 3 ~/trust_example/templates
!tree -L 3 ~/trust_example/bids/ds003745/sub-104
/home/jovyan/trust_example/templates
└── L1_task-trust_model-01_type-act.fsf
1 directory, 1 file
/home/jovyan/trust_example/bids/ds003745/sub-104
├── anat
│ ├── sub-104_T1w.json
│ ├── sub-104_T1w.nii.gz -> ../../.git/annex/objects/wM/31/MD5E-s8381149--5fd51ee8f8b1d0fa00490acab7054f44.nii.gz/MD5E-s8381149--5fd51ee8f8b1d0fa00490acab7054f44.nii.gz
│ ├── sub-104_T2w.json
│ └── sub-104_T2w.nii.gz -> ../../.git/annex/objects/Z3/xJ/MD5E-s9405965--d643b78dc1b963c582be22a5e67576c5.nii.gz/MD5E-s9405965--d643b78dc1b963c582be22a5e67576c5.nii.gz
├── fmap
│ ├── sub-104_magnitude1.json
│ ├── sub-104_magnitude1.nii.gz -> ../../.git/annex/objects/5p/kK/MD5E-s227307--ff542908f56f6acec5e8ef22a84ec4b2.nii.gz/MD5E-s227307--ff542908f56f6acec5e8ef22a84ec4b2.nii.gz
│ ├── sub-104_magnitude2.json
│ ├── sub-104_magnitude2.nii.gz -> ../../.git/annex/objects/fz/8J/MD5E-s225256--6926b13a836ec3487bb68649bf0f36cb.nii.gz/MD5E-s225256--6926b13a836ec3487bb68649bf0f36cb.nii.gz
│ ├── sub-104_phasediff.json
│ └── sub-104_phasediff.nii.gz -> ../../.git/annex/objects/Qw/1v/MD5E-s315320--78621dbba52c9bf69a344e60e82a7c57.nii.gz/MD5E-s315320--78621dbba52c9bf69a344e60e82a7c57.nii.gz
├── func
│ ├── sub-104_task-sharedreward_run-01_bold.json
│ ├── sub-104_task-sharedreward_run-01_bold.nii.gz -> ../../.git/annex/objects/8G/Jk/MD5E-s46088562--9731c3b106760361503f64a140d31914.nii.gz/MD5E-s46088562--9731c3b106760361503f64a140d31914.nii.gz
│ ├── sub-104_task-sharedreward_run-01_events.tsv
│ ├── sub-104_task-sharedreward_run-02_bold.json
│ ├── sub-104_task-sharedreward_run-02_bold.nii.gz -> ../../.git/annex/objects/F7/ZF/MD5E-s46094097--51993b075ce4576cf7d9f87af3ed87fb.nii.gz/MD5E-s46094097--51993b075ce4576cf7d9f87af3ed87fb.nii.gz
│ ├── sub-104_task-sharedreward_run-02_events.tsv
│ ├── sub-104_task-trust_run-01_bold.json
│ ├── sub-104_task-trust_run-01_bold.nii.gz -> ../../.git/annex/objects/qQ/Wf/MD5E-s49583622--5df9c6e76342f61d119f834930f1b106.nii.gz/MD5E-s49583622--5df9c6e76342f61d119f834930f1b106.nii.gz
│ ├── sub-104_task-trust_run-01_events.tsv
│ ├── sub-104_task-trust_run-02_bold.json
│ ├── sub-104_task-trust_run-02_bold.nii.gz -> ../../.git/annex/objects/Zx/1g/MD5E-s49598762--8064d7bae979bf7dce903a5d9566c179.nii.gz/MD5E-s49598762--8064d7bae979bf7dce903a5d9566c179.nii.gz
│ ├── sub-104_task-trust_run-02_events.tsv
│ ├── sub-104_task-trust_run-03_bold.json
│ ├── sub-104_task-trust_run-03_bold.nii.gz -> ../../.git/annex/objects/wg/zf/MD5E-s49517139--ab7192041bf89d0090c5073efde94d35.nii.gz/MD5E-s49517139--ab7192041bf89d0090c5073efde94d35.nii.gz
│ ├── sub-104_task-trust_run-03_events.tsv
│ ├── sub-104_task-trust_run-04_bold.json
│ ├── sub-104_task-trust_run-04_bold.nii.gz -> ../../.git/annex/objects/7j/Z7/MD5E-s49498400--842108100e1e9e1ba319befbf607a742.nii.gz/MD5E-s49498400--842108100e1e9e1ba319befbf607a742.nii.gz
│ ├── sub-104_task-trust_run-04_events.tsv
│ ├── sub-104_task-trust_run-05_bold.json
│ ├── sub-104_task-trust_run-05_bold.nii.gz -> ../../.git/annex/objects/2z/m5/MD5E-s49530982--83aa67c0eeb97763f1a9ed2fed446f5f.nii.gz/MD5E-s49530982--83aa67c0eeb97763f1a9ed2fed446f5f.nii.gz
│ ├── sub-104_task-trust_run-05_events.tsv
│ ├── sub-104_task-ultimatum_run-01_bold.json
│ ├── sub-104_task-ultimatum_run-01_bold.nii.gz -> ../../.git/annex/objects/px/3W/MD5E-s45649089--6c0c75aa15a19bd42fa34aa85f86364c.nii.gz/MD5E-s45649089--6c0c75aa15a19bd42fa34aa85f86364c.nii.gz
│ ├── sub-104_task-ultimatum_run-01_events.tsv
│ ├── sub-104_task-ultimatum_run-02_bold.json
│ ├── sub-104_task-ultimatum_run-02_bold.nii.gz -> ../../.git/annex/objects/mx/Qg/MD5E-s45657152--c4ca6e2d5208031fd9aaf4a8735692a2.nii.gz/MD5E-s45657152--c4ca6e2d5208031fd9aaf4a8735692a2.nii.gz
│ └── sub-104_task-ultimatum_run-02_events.tsv
├── sub-104_scans.json
└── sub-104_scans.tsv
4 directories, 39 files
The example below uses:
subject:
104task:
trustrun:
01
That keeps the notebook manageable, but the same logic can be repeated for the other runs.
For teaching purposes, one run is a nice compromise: the model is still realistic, but the files and paths stay simple enough to follow line by line.
3. Run fMRIPrep for one selected run#
The next cell runs fMRIPrep on one participant for the trust task and run 01. It writes the outputs under ~/trust_example/derivatives/fmriprep.
The task is selected with --task-id trust. The --bids-filter-file narrows fMRIPrep’s BOLD-file query to run-01, so the example processes only the run used later by FEAT.
A few practical notes:
the FreeSurfer license file should exist at
~/.licensethis command will likely take a couple of hours to run
if you are wondering whether it is still running, go back to the Terminal and type
topthe
antsRegistrationstep is especially slow, so long stretches of apparent inactivity are normalwe use
MNI152NLin6Asym:res-2so the preprocessed BOLD file lands on a 2 mm MNI grid that is easy to use alongside standard FSL templates and atlases
One important detail: the res-2 part controls the output grid of the resampled BOLD files. It does not change the resolution used for the underlying nonlinear normalization.
# Request a freesurfer license and store it in your homedirectory.
# This is just an example - please replace with your license id:
!echo "Steffen.Bollmann@cai.uq.edu.au" > ~/.license
!echo "21029" >> ~/.license
!echo "*Cqyn12sqTCxo" >> ~/.license
!echo "FSxgcvGkNR59Y" >> ~/.license
!ls -l ~/.license
-rw-rw-r-- 1 jovyan jovyan 65 Jul 21 07:13 /home/jovyan/.license
%%bash
set -e
EXAMPLE_DIR="$HOME/trust_example"
sub=104
BIDS_DIR="$EXAMPLE_DIR/bids/ds003745"
OUT_DIR="$EXAMPLE_DIR/derivatives/fmriprep"
WORK_DIR="$EXAMPLE_DIR/scratch/fmriprep_work"
BIDS_FILTER="$EXAMPLE_DIR/scratch/bids_filter_task-trust_run-01.json"
FS_LIC="$HOME/.license"
mkdir -p "$OUT_DIR" "$WORK_DIR"
cat > "$BIDS_FILTER" <<'JSON'
{
"bold": {
"datatype": "func",
"suffix": "bold",
"run": "01"
}
}
JSON
mkdir -p "$HOME/freesurfer-subjects-dir"
export SUBJECTS_DIR="$HOME/freesurfer-subjects-dir"
# This command will likely take a couple of hours to finish.
# If you want to confirm that it is still running, go back to the
# Terminal and type: top
# The antsRegistration process is especially slow and can run for
# a long time without printing much new output.
fmriprep \
"$BIDS_DIR" \
"$OUT_DIR" \
participant \
--participant-label "$sub" \
--task-id trust \
--bids-filter-file "$BIDS_FILTER" \
--stop-on-first-crash \
--fs-license-file "$FS_LIC" \
--fs-subjects-dir "$SUBJECTS_DIR" \
--fs-no-reconall \
--output-spaces MNI152NLin6Asym:res-2 \
-w "$WORK_DIR"
bids-validator@1.14.10
This dataset appears to be BIDS compatible.
Summary:
Available Tasks: Available Modalities:
292 Files, 429.42MB sharedreward MRI
50 - Subjects
trust
1 - Session ultimatu
m
If you have any questions, please post on https://neu
rostars.org/tags/bids.
260721-07:16:51,369 nipype.workflow IMPORTANT:
Running fMRIPrep version 25.2.5
License N
OTICE ##################################################
fMRIPrep 25.2.5
Copyright
The NiPreps Developers.
This product includes software developed by
the
NiPreps Community (https://nipreps.org/).
Portions of this software were develop
ed at the Department of
Psychology at Stanford University, Stanford, CA, US.
This software is also distributed as a Docker container image.
The bootstrapping file
for the image ("Dockerfile") is licensed
under the MIT License.
This sof
tware may be distributed through an add-on package called
"Docker Wrapper" that is under th
e BSD 3-clause License.
#################################################################
2
60721-07:16:51,369 nipype.workflow IMPORTANT:
Building fMRIPrep's workflow:
* BIDS data
set path: /home/jovyan/trust_example/bids/ds003745.
* Participants and sessions: sub-104.
* Run identifier: 20260721-071433_115926a0-b4a4-494c-9afb-69bcfb6e0e2b.
* Out
put spaces: MNI152NLin6Asym:res-2.
* Pre-run FreeSurfer's SUBJECTS_DIR: /home/jovyan/free
surfer-subjects-dir.
260721-07:17:19,648 nipype.workflow INFO:
ANAT Stage 1: Adding template workflow
260721-07:17:23,869 nipype.workflow INFO:
ANAT Stage 2: Preparing brain extraction workflow
260721-07:17:38,39 nipype.workflow INFO:
ANAT Stage 3: Preparing segmentation workflow
260721-07:17:38,43 nipype.workflow INFO:
ANAT Stage 4: Preparing normalization workflow for ['MNI1
52NLin6Asym', 'MNI152NLin2009cAsym']
260721-07:17:38,52 nipype.workflow INFO:
ANAT Skipping Stages 5+
260721-07:17:38,757 nipype.workflow INFO:
B0 field inhomogeneity map will be estimated with the fo
llowing 1 estimator(s): [<EstimatorType.PHASEDIFF: 3>].
260721-07:17:39,77 nipype.workflow INFO:
Setting up fieldmap "auto_00000" (EstimatorType.PHASEDIFF
) with <sub-104_phasediff.nii.gz, sub-104_magnitude1.nii.gz, sub-104_magnitude2.nii.gz>
260721-07:17:39,141 nipype.workflow INFO:
No single-band-reference found for sub-104_task-trust_ru
n-01_bold.nii.gz.
260721-07:17:39,346 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
260721-07:17:39,380 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
260721-07:17:39,434 nipype.workflow INFO:
Stage 3: Adding fieldmap reconstruction workflow
260721-07:17:39,435 nipype.workflow INFO:
Stage 3: Registering fieldmap to boldref
260721-07:17:39,504 nipype.workflow INFO:
Stage 4: Adding coregistration boldref workflow
260721-07:17:44,552 nipype.workflow INFO:
Stage 5: Adding coregistration workflow
260721-07:17:44,554 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, register
ing with T1w instead.
260721-07:17:44,566 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an of
fset of 0.972s.
260721-07:17:55,541 nipype.workflow INFO:
fMRIPrep workflow graph with 398 nodes built successfull
y.
260721-07:18:35,230 nipype.workflow IMPORTANT:
fMRIPrep started!
260721-07:18:42,702 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.full_wm" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_w
f/sub_104_wf/anat_fit_wf/brain_extraction_wf/full_wm".
260721-07:18:42,704 nipype.workflow INFO:
[Node] Executing "full_wm" <nipype.interfaces.utility.wr
appers.Function>
260721-07:18:42,779 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.out_merge_fmap_id" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_
104_wf/fmap_preproc_wf/out_merge_fmap_id".
260721-07:18:42,781 nipype.workflow INFO:
[Node] Executing "out_merge_fmap_id" <nipype.interfaces.
utility.base.Merge>
260721-07:18:42,786 nipype.workflow INFO:
[Node] Finished "out_merge_fmap_id", elapsed time 0.0001
9s.
260721-07:18:42,788 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.out_merge_method" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_1
04_wf/fmap_preproc_wf/out_merge_method".
260721-07:18:42,789 nipype.workflow INFO:
[Node] Executing "out_merge_method" <nipype.interfaces.u
tility.base.Merge>
260721-07:18:42,790 nipype.workflow INFO:
[Node] Finished "out_merge_method", elapsed time 0.00012
1s.
260721-07:18:42,925 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.lap_tmpl" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_
wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/lap_tmpl".
260721-07:18:42,926 nipype.workflow INFO:
[Node] Executing "lap_tmpl" <nipype.interfaces.ants.util
s.ImageMath>
260721-07:18:42,939 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.res_tmpl" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_
wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/res_tmpl".
260721-07:18:42,940 nipype.workflow INFO:
[Node] Executing "res_tmpl" <niworkflows.interfaces.niba
bel.RegridToZooms>
260721-07:18:43,109 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_native_wf.bold_source" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_native_wf/bold_source".
260721-07:18:43,111 nipype.workflow INFO:
[Node] Executing "bold_source" <nipype.interfaces.utilit
y.base.Select>
260721-07:18:43,115 nipype.workflow INFO:
[Node] Finished "bold_source", elapsed time 0.000231s.
260721-07:18:43,212 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.hmc_boldref_wf.validation_and_dummies_wf.val_bold" in "/home/jovyan/tru
st_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/h
mc_boldref_wf/validation_and_dummies_wf/val_bold".
260721-07:18:43,214 nipype.workflow INFO:
[Node] Executing "val_bold" <niworkflows.interfaces.head
er.ValidateImage>
260721-07:18:43,237 nipype.workflow INFO:
[Node] Finished "full_wm", elapsed time 0.529074s.
260721-07:18:43,261 nipype.workflow INFO:
[Node] Finished "val_bold", elapsed time 0.046367s.
260721-07:18:43,369 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.hmc_boldref_wf.validation_and_dummies_wf.get_dummy" in "/home/jovyan/tr
ust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/
hmc_boldref_wf/validation_and_dummies_wf/get_dummy".
260721-07:18:43,371 nipype.workflow INFO:
[Node] Executing "get_dummy" <niworkflows.interfaces.bol
d.NonsteadyStatesDetector>
260721-07:18:43,527 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.wf_auto_00000.check_register" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_2
5_2_wf/sub_104_wf/fmap_preproc_wf/wf_auto_00000/check_register".
260721-07:18:43,529 nipype.workflow INFO:
[Node] Executing "check_register" <sdcflows.interfaces.f
map.CheckRegister>
260721-07:18:43,547 nipype.workflow INFO:
[Node] Finished "check_register", elapsed time 0.016693s
.
260721-07:18:43,897 nipype.workflow INFO:
[Node] Finished "res_tmpl", elapsed time 0.952728s.
260721-07:18:44,19 nipype.workflow INFO:
[Node] Finished "get_dummy", elapsed time 0.643676s.
260721-07:18:44,849 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bidssrc"
in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bidssrc".
260721-07:18:44,851 nipype.workflow INFO:
[Node] Executing "bidssrc" <niworkflows.interfaces.bids.
BIDSDataGrabber>
260721-07:18:44,856 nipype.interface INFO:
No "pet" images found for sub-104
260721-07:18:44,856 n
ipype.interface INFO:
No "flair" images found for sub-104
260721-07:18:44,856 nipype.interface INFO:
No "sbref" images found for sub-104
260721-07:18:44,856
nipype.interface INFO:
No "asl" images found for sub-104
260721-07:18:44,856 nipype.interface INF
O:
No "dwi" images found for sub-104
260721-07:18:44,856 nipype.interface INFO:
No "roi" images
found for sub-104
260721-07:18:44,856 nipype.workflow INFO:
[Node] Finished "bidssrc", elapsed tim
e 0.000518s.
260721-07:18:44,879 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.register_template_wf.set_reference" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep
_25_2_wf/sub_104_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin6Asym/set_reference".
260721-07:18:44,880 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.register_template_wf.set_reference" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep
_25_2_wf/sub_104_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/set_reference".
260721-07:18:44,928 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.wf_auto_00000.magnitude_wf.magmrg" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmrip
rep_25_2_wf/sub_104_wf/fmap_preproc_wf/wf_auto_00000/magnitude_wf/magmrg".
260721-07:18:45,68 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task_
trust_run_01_wf.bold_native_wf.validate_bold" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_native_wf/validate_bold".
260721-07:18:45,70 nipype.workflow INFO:
[Node] Executing "validate_bold" <niworkflows.interfaces.
header.ValidateImage>
260721-07:18:45,125 nipype.workflow INFO:
[Node] Finished "validate_bold", elapsed time 0.048696s.
260721-07:18:45,206 nipype.workflow INFO:
[Node] Executing "magmrg" <niworkflows.interfaces.images
.IntraModalMerge>
260721-07:18:45,262 nipype.workflow INFO:
[Node] Finished "magmrg", elapsed time 0.054825s.
260721-07:18:45,393 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.ds_hmc_boldref_wf.sources" in "/home/jovyan/trust_example/scratch/fmrip
rep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/ds_hmc_boldref_wf/sources
".
260721-07:18:45,395 nipype.workflow INFO:
[Node] Executing "sources" <fmriprep.interfaces.bids.BID
SURI>
260721-07:18:45,400 nipype.workflow INFO:
[Node] Finished "sources", elapsed time 0.000389s.
260721-07:18:45,423 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.ds_hmc_wf.sources" in "/home/jovyan/trust_example/scratch/fmriprep_work
/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/ds_hmc_wf/sources".
260721-07:18:45,425 nipype.workflow INFO:
[Node] Executing "sources" <fmriprep.interfaces.bids.BID
SURI>
260721-07:18:45,431 nipype.workflow INFO:
[Node] Finished "sources", elapsed time 0.0004s.
260721-07:18:46,109 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.anat_template_wf.anat_ref_dimensions" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripr
ep_25_2_wf/sub_104_wf/anat_fit_wf/anat_template_wf/anat_ref_dimensions".
260721-07:18:46,293 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.hmc_boldref_wf.gen_avg" in "/home/jovyan/trust_example/scratch/fmriprep
_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/hmc_boldref_wf/gen_avg".
260721-07:18:46,316 nipype.workflow INFO:
[Node] Executing "gen_avg" <niworkflows.interfaces.image
s.RobustAverage>
260721-07:18:46,768 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.wf_auto_00000.magnitude_wf.brainextraction_wf.clipper_pre" in "/home/jovyan/trust_example/scr
atch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/wf_auto_00000/magnitude_wf/brainextra
ction_wf/clipper_pre".
260721-07:18:46,778 nipype.workflow INFO:
[Node] Executing "clipper_pre" <niworkflows.interfaces.n
ibabel.IntensityClip>
260721-07:18:46,983 nipype.workflow INFO:
[Node] Executing "set_reference" <nipype.interfaces.util
ity.wrappers.Function>
260721-07:18:46,984 nipype.workflow INFO:
[Node] Finished "set_reference", elapsed time 0.00039s.
260721-07:18:47,313 nipype.workflow INFO:
[Node] Executing "set_reference" <nipype.interfaces.util
ity.wrappers.Function>
260721-07:18:47,319 nipype.workflow INFO:
[Node] Finished "set_reference", elapsed time 0.000416s.
260721-07:18:47,555 nipype.interface INFO:
stderr 2026-07-21T07:18:47.555631:++ 3dvolreg: AFNI ver
sion=AFNI_25.2.09 (Aug 24 2025) [64-bit]
260721-07:18:47,555 nipype.interface INFO:
stderr 2026-07
-21T07:18:47.555631:++ Authored by: RW Cox
260721-07:18:47,557 nipype.interface INFO:
stderr 2026-07-21T07:18:47.557018:** AFNI converts NIFT
I_datatype=4 (INT16) in file /home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_1
04_wf/bold_task_trust_run_01_wf/bold_fit_wf/hmc_boldref_wf/gen_avg/sub-104_task-trust_run-01_bold_sl
iced.nii.gz to FLOAT32
260721-07:18:47,557 nipype.interface INFO:
stderr 2026-07-21T07:18:47.55701
8: Warnings of this type will be muted for this session.
260721-07:18:47,557 nipype.interface IN
FO:
stderr 2026-07-21T07:18:47.557018: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to
see none.
260721-07:18:47,558 nipype.interface INFO:
stderr 2026-07-21T07:18:47.558755:*+ WARNING:
If you are performing spatial transformations on an oblique dset,
260721-07:18:47,558 nipype.interf
ace INFO:
stderr 2026-07-21T07:18:47.558755: such as /home/jovyan/trust_example/scratch/fmriprep_
work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/hmc_boldref_wf/gen_avg/sub-10
4_task-trust_run-01_bold_sliced.nii.gz,
260721-07:18:47,558 nipype.interface INFO:
stderr 2026-07-
21T07:18:47.558755: or viewing/combining it with volumes of differing obliquity,
260721-07:18:47,55
8 nipype.interface INFO:
stderr 2026-07-21T07:18:47.558755: you should consider running:
260721-
07:18:47,558 nipype.interface INFO:
stderr 2026-07-21T07:18:47.558755: 3dWarp -deoblique
2607
21-07:18:47,558 nipype.interface INFO:
stderr 2026-07-21T07:18:47.558755: on this and other obli
que datasets in the same session.
260721-07:18:47,558 nipype.interface INFO:
stderr 2026-07-21T07:
18:47.558755: See 3dWarp -help for details.
260721-07:18:47,558 nipype.interface INFO:
stderr 2026
-07-21T07:18:47.558755:++ Oblique dataset:/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_
25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/hmc_boldref_wf/gen_avg/sub-104_task-trust_r
un-01_bold_sliced.nii.gz is 16.999994 degrees from plumb.
260721-07:18:47,559 nipype.interface INFO:
stderr 2026-07-21T07:18:47.559235:++ Coarse del was 10, replaced with 4
260721-07:18:47,667 nipype.interface INFO:
stderr 2026-07-21T07:18:47.667560:++ edt_blur: sigx 2,
dx 1, fwhm 4.70964, sfac 2.5, firx 5
260721-07:18:48,127 nipype.workflow INFO:
[Node] Executing "anat_ref_dimensions" <niworkflows.inte
rfaces.images.TemplateDimensions>
260721-07:18:48,204 nipype.workflow INFO:
[Node] Finished "anat_ref_dimensions", elapsed time 0.07
62s.
260721-07:18:48,415 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.source_an
atomical" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/source_an
atomical".
260721-07:18:48,418 nipype.workflow INFO:
[Node] Executing "source_anatomical" <fmriprep.interface
s.bids.BIDSSourceFile>
260721-07:18:48,419 nipype.workflow INFO:
[Node] Finished "source_anatomical", elapsed time 0.0001
22s.
260721-07:18:50,266 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.ds_t1w_mask_wf.raw_sources" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf
/sub_104_wf/anat_fit_wf/ds_t1w_mask_wf/raw_sources".
260721-07:18:50,277 nipype.workflow INFO:
[Node] Executing "raw_sources" <nipype.interfaces.utilit
y.wrappers.Function>
260721-07:18:50,278 nipype.workflow INFO:
[Node] Finished "raw_sources", elapsed time 0.000496s.
260721-07:18:50,305 nipype.workflow INFO:
[Node] Setting-up "_denoise0" in "/home/jovyan/trust_exa
mple/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/anat_template_wf/denoise/mapflow/
_denoise0".
260721-07:18:50,307 nipype.workflow INFO:
[Node] Executing "_denoise0" <nipype.interfaces.ants.seg
mentation.DenoiseImage>
260721-07:18:50,838 nipype.workflow INFO:
[Node] Finished "clipper_pre", elapsed time 4.054803s.
260721-07:18:51,761 nipype.workflow INFO:
[Node] Finished "lap_tmpl", elapsed time 8.456745s.
260721-07:18:52,72 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_w
f.brain_extraction_wf.mrg_tmpl" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_w
f/sub_104_wf/anat_fit_wf/brain_extraction_wf/mrg_tmpl".
260721-07:18:52,121 nipype.workflow INFO:
[Node] Executing "mrg_tmpl" <nipype.interfaces.utility.b
ase.Merge>
260721-07:18:52,122 nipype.workflow INFO:
[Node] Finished "mrg_tmpl", elapsed time 0.000213s.
260721-07:18:52,412 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bids_info
" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bids_info".
260721-07:18:52,422 nipype.workflow INFO:
[Node] Executing "bids_info" <niworkflows.interfaces.bid
s.BIDSInfo>
260721-07:18:52,429 nipype.workflow INFO:
[Node] Finished "bids_info", elapsed time 0.006954s.
260721-07:18:54,14 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task_
trust_run_01_wf.bold_native_wf.bold_stc_wf.slice_timing_correction" in "/home/jovyan/trust_example/s
cratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_native_wf/bold_stc_w
f/slice_timing_correction".
260721-07:18:54,33 nipype.workflow INFO:
[Node] Executing "slice_timing_correction" <fmriprep.work
flows.bold.stc.TShift>
260721-07:18:54,80 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.create_fs_
id" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/create_fs_id".
260721-07:18:54,82 nipype.workflow INFO:
[Node] Executing "create_fs_id" <fmriprep.interfaces.bids
.CreateFreeSurferID>
260721-07:18:54,83 nipype.workflow INFO:
[Node] Finished "create_fs_id", elapsed time 0.000129s.
260721-07:19:01,787 nipype.interface INFO:
stderr 2026-07-21T07:19:01.787043:++ Max displacement i
n automask = 0.32 (mm) at sub-brick 14
260721-07:19:01,787 nipype.interface INFO:
stderr 2026-07-21T07:19:01.787043:++ Max delta displ i
n automask = 0.26 (mm) at sub-brick 14
260721-07:19:02,919 nipype.workflow INFO:
[Node] Finished "gen_avg", elapsed time 16.602109s.
260721-07:19:04,236 nipype.interface WARNING:
Changing /home/jovyan/trust_example/derivatives/fmri
prep/sub-104/func/sub-104_task-trust_run-01_desc-hmc_boldref.nii.gz dtype from int16 to int16
260721-07:19:04,467 nipype.workflow INFO:
[Node] Finished "slice_timing_correction", elapsed time
10.433078s.
260721-07:19:06,208 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.fmapref_buffer" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/fmapref_buffer".
260721-07:19:06,213 nipype.workflow INFO:
[Node] Executing "fmapref_buffer" <nipype.interfaces.uti
lity.wrappers.Function>
260721-07:19:06,214 nipype.workflow INFO:
[Node] Finished "fmapref_buffer", elapsed time 0.001083s
.
260721-07:19:06,228 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_native_wf.bold_stc_wf.copy_xform" in "/home/jovyan/trust_example/scratch/fmrip
rep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_native_wf/bold_stc_wf/copy_xform
".
260721-07:19:06,546 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_hmc_wf.mcflirt" in "/home/jovyan/trust_example/scratch/fmriprep_wo
rk/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_hmc_wf/mcflirt".
260721-07:19:06,566 nipype.workflow INFO:
[Node] Executing "mcflirt" <nipype.interfaces.fsl.prepro
cess.MCFLIRT>
260721-07:19:11,283 nipype.workflow INFO:
[Node] Executing "copy_xform" <niworkflows.interfaces.he
ader.CopyXForm>
260721-07:19:13,342 nipype.workflow INFO:
[Node] Finished "copy_xform", elapsed time 2.058039s.
260721-07:19:14,936 nipype.workflow INFO:
[Node] Finished "_denoise0", elapsed time 24.458782s.
260721-07:19:16,81 nipype.workflow INFO:
[Node] Setting-up "_anat_conform0" in "/home/jovyan/trust
_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/anat_template_wf/anat_conform
/mapflow/_anat_conform0".
260721-07:19:16,82 nipype.workflow INFO:
[Node] Executing "_anat_conform0" <niworkflows.interfaces
.images.Conform>
260721-07:19:16,120 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.wf_auto_00000.magnitude_wf.brainextraction_wf.n4" in "/home/jovyan/trust_example/scratch/fmri
prep_work/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/wf_auto_00000/magnitude_wf/brainextraction_wf/
n4".
260721-07:19:16,123 nipype.workflow INFO:
[Node] Executing "n4" <nipype.interfaces.ants.segmentati
on.N4BiasFieldCorrection>
260721-07:19:16,127 nipype.workflow INFO:
[Node] Finished "_anat_conform0", elapsed time 0.043775s
.
260721-07:19:17,340 nipype.workflow INFO:
[Node] Finished "n4", elapsed time 1.044902s.
260721-07:19:18,88 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_w
f.anat_template_wf.get1st" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub
_104_wf/anat_fit_wf/anat_template_wf/get1st".
260721-07:19:18,90 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task_
trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/home/jovyan/trust_example/
scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhance_and_
skullstrip_bold_wf/init_aff".
260721-07:19:18,93 nipype.workflow INFO:
[Node] Executing "init_aff" <nipype.interfaces.ants.utils
.AI>
260721-07:19:18,99 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prepr
oc_wf.wf_auto_00000.magnitude_wf.brainextraction_wf.clipper_post" in "/home/jovyan/trust_example/scr
atch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/wf_auto_00000/magnitude_wf/brainextra
ction_wf/clipper_post".
260721-07:19:18,139 nipype.workflow INFO:
[Node] Executing "clipper_post" <niworkflows.interfaces.
nibabel.IntensityClip>
260721-07:19:18,397 nipype.workflow INFO:
[Node] Executing "get1st" <nipype.interfaces.utility.bas
e.Select>
260721-07:19:18,399 nipype.workflow INFO:
[Node] Finished "get1st", elapsed time 0.00024s.
260721-07:19:18,710 nipype.workflow INFO:
[Node] Finished "clipper_post", elapsed time 0.570075s.
260721-07:19:20,289 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.wf_auto_00000.magnitude_wf.brainextraction_wf.masker" in "/home/jovyan/trust_example/scratch/
fmriprep_work/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/wf_auto_00000/magnitude_wf/brainextraction
_wf/masker".
260721-07:19:20,300 nipype.workflow INFO:
[Node] Executing "masker" <sdcflows.interfaces.brainmask
.BrainExtraction>
260721-07:19:22,81 nipype.workflow INFO:
[Node] Setting-up "_truncate_images0" in "/home/jovyan/tr
ust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/trunca
te_images/mapflow/_truncate_images0".
260721-07:19:22,83 nipype.workflow INFO:
[Node] Executing "_truncate_images0" <nipype.interfaces.a
nts.utils.ImageMath>
260721-07:19:22,453 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.fmap_derivatives_wf_auto_00000.ds_reference" in "/home/jovyan/trust_example/scratch/fmriprep_
work/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/fmap_derivatives_wf_auto_00000/ds_reference".
260721-07:19:22,457 nipype.workflow INFO:
[Node] Executing "ds_reference" <sdcflows.workflows.outp
uts.DerivativesDataSink>
260721-07:19:22,539 nipype.workflow INFO:
[Node] Finished "ds_reference", elapsed time 0.081015s.
260721-07:19:24,94 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prepr
oc_wf.out_merge_fmap_ref" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_
104_wf/fmap_preproc_wf/out_merge_fmap_ref".
260721-07:19:24,112 nipype.workflow INFO:
[Node] Executing "out_merge_fmap_ref" <nipype.interfaces
.utility.base.Merge>
260721-07:19:24,113 nipype.workflow INFO:
[Node] Finished "out_merge_fmap_ref", elapsed time 0.000
195s.
260721-07:19:24,818 nipype.workflow INFO:
[Node] Finished "masker", elapsed time 4.517482s.
260721-07:19:25,116 nipype.workflow INFO:
[Node] Finished "_truncate_images0", elapsed time 2.7375
96s.
260721-07:19:26,239 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.wf_auto_00000.phdiff_wf.prelude" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripre
p_25_2_wf/sub_104_wf/fmap_preproc_wf/wf_auto_00000/phdiff_wf/prelude".
260721-07:19:26,263 nipype.workflow INFO:
[Node] Executing "prelude" <nipype.interfaces.fsl.prepro
cess.PRELUDE>
260721-07:19:26,648 nipype.workflow INFO:
[Node] Finished "prelude", elapsed time 0.383811s.
260721-07:19:28,364 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.fmap_derivatives_wf_auto_00000.ds_mask" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/fmap_derivatives_wf_auto_00000/ds_mask".
260721-07:19:28,373 nipype.workflow INFO:
[Node] Executing "ds_mask" <sdcflows.workflows.outputs.D
erivativesDataSink>
260721-07:19:28,405 nipype.workflow INFO:
[Node] Finished "ds_mask", elapsed time 0.031431s.
260721-07:19:28,691 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.wf_auto_00000.phdiff_wf.compfmap" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripr
ep_25_2_wf/sub_104_wf/fmap_preproc_wf/wf_auto_00000/phdiff_wf/compfmap".
260721-07:19:28,795 nipype.workflow INFO:
[Node] Executing "compfmap" <sdcflows.interfaces.fmap.Ph
asediff2Fieldmap>
260721-07:19:28,823 nipype.workflow INFO:
[Node] Finished "compfmap", elapsed time 0.026608s.
260721-07:19:30,94 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prepr
oc_wf.out_merge_fmap_mask" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub
_104_wf/fmap_preproc_wf/out_merge_fmap_mask".
260721-07:19:30,687 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.wf_auto_00000.bs_filter" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_w
f/sub_104_wf/fmap_preproc_wf/wf_auto_00000/bs_filter".
260721-07:19:30,768 nipype.workflow INFO:
[Node] Executing "bs_filter" <sdcflows.interfaces.bsplin
e.BSplineApprox>
260721-07:19:32,417 nipype.workflow INFO:
[Node] Executing "out_merge_fmap_mask" <nipype.interface
s.utility.base.Merge>
260721-07:19:32,418 nipype.workflow INFO:
[Node] Finished "out_merge_fmap_mask", elapsed time 0.00
0158s.
260721-07:19:33,94 nipype.interface INFO:
Approximating B-Splines grids (and 16x16x14 [knots]) on
a grid of 74x74x36 (197136) voxels, of which 50938 fall within the mask.
260721-07:19:36,738 nipype.workflow INFO:
[Node] Finished "mcflirt", elapsed time 30.172021s.
260721-07:19:41,687 nipype.workflow INFO:
[Node] Finished "init_aff", elapsed time 23.252005s.
260721-07:19:42,184 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_hmc_wf.fsl2itk" in "/home/jovyan/trust_example/scratch/fmriprep_wo
rk/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_hmc_wf/fsl2itk".
260721-07:19:42,304 nipype.workflow INFO:
[Node] Executing "fsl2itk" <niworkflows.interfaces.itk.M
CFLIRT2ITK>
260721-07:19:42,305 nipype.interface WARNING:
Multithreading is deprecated. Remove the num_threads
input.
260721-07:19:42,437 nipype.workflow INFO:
[Node] Finished "fsl2itk", elapsed time 0.131257s.
260721-07:19:43,896 nipype.workflow INFO:
[Node] Finished "bs_filter", elapsed time 13.126609s.
260721-07:19:44,140 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.norm" in "/home/jovyan/trust_example/scr
atch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhance_and_sku
llstrip_bold_wf/norm".
260721-07:19:44,145 nipype.workflow INFO:
[Node] Executing "norm" <niworkflows.interfaces.fixes.Fi
xHeaderRegistration>
260721-07:19:44,295 nipype.workflow INFO:
[Node] Setting-up "_inu_n40" in "/home/jovyan/trust_exam
ple/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/inu_n4/mapflow
/_inu_n40".
260721-07:19:44,299 nipype.workflow INFO:
[Node] Executing "_inu_n40" <nipype.interfaces.ants.segm
entation.N4BiasFieldCorrection>
260721-07:19:45,236 nipype.workflow INFO:
[Node] Finished "norm", elapsed time 0.762747s.
260721-07:19:46,110 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.motion_params" in "/home/jovyan/trust_example/scratch/fmriprep_wo
rk/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/motion_params".
260721-07:19:46,117 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.fmap_derivatives_wf_auto_00000.merge_fmap" in "/home/jovyan/trust_example/scratch/fmriprep_wo
rk/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/fmap_derivatives_wf_auto_00000/merge_fmap".
260721-07
:19:46,117 nipype.workflow INFO:
[Node] Executing "motion_params" <fmriprep.interfaces.confounds.F
SLMotionParams>
260721-07:19:46,122 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.fmap_derivatives_wf_auto_00000.gen_desc" in "/home/jovyan/trust_example/scratch/fmriprep_work
/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/fmap_derivatives_wf_auto_00000/gen_desc".
260721-07:19:46,125 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.rmsd" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripr
ep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/rmsd".
260721-07:19:46,131 nipype.workflow INFO:
[Node] Executing "rmsd" <fmriprep.interfaces.confounds.F
SLRMSDeviation>
260721-07:19:46,159 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/home/jovyan/trust_ex
ample/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhanc
e_and_skullstrip_bold_wf/map_brainmask".
260721-07:19:46,164 nipype.workflow INFO:
[Node] Executing "map_brainmask" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:19:46,284 nipype.workflow INFO:
[Node] Finished "rmsd", elapsed time 0.1507s.
260721-07:19:46,288 nipype.workflow INFO:
[Node] Finished "motion_params", elapsed time 0.17036s.
260721-07:19:46,437 nipype.workflow INFO:
[Node] Executing "merge_fmap" <niworkflows.interfaces.ni
babel.MergeSeries>
260721-07:19:46,477 nipype.workflow INFO:
[Node] Executing "gen_desc" <nipype.interfaces.utility.w
rappers.Function>
260721-07:19:46,478 nipype.workflow INFO:
[Node] Finished "gen_desc", elapsed time 0.000458s.
260721-07:19:46,488 nipype.workflow INFO:
[Node] Finished "merge_fmap", elapsed time 0.050378s.
260721-07:19:47,329 nipype.workflow INFO:
[Node] Finished "map_brainmask", elapsed time 0.867433s.
260721-07:19:48,307 nipype.workflow INFO:
[Node] Setting-up "_ds_coeff0" in "/home/jovyan/trust_ex
ample/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/fmap_derivatives_wf_auto_000
00/ds_coeff/mapflow/_ds_coeff0".
260721-07:19:48,310 nipype.workflow INFO:
[Node] Executing "_ds_coeff0" <sdcflows.workflows.output
s.DerivativesDataSink>
260721-07:19:48,342 nipype.workflow INFO:
[Node] Finished "_ds_coeff0", elapsed time 0.031114s.
260721-07:19:48,903 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.fmap_reports_wf_auto_00000.fmap_rpt" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmr
iprep_25_2_wf/sub_104_wf/fmap_preproc_wf/fmap_reports_wf_auto_00000/fmap_rpt".
260721-07:19:49,35 nipype.workflow INFO:
[Node] Executing "fmap_rpt" <sdcflows.interfaces.reportle
ts.FieldmapReportlet>
260721-07:19:50,108 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhance_a
nd_skullstrip_bold_wf/n4_correct".
260721-07:19:50,109 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.out_merge_fmap_coeff" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/s
ub_104_wf/fmap_preproc_wf/out_merge_fmap_coeff".
260721-07:19:50,111 nipype.workflow INFO:
[Node]
Executing "out_merge_fmap_coeff" <nipype.interfaces.utility.base.Merge>
260721-07:19:50,113 nipype.w
orkflow INFO:
[Node] Finished "out_merge_fmap_coeff", elapsed time 0.000503s.
260721-07:19:50,118 nipype.workflow INFO:
[Node] Executing "n4_correct" <niworkflows.interfaces.fi
xes.FixN4BiasFieldCorrection>
260721-07:19:51,359 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.fdisp" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmrip
rep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/fdisp".
260721-07:19:51,361 nipype.workflow INFO:
[Node] Executing "fdisp" <fmriprep.interfaces.confounds.
FramewiseDisplacement>
260721-07:19:51,371 nipype.workflow INFO:
[Node] Finished "fdisp", elapsed time 0.009359s.
260721-07:19:51,574 nipype.workflow INFO:
[Node] Finished "n4_correct", elapsed time 1.086296s.
260721-07:19:52,116 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/home/jovyan/
trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_w
f/enhance_and_skullstrip_bold_wf/skullstrip_first_pass".
260721-07:19:52,125 nipype.workflow INFO:
[Node] Executing "skullstrip_first_pass" <nipype.interfa
ces.fsl.preprocess.BET>
260721-07:19:52,284 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.fmap_derivatives_wf_auto_00000.ds_fieldmap" in "/home/jovyan/trust_example/scratch/fmriprep_w
ork/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/fmap_derivatives_wf_auto_00000/ds_fieldmap".
260721-07:19:52,289 nipype.workflow INFO:
[Node] Executing "ds_fieldmap" <sdcflows.workflows.outpu
ts.DerivativesDataSink>
260721-07:19:52,371 nipype.workflow INFO:
[Node] Finished "ds_fieldmap", elapsed time 0.080854s.
260721-07:19:53,944 nipype.workflow INFO:
[Node] Finished "skullstrip_first_pass", elapsed time 1.
818791s.
260721-07:19:54,100 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.out_merge_fmap" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104
_wf/fmap_preproc_wf/out_merge_fmap".
260721-07:19:54,116 nipype.workflow INFO:
[Node] Executing "out_merge_fmap" <nipype.interfaces.uti
lity.base.Merge>
260721-07:19:54,117 nipype.workflow INFO:
[Node] Finished "out_merge_fmap", elapsed time 0.000172s
.
260721-07:19:56,191 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.first_dilate" in "/home/jovyan/trust_exa
mple/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhance
_and_skullstrip_bold_wf/first_dilate".
260721-07:19:56,193 nipype.workflow INFO:
[Node] Executing "first_dilate" <niworkflows.interfaces.
nibabel.BinaryDilation>
260721-07:19:56,376 nipype.workflow INFO:
[Node] Finished "first_dilate", elapsed time 0.182303s.
260721-07:19:56,698 nipype.workflow INFO:
[Node] Finished "_inu_n40", elapsed time 12.127594s.
260721-07:19:56,723 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.fmapreg_wf.dilate_fmap_mask" in "/home/jovyan/trust_example/scratch/fmr
iprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/fmapreg_wf/dilate_fmap_
mask".
260721-07:19:56,737 nipype.workflow INFO:
[Node] Executing "dilate_fmap_mask" <sdcflows.interfaces
.brainmask.BinaryDilation>
260721-07:19:56,861 nipype.workflow INFO:
[Node] Finished "dilate_fmap_mask", elapsed time 0.12332
3s.
260721-07:19:58,125 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.res_target" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_
2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/res_target".
260721-07:19:58,126 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.first_mask" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhance_a
nd_skullstrip_bold_wf/first_mask".
260721-07:19:58,126 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.lap_target" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_
2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/lap_target".
260721-07:19:58,129 nipype.workflow INF
O:
[Node] Executing "res_target" <niworkflows.interfaces.nibabel.RegridToZooms>
260721-07:19:58,13
0 nipype.workflow INFO:
[Node] Executing "lap_target" <nipype.interfaces.ants.utils.ImageMath>
260721-07:19:58,145 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.ds_fmapreg_wf.sources" in "/home/jovyan/trust_example/scratch/fmriprep_
work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/ds_fmapreg_wf/sources".
260721-07:19:58,150 nipype.workflow INFO:
[Node] Executing "sources" <fmriprep.interfaces.bids.BID
SURI>
260721-07:19:58,153 nipype.workflow INFO:
[Node] Finished "sources", elapsed time 0.000527s.
260721-07:19:58,235 nipype.workflow INFO:
[Node] Executing "first_mask" <niworkflows.interfaces.ni
babel.ApplyMask>
260721-07:19:58,262 nipype.workflow INFO:
[Node] Finished "first_mask", elapsed time 0.025944s.
260721-07:19:58,741 nipype.workflow INFO:
[Node] Finished "res_target", elapsed time 0.611324s.
260721-07:20:00,103 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.init_aff" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_
wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/init_aff".
260721-07:20:00,109 nipype.workflow INFO:
[Node] Executing "init_aff" <nipype.interfaces.ants.util
s.AI>
260721-07:20:00,354 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.unifize" in "/home/jovyan/trust_example/
scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhance_and_
skullstrip_bold_wf/unifize".
260721-07:20:00,357 nipype.workflow INFO:
[Node] Executing "unifize" <nipype.interfaces.afni.utils
.Unifize>
260721-07:20:02,844 nipype.workflow INFO:
[Node] Finished "lap_target", elapsed time 4.713192s.
260721-07:20:03,702 nipype.workflow INFO:
[Node] Finished "fmap_rpt", elapsed time 14.665577s.
260721-07:20:04,123 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.mrg_target" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_
2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/mrg_target".
260721-07:20:04,124 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.fmap_prep
roc_wf.fmap_reports_wf_auto_00000.ds_fmap_report" in "/home/jovyan/trust_example/scratch/fmriprep_wo
rk/fmriprep_25_2_wf/sub_104_wf/fmap_preproc_wf/fmap_reports_wf_auto_00000/ds_fmap_report".
260721-07:20:04,127 nipype.workflow INFO:
[Node] Executing "mrg_target" <nipype.interfaces.utility
.base.Merge>
260721-07:20:04,128 nipype.workflow INFO:
[Node] Finished "mrg_target", elapsed time
0.000264s.
260721-07:20:04,133 nipype.workflow INFO:
[Node] Executing "ds_fmap_report" <sdcflows.workflows.ou
tputs.DerivativesDataSink>
260721-07:20:04,149 nipype.workflow INFO:
[Node] Finished "ds_fmap_report", elapsed time 0.015677s
.
260721-07:20:15,234 nipype.workflow INFO:
[Node] Finished "init_aff", elapsed time 15.123745s.
260721-07:20:16,169 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.norm" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/s
ub_104_wf/anat_fit_wf/brain_extraction_wf/norm".
260721-07:20:16,174 nipype.workflow INFO:
[Node] Executing "norm" <niworkflows.interfaces.fixes.Fi
xHeaderRegistration>
260721-07:21:35,17 nipype.workflow INFO:
[Node] Finished "unifize", elapsed time 94.659304s.
260721-07:21:36,279 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/home/jovyan/trust_e
xample/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhan
ce_and_skullstrip_bold_wf/fixhdr_unifize".
260721-07:21:36,333 nipype.workflow INFO:
[Node] Executing "fixhdr_unifize" <niworkflows.interface
s.header.CopyXForm>
260721-07:21:36,361 nipype.workflow INFO:
[Node] Finished "fixhdr_unifize", elapsed time 0.027157s
.
260721-07:21:38,315 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/home/jovyan
/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_
wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass".
260721-07:21:38,332 nipype.workflow INFO:
[Node] Executing "skullstrip_second_pass" <nipype.interf
aces.afni.preprocess.Automask>
260721-07:21:38,724 nipype.workflow INFO:
[Node] Finished "skullstrip_second_pass", elapsed time 0
.391381s.
260721-07:21:40,119 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/home/jovyan/tru
st_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/e
nhance_and_skullstrip_bold_wf/fixhdr_skullstrip2".
260721-07:21:40,191 nipype.workflow INFO:
[Node] Executing "fixhdr_skullstrip2" <niworkflows.inter
faces.header.CopyXForm>
260721-07:21:40,214 nipype.workflow INFO:
[Node] Finished "fixhdr_skullstrip2", elapsed time 0.021
94s.
260721-07:21:42,173 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/home/jovyan/trust_ex
ample/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhanc
e_and_skullstrip_bold_wf/combine_masks".
260721-07:21:42,176 nipype.workflow INFO:
[Node] Executing "combine_masks" <nipype.interfaces.fsl.
maths.BinaryMaths>
260721-07:21:42,370 nipype.workflow INFO:
[Node] Finished "combine_masks", elapsed time 0.189887s.
260721-07:21:44,225 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/enhance_a
nd_skullstrip_bold_wf/apply_mask".
260721-07:21:44,236 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.fmapreg_wf.dilate_target_mask" in "/home/jovyan/trust_example/scratch/f
mriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/fmapreg_wf/dilate_tar
get_mask".
260721-07:21:44,328 nipype.workflow INFO:
[Node] Executing "apply_mask" <niworkflows.interfaces.ni
babel.ApplyMask>
260721-07:21:44,347 nipype.workflow INFO:
[Node] Executing "dilate_target_mask" <sdcflows.interfac
es.brainmask.BinaryDilation>
260721-07:21:44,356 nipype.workflow INFO:
[Node] Finished "apply_mask", elapsed time 0.026815s.
260721-07:21:44,616 nipype.workflow INFO:
[Node] Finished "dilate_target_mask", elapsed time 0.267
433s.
260721-07:21:46,235 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.fmapreg_wf.coregister" in "/home/jovyan/trust_example/scratch/fmriprep_
work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/fmapreg_wf/coregister".
260721-07:21:46,252 nipype.workflow INFO:
[Node] Executing "coregister" <niworkflows.interfaces.fi
xes.FixHeaderRegistration>
260721-07:21:46,850 nipype.workflow INFO:
[Node] Finished "coregister", elapsed time 0.596616s.
260721-07:21:48,258 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.itk_mat2txt" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmrip
rep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/itk_mat2txt".
260721-07:21:48,260 nipype.workflow INFO:
[Node] Executing "itk_mat2txt" <niworkflows.interfaces.n
itransforms.ConcatenateXFMs>
260721-07:21:48,262 nipype.workflow INFO:
[Node] Finished "itk_mat2txt", elapsed time 0.001047s.
260721-07:21:52,299 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.boldref_fmap" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmri
prep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/boldref_fmap".
260721-07:21:52,312 nipype.workflow INFO:
[Node] Executing "boldref_fmap" <fmriprep.interfaces.res
ampling.ReconstructFieldmap>
260721-07:21:52,629 nipype.workflow INFO:
[Node] Finished "boldref_fmap", elapsed time 0.316433s.
260721-07:21:54,584 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.unwarp_boldref" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/unwarp_boldref".
260721-07:21:54,588 nipype.workflow INFO:
[Node] Executing "unwarp_boldref" <fmriprep.interfaces.r
esampling.ResampleSeries>
260721-07:21:54,776 nipype.workflow INFO:
[Node] Finished "unwarp_boldref", elapsed time 0.187847s
.
260721-07:21:56,236 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.ds_coreg_boldref_wf.sources" in "/home/jovyan/trust_example/scratch/fmr
iprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/ds_coreg_boldref_wf/sou
rces".
260721-07:21:56,241 nipype.workflow INFO:
[Node] Executing "sources" <fmriprep.interfaces.bids.BID
SURI>
260721-07:21:56,247 nipype.workflow INFO:
[Node] Finished "sources", elapsed time 0.004784s.
260721-07:22:00,127 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.ds_boldreg_wf.sources" in "/home/jovyan/trust_example/scratch/fmriprep_
work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/ds_boldreg_wf/sources".
260721-07:22:00,132 nipype.workflow INFO:
[Node] Executing "sources" <fmriprep.interfaces.bids.BID
SURI>
260721-07:22:00,133 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.ds_boldmask_wf.sources" in "/home/jovyan/trust_example/scratch/fmriprep
_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/ds_boldmask_wf/sources".
260721-07:22:00,135 nipype.workflow INFO:
[Node] Finished "sources", elapsed time 0.003337s.
26072
1-07:22:00,136 nipype.workflow INFO:
[Node] Executing "sources" <fmriprep.interfaces.bids.BIDSURI>
260721-07:22:00,138 nipype.workflow INFO:
[Node] Finished "sources", elapsed time 0.000623s.
260721-07:22:00,230 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/home/jovyan/trust_exampl
e/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/skullstrip
_bold_wf/skullstrip_first_pass".
260721-07:22:00,235 nipype.workflow INFO:
[Node] Executing "skullstrip_first_pass" <nipype.interfa
ces.fsl.preprocess.BET>
260721-07:22:00,336 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.fmapref_boldref" in "/home/jovyan/trust_example/scr
atch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_report
s_wf/fmapref_boldref".
260721-07:22:00,337 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.fmap_boldref" in "/home/jovyan/trust_example/scratc
h/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_reports_w
f/fmap_boldref".
260721-07:22:00,337 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub
_104_wf.bold_task_trust_run_01_wf.bold_std_wf.gen_ref" in "/home/jovyan/trust_example/scratch/fmripr
ep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_std_wf/_in_tuple_MNI152NLin6Asym.
res2/gen_ref".
260721-07:22:00,349 nipype.workflow INFO:
[Node] Executing "gen_ref" <niworkflows.interfaces.nibab
el.GenerateSamplingReference>
260721-07:22:00,349 nipype.workflow INFO:
[Node] Finished "gen_ref",
elapsed time 0.00016s.
260721-07:22:00,350 nipype.workflow INFO:
[Node] Executing "fmapref_boldre
f" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
260721-07:22:00,481 nipype.workflow INFO:
[Node] Executing "fmap_boldref" <niworkflows.interfaces.
fixes.FixHeaderApplyTransforms>
260721-07:22:00,729 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_native_wf.boldref_fmap" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_native_wf/boldref_fmap".
260721-07:22:00,741 nipype.workflow INFO:
[Node] Executing "boldref_fmap" <fmriprep.interfaces.res
ampling.ReconstructFieldmap>
260721-07:22:01,44 nipype.workflow INFO:
[Node] Finished "boldref_fmap", elapsed time 0.303156s.
260721-07:22:01,256 nipype.workflow INFO:
[Node] Finished "fmapref_boldref", elapsed time 0.906022
s.
260721-07:22:01,394 nipype.workflow INFO:
[Node] Finished "fmap_boldref", elapsed time 0.910303s.
260721-07:22:01,538 nipype.workflow INFO:
[Node] Finished "skullstrip_first_pass", elapsed time 1.
3019319999999999s.
260721-07:22:02,115 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/skullstri
p_bold_wf/skullstrip_second_pass".
260721-07:22:02,117 nipype.workflow INFO:
[Node] Executing "skullstrip_second_pass" <nipype.interf
aces.afni.preprocess.Automask>
260721-07:22:02,291 nipype.workflow INFO:
[Node] Finished "skullstrip_second_pass", elapsed time 0
.173252s.
260721-07:22:04,135 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_native_wf.boldref_bold" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_native_wf/boldref_bold".
260721-07:22:04,139 nipype.workflow INFO:
[Node] Executing "boldref_bold" <fmriprep.interfaces.res
ampling.ResampleSeries>
260721-07:22:13,760 nipype.workflow INFO:
[Node] Finished "boldref_bold", elapsed time 9.620454s.
260721-07:22:14,258 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.skullstrip_bold_wf.combine_masks" in "/home/jovyan/trust_example/scratc
h/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/skullstrip_bold_wf
/combine_masks".
260721-07:22:14,340 nipype.workflow INFO:
[Node] Executing "combine_masks" <nipype.interfaces.fsl.
maths.BinaryMaths>
260721-07:22:14,499 nipype.workflow INFO:
[Node] Finished "combine_masks", elapsed time 0.157628s.
260721-07:22:16,133 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.skullstrip_bold_wf.apply_mask" in "/home/jovyan/trust_example/scratch/f
mriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/skullstrip_bold_wf/ap
ply_mask".
260721-07:22:16,148 nipype.interface WARNING:
Changing /home/jovyan/trust_example/derivatives/fmri
prep/sub-104/func/sub-104_task-trust_run-01_desc-brain_mask.nii.gz dtype from float32 to float32
260721-07:22:16,202 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.skullstrip_bold_wf.mask_reportlet" in "/home/jovyan/trust_example/scrat
ch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/skullstrip_bold_w
f/mask_reportlet".
260721-07:22:16,204 nipype.workflow INFO:
[Node] Executing "mask_reportlet" <niworkflows.interface
s.reportlets.masks.SimpleShowMaskRPT>
260721-07:22:16,228 nipype.workflow INFO:
[Node] Executing "apply_mask" <niworkflows.interfaces.ni
babel.ApplyMask>
260721-07:22:16,262 nipype.workflow INFO:
[Node] Finished "apply_mask", elapsed time 0.032679s.
260721-07:22:18,165 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.tcompcor" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/tcompcor".
260721-07:22:18,170 nipype.workflow INFO:
[Node] Executing "tcompcor" <niworkflows.interfaces.patc
hes.RobustTCompCor>
260721-07:22:18,176 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.dvars" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmrip
rep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/dvars".
260721-07:22:18,190 nipype.workflow INFO:
[Node] Executing "dvars" <nipype.algorithms.confounds.Co
mputeDVARS>
260721-07:22:20,67 nipype.workflow INFO:
[Node] Finished "tcompcor", elapsed time 1.896685s.
260721-07:22:20,612 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.sdcreg_report" in "/home/jovyan/trust_example/scrat
ch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_reports_
wf/sdcreg_report".
260721-07:22:20,619 nipype.workflow INFO:
[Node] Executing "sdcreg_report" <sdcflows.interfaces.re
portlets.FieldmapReportlet>
260721-07:22:22,132 nipype.workflow INFO:
[Node] Finished "mask_reportlet", elapsed time 5.927017s
.
260721-07:22:25,502 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.tcc_metadata_filter" in "/home/jovyan/trust_example/scratch/fmrip
rep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/tcc_metadata_filter
".
260721-07:22:25,506 nipype.workflow INFO:
[Node] Executing "tcc_metadata_filter" <fmriprep.interfa
ces.confounds.FilterDropped>
260721-07:22:25,513 nipype.workflow INFO:
[Node] Finished "tcc_metadata_filter", elapsed time 0.00
6445s.
260721-07:22:26,152 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.tcc_metadata_fmt" in "/home/jovyan/trust_example/scratch/fmriprep
_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/tcc_metadata_fmt".
260721-07:22:29,16 nipype.workflow INFO:
[Node] Executing "tcc_metadata_fmt" <niworkflows.interfac
es.utility.TSV2JSON>
260721-07:22:29,21 nipype.workflow INFO:
[Node] Finished "tcc_metadata_fmt", elapsed time 0.004286
s.
260721-07:22:29,445 nipype.workflow INFO:
[Node] Finished "dvars", elapsed time 11.254611s.
260721-07:22:34,345 nipype.workflow INFO:
[Node] Finished "sdcreg_report", elapsed time 13.725759s
.
260721-07:22:36,238 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.ds_sdcreg_report" in "/home/jovyan/trust_example/sc
ratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_repor
ts_wf/ds_sdcreg_report".
260721-07:22:39,124 nipype.workflow INFO:
[Node] Executing "ds_sdcreg_report" <fmriprep.interfaces
.DerivativesDataSink>
260721-07:22:39,136 nipype.workflow INFO:
[Node] Finished "ds_sdcreg_report", elapsed time 0.01164
3s.
260721-07:25:43,45 nipype.workflow INFO:
[Node] Finished "norm", elapsed time 326.618947s.
260721-07:25:44,184 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.map_wmmask" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_
2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/map_wmmask".
260721-07:25:44,186 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.map_brainmask" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_
25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/map_brainmask".
260721-07:25:44,189 nipype.workflow INFO:
[Node] Executing "map_wmmask" <niworkflows.interfaces.fi
xes.FixHeaderApplyTransforms>
260721-07:25:44,191 nipype.workflow INFO:
[Node] Executing "map_brainmask" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:25:55,64 nipype.workflow INFO:
[Node] Finished "map_wmmask", elapsed time 10.874251s.
260721-07:25:55,82 nipype.workflow INFO:
[Node] Finished "map_brainmask", elapsed time 10.660307s.
260721-07:25:56,160 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.thr_brainmask" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_
25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/thr_brainmask".
260721-07:25:56,162 nipype.workflow INFO:
[Node] Executing "thr_brainmask" <nipype.interfaces.ants
.utils.ThresholdImage>
260721-07:25:57,140 nipype.workflow INFO:
[Node] Finished "thr_brainmask", elapsed time 0.977089s.
260721-07:25:58,172 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
260721-07:25:58,173 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.dil_brainmask" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/dil_brainmask".
260721-07:25:58,174 nipype.workflow INFO:
[Node] Executing "03_pad_mask" <nipype.interfaces.ants.u
tils.ImageMath>
260721-07:25:58,176 nipype.workflow INFO:
[Node] Executing "dil_brainmask" <nipype.interfaces.ants
.utils.ImageMath>
260721-07:25:58,654 nipype.workflow INFO:
[Node] Finished "03_pad_mask", elapsed time 0.479609s.
260721-07:25:58,983 nipype.workflow INFO:
[Node] Finished "dil_brainmask", elapsed time 0.80684s.
260721-07:26:00,167 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.get_brainmask" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/get_brainmask".
260721-07:26:00,170 nipype.workflow INFO:
[Node] Executing "get_brainmask" <nipype.interfaces.ants
.utils.ImageMath>
260721-07:26:01,167 nipype.workflow INFO:
[Node] Finished "get_brainmask", elapsed time 0.780073s.
260721-07:26:02,171 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.01_atropos" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/01_atropos".
260721-07:26:02,175 nipype.workflow INFO:
[Node] Executing "01_atropos" <nipype.interfaces.ants.se
gmentation.Atropos>
260721-07:26:20,582 nipype.workflow INFO:
[Node] Finished "01_atropos", elapsed time 18.406357s.
260721-07:26:22,152 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
260721-07:26:22,156 nipype.workflow INFO:
[Node] Executing "02_pad_segm" <nipype.interfaces.ants.u
tils.ImageMath>
260721-07:26:22,842 nipype.workflow INFO:
[Node] Finished "02_pad_segm", elapsed time 0.685341s.
260721-07:26:24,132 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
260721-07:26:24,134 nipype.workflow INFO:
[Node] Executing "04_sel_labels" <nipype.interfaces.util
ity.wrappers.Function>
260721-07:26:24,337 nipype.workflow INFO:
[Node] Finished "04_sel_labels", elapsed time 0.202005s.
260721-07:26:26,151 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/05_get_wm".
260721-07:26:26,151
nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_wf.brain_extraction
_wf.atropos_wf.06_get_gm" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_
104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/06_get_gm".
260721-07:26:26,151 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/home/jovyan/trust_example/scratch/fmriprep_work
/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
260721-07:26:
26,151 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_wf.brain_extr
action_wf.atropos_wf.10_me_csf" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_w
f/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/10_me_csf".
260721-07:26:26,154 nipype.workflow INFO:
[Node] Executing "06_get_gm" <nipype.interfaces.ants.uti
ls.ImageMath>
260721-07:26:26,154 nipype.workflow INFO:
[Node] Executing "10_me_csf" <nipype.inter
faces.ants.utils.ImageMath>
260721-07:26:26,154 nipype.workflow INFO:
[Node] Executing "27_depad_c
sf" <nipype.interfaces.ants.utils.ImageMath>
260721-07:26:26,154 nipype.workflow INFO:
[Node] Exec
uting "05_get_wm" <nipype.interfaces.ants.utils.ImageMath>
260721-07:26:26,648 nipype.workflow INFO:
[Node] Finished "27_depad_csf", elapsed time 0.493217s.
260721-07:26:27,179 nipype.workflow INFO:
[Node] Finished "06_get_gm", elapsed time 1.024554s.
260721-07:26:27,193 nipype.workflow INFO:
[Node] Finished "05_get_wm", elapsed time 1.037819s.
260721-07:26:28,167 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
260721-07:2
6:28,167 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_wf.brain_ex
traction_wf.atropos_wf.07_fill_gm" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_
2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
260721-07:26:28,169 nipype.w
orkflow INFO:
[Node] Executing "09_relabel_wm" <nipype.interfaces.ants.utils.MultiplyImages>
260721-07:26:28,169 nipype.workflow INFO:
[Node] Executing "07_fill_gm" <nipype.interfaces.ants.ut
ils.ImageMath>
260721-07:26:28,864 nipype.workflow INFO:
[Node] Finished "10_me_csf", elapsed time 2.709896s.
260721-07:26:28,900 nipype.workflow INFO:
[Node] Finished "09_relabel_wm", elapsed time 0.728986s.
260721-07:26:30,181 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
260721-07:26:30,181 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.apply_wm_prior" in "/home/jovyan/trust_example/scratch/fmriprep_wo
rk/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/apply_wm_prior".
260721-07:26:30,183 nipype.workflow INFO:
[Node] Executing "26_depad_wm" <nipype.interfaces.ants.u
tils.ImageMath>
260721-07:26:30,202 nipype.workflow INFO:
[Node] Executing "apply_wm_prior" <nipype.interfaces.uti
lity.wrappers.Function>
260721-07:26:30,616 nipype.workflow INFO:
[Node] Finished "apply_wm_prior", elapsed time 0.413417s
.
260721-07:26:30,728 nipype.workflow INFO:
[Node] Finished "26_depad_wm", elapsed time 0.544292s.
260721-07:26:32,175 nipype.workflow INFO:
[Node] Setting-up "_inu_n4_final0" in "/home/jovyan/trus
t_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_
wf/inu_n4_final/mapflow/_inu_n4_final0".
260721-07:26:32,176 nipype.workflow INFO:
[Node] Executing "_inu_n4_final0" <nipype.interfaces.ant
s.segmentation.N4BiasFieldCorrection>
260721-07:26:34,947 nipype.workflow INFO:
[Node] Finished "07_fill_gm", elapsed time 6.77742800000
00005s.
260721-07:26:36,185 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
260721-07:26:36,188 nipype.workflow INFO:
[Node] Executing "08_mult_gm" <nipype.interfaces.ants.ut
ils.MultiplyImages>
260721-07:26:36,858 nipype.workflow INFO:
[Node] Finished "08_mult_gm", elapsed time 0.669732s.
260721-07:26:38,144 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/11_add_gm".
260721-07:26:38,146 nipype.workflow INFO:
[Node] Executing "11_add_gm" <nipype.interfaces.ants.uti
ls.ImageMath>
260721-07:26:39,314 nipype.workflow INFO:
[Node] Finished "11_add_gm", elapsed time 1.166664s.
260721-07:26:40,183 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
260721-07:26:40,186 nipype.workflow INFO:
[Node] Executing "12_relabel_gm" <nipype.interfaces.ants
.utils.MultiplyImages>
260721-07:26:40,422 nipype.workflow INFO:
[Node] Finished "_inu_n4_final0", elapsed time 8.245132s
.
260721-07:26:40,859 nipype.workflow INFO:
[Node] Finished "12_relabel_gm", elapsed time 0.67195s.
260721-07:26:42,144 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
260721-07:26:42,144 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/home/jovyan/trust_example/scratch/fmriprep_work
/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
260721-07:26:42,148 nipype.workflow INFO:
[Node] Executing "25_depad_gm" <nipype.interfaces.ants.u
tils.ImageMath>
260721-07:26:42,148 nipype.workflow INFO:
[Node] Executing "13_add_gm_wm" <nipype.interfaces.ants.
utils.ImageMath>
260721-07:26:42,827 nipype.workflow INFO:
[Node] Finished "25_depad_gm", elapsed time 0.677684s.
260721-07:26:43,507 nipype.workflow INFO:
[Node] Finished "13_add_gm_wm", elapsed time 1.358413s.
260721-07:26:44,149 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/home/jovyan/trust_example/scratch/fmriprep_wo
rk/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
260721-07
:26:44,149 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_wf.brain_
extraction_wf.atropos_wf.24_depad_segm" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripre
p_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
260721-07:26:44,149
nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_wf.brain_extraction_
wf.atropos_wf.merge_tpms" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_
104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/merge_tpms".
260721-07:26:44,151 nipype.workflow I
NFO:
[Node] Executing "24_depad_segm" <nipype.interfaces.ants.utils.ImageMath>
260721-07:26:44,151
nipype.workflow INFO:
[Node] Executing "14_sel_labels2" <nipype.interfaces.utility.wrappers.Funct
ion>
260721-07:26:44,152 nipype.workflow INFO:
[Node] Executing "merge_tpms" <nipype.interfaces.utility
.base.Merge>
260721-07:26:44,153 nipype.workflow INFO:
[Node] Finished "merge_tpms", elapsed time
0.000166s.
260721-07:26:44,260 nipype.workflow INFO:
[Node] Finished "14_sel_labels2", elapsed time 0.108182s
.
260721-07:26:44,705 nipype.workflow INFO:
[Node] Finished "24_depad_segm", elapsed time 0.552914s.
260721-07:26:46,152 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.15_add_7" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmr
iprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/15_add_7".
260721-07:26:46,156 nipype.workflow INFO:
[Node] Executing "15_add_7" <nipype.interfaces.ants.util
s.ImageMath>
260721-07:26:47,70 nipype.workflow INFO:
[Node] Finished "15_add_7", elapsed time 0.913296s.
260721-07:26:48,151 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.16_me_7" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmri
prep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/16_me_7".
260721-07:26:48,155 nipype.workflow INFO:
[Node] Executing "16_me_7" <nipype.interfaces.ants.utils
.ImageMath>
260721-07:26:49,694 nipype.workflow INFO:
[Node] Finished "16_me_7", elapsed time 1.538152s.
260721-07:26:50,154 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/17_comp_7".
260721-07:26:50,157
nipype.workflow INFO:
[Node] Executing "17_comp_7" <nipype.interfaces.ants.utils.ImageMath>
260721-07:26:51,127 nipype.workflow INFO:
[Node] Finished "17_comp_7", elapsed time 0.970122s.
260721-07:26:52,147 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.18_md_7" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmri
prep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/18_md_7".
260721-07:26:52,149 nipype.workflow INFO:
[Node] Executing "18_md_7" <nipype.interfaces.ants.utils
.ImageMath>
260721-07:26:53,238 nipype.workflow INFO:
[Node] Finished "18_md_7", elapsed time 1.087486s.
260721-07:26:54,135 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/19_fill_7".
260721-07:26:54,138
nipype.workflow INFO:
[Node] Executing "19_fill_7" <nipype.interfaces.ants.utils.ImageMath>
260721-07:27:00,403 nipype.workflow INFO:
[Node] Finished "19_fill_7", elapsed time 6.264847s.
260721-07:27:02,139 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
260721-07:27:02,143 nipype.workflow INFO:
[Node] Executing "20_add_7_2" <nipype.interfaces.ants.ut
ils.ImageMath>
260721-07:27:03,162 nipype.workflow INFO:
[Node] Finished "20_add_7_2", elapsed time 1.018917s.
260721-07:27:04,267 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
260721-07:27:04,269 nipype.workflow INFO:
[Node] Executing "21_md_7_2" <nipype.interfaces.ants.uti
ls.ImageMath>
260721-07:27:05,329 nipype.workflow INFO:
[Node] Finished "21_md_7_2", elapsed time 1.05928s.
260721-07:27:06,146 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
260721-07:27:06,149 nipype.workflow INFO:
[Node] Executing "22_me_7_2" <nipype.interfaces.ants.uti
ls.ImageMath>
260721-07:27:07,826 nipype.workflow INFO:
[Node] Finished "22_me_7_2", elapsed time 1.675892000000
0002s.
260721-07:27:08,141 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
260721-07:27:08,144 nipype.workflow INFO:
[Node] Executing "23_depad_mask" <nipype.interfaces.ants
.utils.ImageMath>
260721-07:27:08,665 nipype.workflow INFO:
[Node] Finished "23_depad_mask", elapsed time 0.52066s.
260721-07:27:10,162 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.brain_extraction_wf.atropos_wf.msk_conform" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf/msk_conform".
260721-07:27:10,167 nipype.workflow INFO:
[Node] Executing "msk_conform" <nipype.interfaces.utilit
y.wrappers.Function>
260721-07:27:10,324 nipype.workflow INFO:
[Node] Finished "msk_conform", elapsed time 0.156324s.
260721-07:27:15,473 nipype.workflow INFO:
[Node] Setting-up "_apply_mask0" in "/home/jovyan/trust_
example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/brain_extraction_wf/atropos_wf
/apply_mask/mapflow/_apply_mask0".
260721-07:27:15,475 nipype.workflow INFO:
[Node] Executing "_apply_mask0" <niworkflows.interfaces.
nibabel.ApplyMask>
260721-07:27:15,906 nipype.workflow INFO:
[Node] Finished "_apply_mask0", elapsed time 0.430401s.
260721-07:27:17,956 nipype.interface WARNING:
Changing /home/jovyan/trust_example/derivatives/fmri
prep/sub-104/anat/sub-104_desc-brain_mask.nii.gz dtype from int16 to int16
260721-07:27:18,531 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.register_template_wf.trunc_mov" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_
2_wf/sub_104_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin6Asym/trunc_mov".
260721-07:27:18,550 nipype.workflow INFO:
[Node] Executing "trunc_mov" <nipype.interfaces.ants.uti
ls.ImageMath>
260721-07:27:18,687 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.register_template_wf.trunc_mov" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_
2_wf/sub_104_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/trunc_mov".
260721-07:27:18,690 nipype.workflow INFO:
[Node] Executing "trunc_mov" <nipype.interfaces.ants.uti
ls.ImageMath>
260721-07:27:18,691 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.ds_std_vo
lumes_wf.gen_ref" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/d
s_std_volumes_wf/_in_tuple_MNI152NLin6Asym.res2/gen_ref".
260721-07:27:18,697 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.fast" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/anat_fit_w
f/fast".
260721-07:27:18,703 nipype.workflow INFO:
[Node] Executing "gen_ref" <niworkflows.interfaces.nibab
el.GenerateSamplingReference>
260721-07:27:18,704 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_anat_wf.gen_ref" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep
_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_anat_wf/gen_ref".
260721-07:27:18,704 nipype.work
flow INFO:
[Node] Finished "gen_ref", elapsed time 0.000138s.
260721-07:27:18,705 nipype.workflow
INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.ds_std_volumes_wf.mask_anat" in "/home/jovyan
/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/ds_std_volumes_wf/mask_anat".
26072
1-07:27:18,705 nipype.workflow INFO:
[Node] Executing "fast" <smriprep.interfaces.fsl.FAST>
260721-07:27:18,710 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_reg_wf.fsl_bbr_wf.mask_t1w_brain" in "/home/jovyan/trust_example/s
cratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_reg_wf/f
sl_bbr_wf/mask_t1w_brain".
260721-07:27:18,712 nipype.workflow INFO:
[Node] Executing "gen_ref" <niworkflows.interfaces.nibab
el.GenerateSamplingReference>
260721-07:27:18,712 nipype.workflow INFO:
[Node] Executing "mask_ana
t" <niworkflows.interfaces.nibabel.ApplyMask>
260721-07:27:18,715 nipype.workflow INFO:
[Node] Executing "mask_t1w_brain" <niworkflows.interface
s.nibabel.ApplyMask>
260721-07:27:19,145 nipype.workflow INFO:
[Node] Finished "mask_anat", elapsed time 0.432666s.
260721-07:27:19,153 nipype.workflow INFO:
[Node] Finished "mask_t1w_brain", elapsed time 0.43821s.
260721-07:27:19,167 nipype.workflow INFO:
[Node] Finished "gen_ref", elapsed time 0.453922s.
260721-07:27:20,802 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_reg_wf.fsl_bbr_wf.mri_coreg" in "/home/jovyan/trust_example/scratc
h/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_reg_wf/fsl_bb
r_wf/mri_coreg".
260721-07:27:20,806 nipype.workflow INFO:
[Node] Executing "mri_coreg" <nipype.interfaces.freesurf
er.registration.MRICoreg>
260721-07:27:21,131 nipype.workflow INFO:
[Node] Finished "trunc_mov", elapsed time 2.579466s.
260721-07:27:21,298 nipype.workflow INFO:
[Node] Finished "trunc_mov", elapsed time 2.607136s.
260721-07:27:34,959 nipype.workflow INFO:
[Node] Finished "mri_coreg", elapsed time 14.151798s.
260721-07:27:36,682 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_reg_wf.fsl_bbr_wf.lta_to_fsl" in "/home/jovyan/trust_example/scrat
ch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_reg_wf/fsl_b
br_wf/lta_to_fsl".
260721-07:27:36,685 nipype.workflow INFO:
[Node] Executing "lta_to_fsl" <niworkflows.interfaces.fr
eesurfer.PatchedLTAConvert>
260721-07:27:36,689 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.register_template_wf.registration" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_
25_2_wf/sub_104_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin6Asym/registration".
260721-07:27:36,693 nipype.workflow INFO:
[Node] Executing "registration" <niworkflows.interfaces.
norm.SpatialNormalization>
260721-07:27:37,68 nipype.workflow INFO:
[Node] Finished "lta_to_fsl", elapsed time 0.38225s.
260721-07:28:26,266 nipype.workflow INFO:
[Node] Finished "fast", elapsed time 67.559866s.
260721-07:28:26,702 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.register_template_wf.registration" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_
25_2_wf/sub_104_wf/anat_fit_wf/register_template_wf/_template_MNI152NLin2009cAsym/registration".
260721-07:28:26,714 nipype.workflow INFO:
[Node] Executing "registration" <niworkflows.interfaces.
norm.SpatialNormalization>
260721-07:43:09,414 nipype.workflow INFO:
[Node] Finished "registration", elapsed time 932.720129s
.
260721-07:43:11,261 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.lut_t1w_dseg" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/an
at_fit_wf/lut_t1w_dseg".
260721-07:43:11,399 nipype.workflow INFO:
[Node] Executing "lut_t1w_dseg" <nipype.interfaces.utili
ty.wrappers.Function>
260721-07:43:11,535 nipype.workflow INFO:
[Node] Finished "lut_t1w_dseg", elapsed time 0.134893s.
260721-07:43:18,520 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_reg_wf.fsl_bbr_wf.wm_mask" in "/home/jovyan/trust_example/scratch/
fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_reg_wf/fsl_bbr_
wf/wm_mask".
260721-07:43:18,520 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.t1w_wm" in "/home/jovyan/trust_example/scratch/fmri
prep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_reports_wf/t1w_
wm".
260721-07:43:18,523 nipype.workflow INFO:
[Node] Executing "wm_mask" <nipype.interfaces.utili
ty.wrappers.Function>
260721-07:43:18,524 nipype.workflow INFO:
[Node] Executing "t1w_wm" <nipype.interfaces.utility.wra
ppers.Function>
260721-07:43:18,529 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.acc_masks" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acc_masks".
260721-07:43:18,611 nipype.workflow INFO:
[Node] Finished "wm_mask", elapsed time 0.087956s.
260721-07:43:18,612 nipype.workflow INFO:
[Node] Finished "t1w_wm", elapsed time 0.087741s.
260721-07:43:18,637 nipype.workflow INFO:
[Node] Executing "acc_masks" <fmriprep.interfaces.confou
nds.aCompCorMasks>
260721-07:43:20,139 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.anat_reports_wf.seg_rpt" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/su
b_104_wf/anat_fit_wf/anat_reports_wf/seg_rpt".
260721-07:43:20,143 nipype.workflow INFO:
[Node] Executing "seg_rpt" <niworkflows.interfaces.repor
tlets.masks.ROIsPlot>
260721-07:43:20,295 nipype.workflow INFO:
[Node] Finished "acc_masks", elapsed time 1.657560999999
9998s.
260721-07:43:20,597 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr" in "/home/jovyan/trust_example/scratch/
fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_reg_wf/fsl_bbr_
wf/flt_bbr".
260721-07:43:22,274 nipype.workflow INFO:
[Node] Executing "flt_bbr" <nipype.interfaces.fsl.prepro
cess.FLIRT>
260721-07:43:29,600 nipype.workflow INFO:
[Node] Finished "seg_rpt", elapsed time 9.456745s.
260721-07:44:11,210 nipype.workflow INFO:
[Node] Finished "flt_bbr", elapsed time 48.934526s.
260721-07:44:16,625 nipype.workflow INFO:
[Node] Setting-up "_fsl_to_lta1" in "/home/jovyan/trust_
example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold
_reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta1".
260721-07:44:16,628 nipype.workflow INFO:
[Node] Executing "_fsl_to_lta1" <niworkflows.interfaces.
freesurfer.PatchedLTAConvert>
260721-07:44:16,770 nipype.workflow INFO:
[Node] Finished "_fsl_to_lta1", elapsed time 0.141957s.
260721-07:44:17,53 nipype.workflow INFO:
[Node] Setting-up "_fsl_to_lta0" in "/home/jovyan/trust_e
xample/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_
reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta0".
260721-07:44:17,55 nipype.workflow INFO:
[Node] Executing "_fsl_to_lta0" <niworkflows.interfaces.f
reesurfer.PatchedLTAConvert>
260721-07:44:17,156 nipype.workflow INFO:
[Node] Finished "_fsl_to_lta0", elapsed time 0.099657s.
260721-07:44:18,502 nipype.workflow INFO:
[Node] Setting-up "_fsl_to_lta0" in "/home/jovyan/trust_
example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold
_reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta0".
260721-07:44:18,504 nipype.workflow INFO:
[Node] Cached "_fsl_to_lta0" - collecting precomputed ou
tputs
260721-07:44:18,504 nipype.workflow INFO:
[Node] "_fsl_to_lta0" found cached.
260721-07:44:1
8,505 nipype.workflow INFO:
[Node] Setting-up "_fsl_to_lta1" in "/home/jovyan/trust_example/scratc
h/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_reg_wf/fsl_bb
r_wf/fsl_to_lta/mapflow/_fsl_to_lta1".
260721-07:44:18,506 nipype.workflow INFO:
[Node] Cached "_f
sl_to_lta1" - collecting precomputed outputs
260721-07:44:18,506 nipype.workflow INFO:
[Node] "_fs
l_to_lta1" found cached.
260721-07:44:20,496 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_reg_
wf/fsl_bbr_wf/compare_transforms".
260721-07:44:22,241 nipype.workflow INFO:
[Node] Executing "compare_transforms" <nipype.interfaces
.utility.wrappers.Function>
260721-07:44:22,287 nipype.workflow INFO:
[Node] Finished "compare_transforms", elapsed time 0.043
972s.
260721-07:44:24,512 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.bold_reg_wf.fsl_bbr_wf.xfm2itk" in "/home/jovyan/trust_example/scratch/
fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/bold_reg_wf/fsl_bbr_
wf/xfm2itk".
260721-07:44:24,519 nipype.workflow INFO:
[Node] Executing "xfm2itk" <fmriprep.interfaces.nitransf
orms.ConvertAffine>
260721-07:44:24,643 nipype.workflow INFO:
[Node] Finished "xfm2itk", elapsed time 0.122995s.
260721-07:44:28,489 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.t1w_boldref" in "/home/jovyan/trust_example/scratch
/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_reports_wf
/t1w_boldref".
260721-07:44:28,489 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_1
04_wf.bold_task_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.boldref_wm" in "/home/jovyan/trust_e
xample/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_
fit_reports_wf/boldref_wm".
260721-07:44:28,493 nipype.workflow INFO:
[Node] Executing "t1w_boldref" <niworkflows.interfaces.f
ixes.FixHeaderApplyTransforms>
260721-07:44:28,493 nipype.workflow INFO:
[Node] Executing "boldref
_wm" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
260721-07:44:28,648 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.t1w_mask_tfm" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/t1w_mask_tfm".
260721-07:44:28,654 nipype.workflow INFO:
[Node] Executing "t1w_mask_tfm" <niworkflows.interfaces.
fixes.FixHeaderApplyTransforms>
260721-07:44:28,772 nipype.workflow INFO:
[Node] Finished "boldref_wm", elapsed time 0.278064s.
260721-07:44:29,379 nipype.workflow INFO:
[Node] Finished "t1w_boldref", elapsed time 0.885125s.
260721-07:44:29,730 nipype.workflow INFO:
[Node] Finished "t1w_mask_tfm", elapsed time 1.075191s.
260721-07:44:30,540 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.sdc_report" in "/home/jovyan/trust_example/scratch/
fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_reports_wf/
sdc_report".
260721-07:44:30,547 nipype.workflow INFO:
[Node] Executing "sdc_report" <nireports.interfaces.repo
rting.base.SimpleBeforeAfterRPT>
260721-07:44:30,547 nipype.interface INFO:
Report - setting before (/home/jovyan/trust_example/der
ivatives/fmriprep/sub-104/func/sub-104_task-trust_run-01_desc-coreg_boldref.nii.gz) and after (/home
/jovyan/trust_example/derivatives/fmriprep/sub-104/func/sub-104_task-trust_run-01_desc-hmc_boldref.n
ii.gz) images
260721-07:44:30,547 nipype.interface INFO:
Generating visual report
260721-07:44:30,954 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.epi_t1_report" in "/home/jovyan/trust_example/scrat
ch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_reports_
wf/epi_t1_report".
260721-07:44:30,957 nipype.workflow INFO:
[Node] Executing "epi_t1_report" <nireports.interfaces.r
eporting.base.SimpleBeforeAfterRPT>
260721-07:44:30,957 nipype.interface INFO:
Report - setting be
fore (/home/jovyan/trust_example/derivatives/fmriprep/sub-104/func/sub-104_task-trust_run-01_desc-co
reg_boldref.nii.gz) and after (/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub
_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_reports_wf/t1w_boldref/sub-104_desc-preproc_T
1w_trans.nii.gz) images
260721-07:44:30,957 nipype.interface INFO:
Generating visual report
260721-07:44:30,977 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.union_mask" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/union_mask".
260721-07:44:30,980 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_tfm0" in "/home/jovyan/trust
_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_
wf/acc_msk_tfm/mapflow/_acc_msk_tfm0".
260721-07:44:30,980 nipype.workflow INFO:
[Node] Executing
"union_mask" <nipype.interfaces.utility.wrappers.Function>
260721-07:44:30,981 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_tfm1" in "/home/jovyan/trust
_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_
wf/acc_msk_tfm/mapflow/_acc_msk_tfm1".
260721-07:44:30,982 nipype.workflow INFO:
[Node] Executing "_acc_msk_tfm0" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:44:30,983 nipype.workflow INFO:
[Node] Executing "_acc_msk_tfm1" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:44:30,983 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_tfm2" in "/home/jovyan/trust
_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_
wf/acc_msk_tfm/mapflow/_acc_msk_tfm2".
260721-07:44:30,988 nipype.workflow INFO:
[Node] Executing "_acc_msk_tfm2" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:44:31,5 nipype.workflow INFO:
[Node] Finished "union_mask", elapsed time 0.025286s.
260721-07:44:31,479 nipype.workflow INFO:
[Node] Finished "_acc_msk_tfm1", elapsed time 0.49615s.
260721-07:44:31,488 nipype.workflow INFO:
[Node] Finished "_acc_msk_tfm2", elapsed time 0.499487s.
260721-07:44:31,522 nipype.workflow INFO:
[Node] Finished "_acc_msk_tfm0", elapsed time 0.539923s.
260721-07:44:32,508 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_tfm0" in "/home/jovyan/trust
_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_
wf/acc_msk_tfm/mapflow/_acc_msk_tfm0".
260721-07:44:32,509 nipype.workflow INFO:
[Node] Cached "_acc_msk_tfm0" - collecting precomputed o
utputs
260721-07:44:32,509 nipype.workflow INFO:
[Node] "_acc_msk_tfm0" found cached.
260721-07:44
:32,510 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_tfm1" in "/home/jovyan/trust_example/scr
atch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acc_msk_t
fm/mapflow/_acc_msk_tfm1".
260721-07:44:32,511 nipype.workflow INFO:
[Node] Cached "_acc_msk_tfm1"
- collecting precomputed outputs
260721-07:44:32,511 nipype.workflow INFO:
[Node] "_acc_msk_tfm1"
found cached.
260721-07:44:32,512 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_tfm2" in "/ho
me/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/
bold_confounds_wf/acc_msk_tfm/mapflow/_acc_msk_tfm2".
260721-07:44:32,512 nipype.workflow INFO:
[N
ode] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task_trust_run_01_wf.bold_confounds_wf.dilated_mas
k" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_
run_01_wf/bold_confounds_wf/dilated_mask".
260721-07:44:32,512 nipype.workflow INFO:
[Node] Cached
"_acc_msk_tfm2" - collecting precomputed outputs
260721-07:44:32,512 nipype.workflow INFO:
[Node]
"_acc_msk_tfm2" found cached.
260721-07:44:32,514 nipype.workflow INFO:
[Node] Executing "dilated_mask" <niworkflows.interfaces.
morphology.BinaryDilation>
260721-07:44:32,557 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_anat_wf.fmap_recon" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmrip
rep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_anat_wf/fmap_recon".
260721-07:44:32,573 nipype.workflow INFO:
[Node] Executing "fmap_recon" <fmriprep.interfaces.resam
pling.ReconstructFieldmap>
260721-07:44:32,595 nipype.workflow INFO:
[Node] Finished "dilated_mask", elapsed time 0.080707s.
260721-07:44:32,837 nipype.workflow INFO:
[Node] Finished "fmap_recon", elapsed time 0.264136s.
260721-07:44:34,511 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.subtract_mask" in "/home/jovyan/trust_example/scratch/fmriprep_wo
rk/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/subtract_mask".
260721-07:44:34,514 nipype.workflow INFO:
[Node] Executing "subtract_mask" <niworkflows.interfaces
.morphology.BinarySubtraction>
260721-07:44:34,521 nipype.workflow INFO:
[Node] Finished "subtract_mask", elapsed time 0.007323s.
260721-07:44:36,510 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_brain0" in "/home/jovyan/tru
st_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confound
s_wf/acc_msk_brain/mapflow/_acc_msk_brain0".
260721-07:44:36,512 nipype.workflow INFO:
[Node] Executing "_acc_msk_brain0" <niworkflows.interfac
es.nibabel.ApplyMask>
260721-07:44:36,512 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_brain1
" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_r
un_01_wf/bold_confounds_wf/acc_msk_brain/mapflow/_acc_msk_brain1".
260721-07:44:36,513 nipype.workfl
ow INFO:
[Node] Setting-up "_acc_msk_brain2" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acc_msk_brain/mapflow/_acc_m
sk_brain2".
260721-07:44:36,514 nipype.workflow INFO:
[Node] Executing "_acc_msk_brain1" <niworkfl
ows.interfaces.nibabel.ApplyMask>
260721-07:44:36,515 nipype.workflow INFO:
[Node] Executing "_acc
_msk_brain2" <niworkflows.interfaces.nibabel.ApplyMask>
260721-07:44:36,522 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.crowncompcor" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/crowncompcor".
260721-07:4
4:36,527 nipype.workflow INFO:
[Node] Executing "crowncompcor" <niworkflows.interfaces.patches.Rob
ustACompCor>
260721-07:44:36,538 nipype.workflow INFO:
[Node] Finished "_acc_msk_brain0", elapsed time 0.025367
s.
260721-07:44:36,541 nipype.workflow INFO:
[Node] Finished "_acc_msk_brain2", elapsed time 0.025447
s.
260721-07:44:36,545 nipype.workflow INFO:
[Node] Finished "_acc_msk_brain1", elapsed time 0.030209
s.
260721-07:44:38,531 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_brain0" in "/home/jovyan/tru
st_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confound
s_wf/acc_msk_brain/mapflow/_acc_msk_brain0".
260721-07:44:38,531 nipype.workflow INFO:
[Node] Cached "_acc_msk_brain0" - collecting precomputed
outputs
260721-07:44:38,532 nipype.workflow INFO:
[Node] "_acc_msk_brain0" found cached.
260721-0
7:44:38,532 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_brain1" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acc
_msk_brain/mapflow/_acc_msk_brain1".
260721-07:44:38,533 nipype.workflow INFO:
[Node] Cached "_acc_msk_brain1" - collecting precomputed
outputs
260721-07:44:38,533 nipype.workflow INFO:
[Node] Finished "crowncompcor", elapsed time 2.
005369s.
260721-07:44:38,533 nipype.workflow INFO:
[Node] "_acc_msk_brain1" found cached.
260721-0
7:44:38,533 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_brain2" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acc
_msk_brain/mapflow/_acc_msk_brain2".
260721-07:44:38,534 nipype.workflow INFO:
[Node] Cached "_acc
_msk_brain2" - collecting precomputed outputs
260721-07:44:38,534 nipype.workflow INFO:
[Node] "_a
cc_msk_brain2" found cached.
260721-07:44:38,575 nipype.workflow INFO:
[Node] Finished "sdc_report", elapsed time 8.02799s.
260721-07:44:38,995 nipype.workflow INFO:
[Node] Finished "epi_t1_report", elapsed time 8.037469s.
260721-07:44:40,508 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.ds_sdc_report" in "/home/jovyan/trust_example/scrat
ch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_reports_
wf/ds_sdc_report".
260721-07:44:40,515 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.crowncc_metadata_fmt" in "/home/jovyan/trust_example/scratch/fmri
prep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/crowncc_metadata_f
mt".
260721-07:44:40,515 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_fit_wf.func_fit_reports_wf.ds_epi_t1_report" in "/home/jovyan/trust_example/sc
ratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_fit_wf/func_fit_repor
ts_wf/ds_epi_t1_report".
260721-07:44:40,545 nipype.workflow INFO:
[Node] Executing "crowncc_metadata_fmt" <niworkflows.int
erfaces.utility.TSV2JSON>
260721-07:44:40,556 nipype.workflow INFO:
[Node] Finished "crowncc_metadata_fmt", elapsed time 0.0
11001s.
260721-07:44:42,30 nipype.workflow INFO:
[Node] Executing "ds_epi_t1_report" <fmriprep.interfaces.
DerivativesDataSink>
260721-07:44:42,42 nipype.workflow INFO:
[Node] Finished "ds_epi_t1_report", elapsed time 0.011186
s.
260721-07:44:42,533 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_bin0" in "/home/jovyan/trust
_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_
wf/acc_msk_bin/mapflow/_acc_msk_bin0".
260721-07:44:42,533 nipype.workflow INFO:
[Node] Setting-up
"_acc_msk_bin1" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bo
ld_task_trust_run_01_wf/bold_confounds_wf/acc_msk_bin/mapflow/_acc_msk_bin1".
260721-07:44:42,533 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_bin2" in "/home/jovyan/trust
_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_
wf/acc_msk_bin/mapflow/_acc_msk_bin2".
260721-07:44:42,534 nipype.workflow INFO:
[Node] Executing
"_acc_msk_bin1" <niworkflows.interfaces.nibabel.Binarize>
260721-07:44:42,534 nipype.workflow INFO:
[Node] Executing "_acc_msk_bin2" <niworkflows.interfaces.nibabel.Binarize>
260721-07:44:42,535 nip
ype.workflow INFO:
[Node] Executing "_acc_msk_bin0" <niworkflows.interfaces.nibabel.Binarize>
260721-07:44:42,547 nipype.workflow INFO:
[Node] Finished "_acc_msk_bin2", elapsed time 0.012234s.
260721-07:44:42,547 nipype.workflow INFO:
[Node] Finished "_acc_msk_bin1", elapsed time 0.012531s
.
260721-07:44:42,564 nipype.workflow INFO:
[Node] Finished "_acc_msk_bin0", elapsed time 0.028341s.
260721-07:44:43,319 nipype.workflow INFO:
[Node] Executing "ds_sdc_report" <fmriprep.interfaces.De
rivativesDataSink>
260721-07:44:43,331 nipype.workflow INFO:
[Node] Finished "ds_sdc_report", elapsed time 0.011273s.
260721-07:44:44,535 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_bin0" in "/home/jovyan/trust
_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_
wf/acc_msk_bin/mapflow/_acc_msk_bin0".
260721-07:44:44,535 nipype.workflow INFO:
[Node] Cached "_acc_msk_bin0" - collecting precomputed o
utputs
260721-07:44:44,536 nipype.workflow INFO:
[Node] "_acc_msk_bin0" found cached.
260721-07:44
:44,536 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_bin1" in "/home/jovyan/trust_example/scr
atch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acc_msk_b
in/mapflow/_acc_msk_bin1".
260721-07:44:44,537 nipype.workflow INFO:
[Node] Cached "_acc_msk_bin1"
- collecting precomputed outputs
260721-07:44:44,537 nipype.workflow INFO:
[Node] "_acc_msk_bin1"
found cached.
260721-07:44:44,537 nipype.workflow INFO:
[Node] Setting-up "_acc_msk_bin2" in "/ho
me/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/
bold_confounds_wf/acc_msk_bin/mapflow/_acc_msk_bin2".
260721-07:44:44,538 nipype.workflow INFO:
[Node] Cached "_acc_msk_bin2" - collecting precomputed o
utputs
260721-07:44:44,538 nipype.workflow INFO:
[Node] "_acc_msk_bin2" found cached.
260721-07:44:46,527 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_anat_wf.resample" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripre
p_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_anat_wf/resample".
260721-07:44:46,535 nipype.workflow INFO:
[Node] Executing "resample" <fmriprep.interfaces.resampl
ing.ResampleSeries>
260721-07:44:53,593 nipype.workflow INFO:
[Node] Finished "resample", elapsed time 7.057699s.
260721-07:44:54,502 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.acompcor" in "/home/jovyan/trust_example/scratch/fmriprep_work/fm
riprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acompcor".
260721-07:44:54,506 nipype.workflow INFO:
[Node] Executing "acompcor" <niworkflows.interfaces.patc
hes.RobustACompCor>
260721-07:44:56,259 nipype.workflow INFO:
[Node] Finished "acompcor", elapsed time 1.7524790000000
001s.
260721-07:44:56,501 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.rename_acompcor" in "/home/jovyan/trust_example/scratch/fmriprep_
work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/rename_acompcor".
260721-07:44:56,506 nipype.workflow INFO:
[Node] Executing "rename_acompcor" <fmriprep.interfaces.
confounds.RenameACompCor>
260721-07:44:56,509 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.signals" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmr
iprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/signals".
260721-07:44:56,514 nipype.workflow INFO:
[Node] Executing "signals" <niworkflows.interfaces.image
s.SignalExtraction>
260721-07:44:56,561 nipype.workflow INFO:
[Node] Finished "rename_acompcor", elapsed time 0.054573
s.
260721-07:44:57,261 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.rois_plot" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/rois_plot".
260721-07:44:57,266 nipype.workflow INFO:
[Node] Executing "rois_plot" <niworkflows.interfaces.rep
ortlets.masks.ROIsPlot>
260721-07:44:57,544 nipype.workflow INFO:
[Node] Finished "signals", elapsed time 1.030051s.
260721-07:44:58,502 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.acc_metadata_filter" in "/home/jovyan/trust_example/scratch/fmrip
rep_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acc_metadata_filter
".
260721-07:44:58,508 nipype.workflow INFO:
[Node] Executing "acc_metadata_filter" <fmriprep.interfa
ces.confounds.FilterDropped>
260721-07:44:58,515 nipype.workflow INFO:
[Node] Finished "acc_metadata_filter", elapsed time 0.00
4789s.
260721-07:44:58,764 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.compcor_plot" in "/home/jovyan/trust_example/scratch/fmriprep_wor
k/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/compcor_plot".
260721-07:44:58,767 nipype.workflow INFO:
[Node] Executing "compcor_plot" <nireports.interfaces.nu
isance.CompCorVariancePlot>
260721-07:44:59,36 nipype.workflow INFO:
[Node] Finished "compcor_plot", elapsed time 0.269043s.
260721-07:45:00,502 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.conf_corr_plot" in "/home/jovyan/trust_example/scratch/fmriprep_w
ork/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/conf_corr_plot".
260721-07:45:00,510 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.model_expansion" in "/home/jovyan/trust_example/scratch/fmriprep_
work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/model_expansion".
260721-07:45:00,513 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.acc_metadata_fmt" in "/home/jovyan/trust_example/scratch/fmriprep
_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/acc_metadata_fmt".
260721-07:45:00,518 nipype.workflow INFO:
[Node] Executing "conf_corr_plot" <nireports.interfaces.
nuisance.ConfoundsCorrelationPlot>
260721-07:45:01,98 nipype.workflow INFO:
[Node] Executing "model_expansion" <niworkflows.interface
s.confounds.ExpandModel>
260721-07:45:01,212 nipype.workflow INFO:
[Node] Finished "model_expansion", elapsed time 0.113323
s.
260721-07:45:01,326 nipype.workflow INFO:
[Node] Finished "conf_corr_plot", elapsed time 0.807698s
.
260721-07:45:01,650 nipype.workflow INFO:
[Node] Executing "acc_metadata_fmt" <niworkflows.interfa
ces.utility.TSV2JSON>
260721-07:45:01,657 nipype.workflow INFO:
[Node] Finished "acc_metadata_fmt", elapsed time 0.00528
6s.
260721-07:45:02,749 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_confounds_wf.spike_regressors" in "/home/jovyan/trust_example/scratch/fmriprep
_work/fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_confounds_wf/spike_regressors".
260721-07:45:02,751 nipype.workflow INFO:
[Node] Executing "spike_regressors" <niworkflows.interfa
ces.confounds.SpikeRegressors>
260721-07:45:02,833 nipype.workflow INFO:
[Node] Finished "spike_regressors", elapsed time 0.08113
s.
260721-07:45:04,537 nipype.workflow INFO:
[Node] Finished "rois_plot", elapsed time 7.270752s.
260721-07:47:27,254 nipype.workflow INFO:
[Node] Finished "registration", elapsed time 1140.539125
s.
260721-07:47:28,520 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.register_template_wf.outputnode" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25
_2_wf/sub_104_wf/anat_fit_wf/register_template_wf/outputnode".
260721-07:47:28,529 nipype.workflow INFO:
[Node] Executing "outputnode" <nipype.interfaces.utility
.base.IdentityInterface>
260721-07:47:28,530 nipype.workflow INFO:
[Node] Finished "outputnode", elapsed time 0.000219s.
260721-07:47:30,577 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.template_buffer" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf
/anat_fit_wf/template_buffer".
260721-07:47:30,579 nipype.workflow INFO:
[Node] Executing "template_buffer" <nipype.interfaces.ut
ility.base.Merge>
260721-07:47:30,580 nipype.workflow INFO:
[Node] Finished "template_buffer", elapsed time 0.000168
s.
260721-07:47:36,522 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.anat2std_buffer" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf
/anat_fit_wf/anat2std_buffer".
260721-07:47:36,523 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.std2anat_buffer" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf
/anat_fit_wf/std2anat_buffer".
260721-07:47:36,525 nipype.workflow INFO:
[Node] Executing "anat2std_buffer" <nipype.interfaces.ut
ility.base.Merge>
260721-07:47:36,525 nipype.workflow INFO:
[Node] Executing "std2anat_buffer" <nipype.interfaces.ut
ility.base.Merge>
260721-07:47:36,526 nipype.workflow INFO:
[Node] Finished "anat2std_buffer", elapsed time 0.000191
s.
260721-07:47:36,526 nipype.workflow INFO:
[Node] Finished "std2anat_buffer", elapsed time 0.000
153s.
260721-07:47:40,517 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.ds_std_vo
lumes_wf.anat2std_mask" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_10
4_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6Asym.res2/anat2std_mask".
260721-07:47:40,517 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.ds_std_vo
lumes_wf.anat2std_dseg" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_10
4_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6Asym.res2/anat2std_dseg".
260721-07:47:40,521 nipype.workflow INFO:
[Node] Executing "anat2std_mask" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:47:40,522 nipype.workflow INFO:
[Node] Executing "anat2std_dseg" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:47:40,525 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.anat_reports_wf.t1w_std" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/su
b_104_wf/anat_fit_wf/anat_reports_wf/_in_tuple_MNI152NLin6Asym.res2/t1w_std".
260721-07:47:40,526 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.ds_std_vo
lumes_wf.anat2std_t1w" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104
_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6Asym.res2/anat2std_t1w".
260721-07:47:40,526 nipype.workf
low INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_wf.anat_reports_wf.mask_std" in
"/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/anat_fit_wf/anat_repor
ts_wf/_in_tuple_MNI152NLin6Asym.res2/mask_std".
260721-07:47:40,527 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.carpetplot_wf.mrg_xfms" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripr
ep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/carpetplot_wf/mrg_xfms".
260721-07:47:40,528 nipype.
workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task_trust_run_01_wf.ds_bold_st
d_wf.boldref2target" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_w
f/bold_task_trust_run_01_wf/ds_bold_std_wf/_in_tuple_MNI152NLin6Asym.res2/boldref2target".
260721-07
:47:40,530 nipype.workflow INFO:
[Node] Executing "anat2std_t1w" <niworkflows.interfaces.fixes.Fix
HeaderApplyTransforms>
260721-07:47:40,533 nipype.workflow INFO:
[Node] Executing "boldref2target" <nipype.interfaces.uti
lity.base.Merge>
260721-07:47:40,534 nipype.workflow INFO:
[Node] Finished "boldref2target", elaps
ed time 0.000159s.
260721-07:47:40,534 nipype.workflow INFO:
[Node] Executing "t1w_std" <niworkflo
ws.interfaces.fixes.FixHeaderApplyTransforms>
260721-07:47:40,539 nipype.workflow INFO:
[Node] Executing "mask_std" <niworkflows.interfaces.fixe
s.FixHeaderApplyTransforms>
260721-07:47:40,546 nipype.workflow INFO:
[Node] Executing "mrg_xfms" <nipype.interfaces.utility.b
ase.Merge>
260721-07:47:40,546 nipype.workflow INFO:
[Node] Finished "mrg_xfms", elapsed time 0.000154s.
260721-07:47:40,710 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.ds_bold_std_wf.sources" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripr
ep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/ds_bold_std_wf/_in_tuple_MNI152NLin6Asym.res2/source
s".
260721-07:47:40,727 nipype.workflow INFO:
[Node] Executing "sources" <fmriprep.interfaces.bids.BID
SURI>
260721-07:47:40,730 nipype.workflow INFO:
[Node] Finished "sources", elapsed time 0.001172s.
260721-07:47:42,517 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.carpetplot_wf.resample_parc" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/carpetplot_wf/resample_parc".
260721-07:47:42,519 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.ds_bold_std_wf.resample_ref" in "/home/jovyan/trust_example/scratch/fmriprep_work/f
mriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/ds_bold_std_wf/_in_tuple_MNI152NLin6Asym.res2/r
esample_ref".
260721-07:47:42,520 nipype.workflow INFO:
[Node] Executing "resample_parc" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:47:42,521 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.ds_bold_std_wf.resample_mask" in "/home/jovyan/trust_example/scratch/fmriprep_work/
fmriprep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/ds_bold_std_wf/_in_tuple_MNI152NLin6Asym.res2/
resample_mask".
260721-07:47:42,522 nipype.workflow INFO:
[Node] Executing "resample_ref" <niworkflows.interfaces.
fixes.FixHeaderApplyTransforms>
260721-07:47:42,524 nipype.workflow INFO:
[Node] Executing "resample_mask" <niworkflows.interfaces
.fixes.FixHeaderApplyTransforms>
260721-07:47:42,977 nipype.workflow INFO:
[Node] Setting-up "_anat2std_tpms0" in "/home/jovyan/tru
st_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6
Asym.res2/anat2std_tpms/mapflow/_anat2std_tpms0".
260721-07:47:42,979 nipype.workflow INFO:
[Node] Setting-up "_anat2std_tpms1" in "/home/jovyan/tru
st_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6
Asym.res2/anat2std_tpms/mapflow/_anat2std_tpms1".
260721-07:47:42,979 nipype.workflow INFO:
[Node]
Executing "_anat2std_tpms0" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
260721-07:47:42
,980 nipype.workflow INFO:
[Node] Setting-up "_anat2std_tpms2" in "/home/jovyan/trust_example/scra
tch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6Asym.res2/anat2
std_tpms/mapflow/_anat2std_tpms2".
260721-07:47:42,981 nipype.workflow INFO:
[Node] Executing "_anat2std_tpms2" <niworkflows.interfac
es.fixes.FixHeaderApplyTransforms>
260721-07:47:42,982 nipype.workflow INFO:
[Node] Executing "_an
at2std_tpms1" <niworkflows.interfaces.fixes.FixHeaderApplyTransforms>
260721-07:47:43,945 nipype.workflow INFO:
[Node] Finished "anat2std_t1w", elapsed time 3.414753s.
260721-07:47:44,236 nipype.workflow INFO:
[Node] Finished "t1w_std", elapsed time 3.701899s.
260721-07:47:44,515 nipype.workflow INFO:
[Node] Finished "resample_parc", elapsed time 1.994337s.
260721-07:47:44,897 nipype.workflow INFO:
[Node] Finished "_anat2std_tpms2", elapsed time 1.914708
s.
260721-07:47:44,901 nipype.workflow INFO:
[Node] Finished "_anat2std_tpms1", elapsed time 1.917827
s.
260721-07:47:44,909 nipype.workflow INFO:
[Node] Finished "_anat2std_tpms0", elapsed time 1.92912s
.
260721-07:47:44,917 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_std_wf.fmap_recon" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripr
ep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_std_wf/_in_tuple_MNI152NLin6Asym.res2/fmap_reco
n".
260721-07:47:44,921 nipype.workflow INFO:
[Node] Executing "fmap_recon" <fmriprep.interfaces.resam
pling.ReconstructFieldmap>
260721-07:47:45,674 nipype.workflow INFO:
[Node] Finished "mask_std", elapsed time 5.134054s.
260721-07:47:45,750 nipype.workflow INFO:
[Node] Finished "resample_ref", elapsed time 3.227482s.
260721-07:47:45,965 nipype.workflow INFO:
[Node] Finished "anat2std_mask", elapsed time 5.443881s.
260721-07:47:46,452 nipype.workflow INFO:
[Node] Finished "anat2std_dseg", elapsed time 5.930026s.
260721-07:47:46,545 nipype.workflow INFO:
[Node] Setting-up "_anat2std_tpms0" in "/home/jovyan/tru
st_example/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6
Asym.res2/anat2std_tpms/mapflow/_anat2std_tpms0".
260721-07:47:46,546 nipype.workflow INFO:
[Node] Cached "_anat2std_tpms0" - collecting precomputed
outputs
260721-07:47:46,546 nipype.workflow INFO:
[Node] "_anat2std_tpms0" found cached.
260721-0
7:47:46,547 nipype.workflow INFO:
[Node] Setting-up "_anat2std_tpms1" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6Asym.res
2/anat2std_tpms/mapflow/_anat2std_tpms1".
260721-07:47:46,547 nipype.workflow INFO:
[Node] Cached "_anat2std_tpms1" - collecting precomputed
outputs
260721-07:47:46,548 nipype.workflow INFO:
[Node] "_anat2std_tpms1" found cached.
260721-0
7:47:46,548 nipype.workflow INFO:
[Node] Setting-up "_anat2std_tpms2" in "/home/jovyan/trust_examp
le/scratch/fmriprep_work/fmriprep_25_2_wf/sub_104_wf/ds_std_volumes_wf/_in_tuple_MNI152NLin6Asym.res
2/anat2std_tpms/mapflow/_anat2std_tpms2".
260721-07:47:46,549 nipype.workflow INFO:
[Node] Cached "_anat2std_tpms2" - collecting precomputed
outputs
260721-07:47:46,549 nipype.workflow INFO:
[Node] "_anat2std_tpms2" found cached.
260721-07:47:46,559 nipype.interface WARNING:
Changing /home/jovyan/trust_example/derivatives/fmri
prep/sub-104/anat/sub-104_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz dtype from float64 to f
loat64
260721-07:47:46,644 nipype.workflow INFO:
[Node] Finished "fmap_recon", elapsed time 1.72244399999
99999s.
260721-07:47:46,799 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.anat_reports_wf.norm_msk" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/s
ub_104_wf/anat_fit_wf/anat_reports_wf/_in_tuple_MNI152NLin6Asym.res2/norm_msk".
260721-07:47:46,804 nipype.workflow INFO:
[Node] Executing "norm_msk" <nipype.interfaces.utility.w
rappers.Function>
260721-07:47:46,900 nipype.workflow INFO:
[Node] Finished "resample_mask", elapsed time 4.375187s.
260721-07:47:46,998 nipype.workflow INFO:
[Node] Finished "norm_msk", elapsed time 0.192468s.
260721-07:47:47,204 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.carpetplot_wf.parcels" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripre
p_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/carpetplot_wf/parcels".
260721-07:47:47,207 nipype.workflow INFO:
[Node] Executing "parcels" <nipype.interfaces.utility.wr
appers.Function>
260721-07:47:47,226 nipype.workflow INFO:
[Node] Finished "parcels", elapsed time 0.018419s.
260721-07:47:48,549 nipype.interface WARNING:
Changing /home/jovyan/trust_example/derivatives/fmri
prep/sub-104/anat/sub-104_space-MNI152NLin6Asym_res-2_dseg.nii.gz dtype from float64 to float64
260721-07:47:49,741 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.anat_fit_
wf.anat_reports_wf.norm_rpt" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep_25_2_wf/s
ub_104_wf/anat_fit_wf/anat_reports_wf/_in_tuple_MNI152NLin6Asym.res2/norm_rpt".
260721-07:47:49,745 nipype.workflow INFO:
[Node] Executing "norm_rpt" <niworkflows.interfaces.repo
rtlets.registration.SimpleBeforeAfterRPT>
260721-07:47:49,761 nipype.interface WARNING:
Changing /home/jovyan/trust_example/derivatives/fmri
prep/sub-104/func/sub-104_task-trust_run-01_space-MNI152NLin6Asym_res-2_desc-brain_mask.nii.gz dtype
from float64 to float64
260721-07:47:49,995 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.bold_std_wf.resample" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmriprep
_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/bold_std_wf/_in_tuple_MNI152NLin6Asym.res2/resample".
260721-07:47:49,995 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.carpetplot_wf.conf_plot" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmrip
rep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/carpetplot_wf/conf_plot".
260721-07:47:49,999 nipype.workflow INFO:
[Node] Executing "resample" <fmriprep.interfaces.resampl
ing.ResampleSeries>
260721-07:47:50,4 nipype.workflow INFO:
[Node] Executing "conf_plot" <fmriprep.interfaces.confound
s.FMRISummary>
260721-07:47:52,154 nipype.workflow INFO:
[Node] Finished "conf_plot", elapsed time 2.148517s.
260721-07:47:57,496 nipype.workflow INFO:
[Node] Finished "norm_rpt", elapsed time 7.750288s.
260721-07:48:30,867 nipype.workflow INFO:
[Node] Finished "resample", elapsed time 40.867387s.
260721-07:48:32,574 nipype.workflow INFO:
[Node] Setting-up "fmriprep_25_2_wf.sub_104_wf.bold_task
_trust_run_01_wf.ds_bold_std_wf.ds_bold" in "/home/jovyan/trust_example/scratch/fmriprep_work/fmripr
ep_25_2_wf/sub_104_wf/bold_task_trust_run_01_wf/ds_bold_std_wf/_in_tuple_MNI152NLin6Asym.res2/ds_bol
d".
260721-07:48:32,585 nipype.workflow INFO:
[Node] Executing "ds_bold" <fmriprep.interfaces.Derivati
vesDataSink>
260721-07:49:04,832 nipype.workflow INFO:
[Node] Finished "ds_bold", elapsed time 32.246415s.
260721-07:49:08,461 nipype.workflow IMPORTANT:
fMRIPrep finished successfully!
260721-07:49:08,466 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should i
nclude the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
(node:2381) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...`
to show where the warning was created)
Matplotlib is building the font cache; this may take a moment.
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_T1w
.nii.gz
0%| | 0.00/11.0M [00:00<?, ?B/s]
0%| | 17.4k/11.0M [00:00<02:07, 86.5kB/s]
0%| | 54.3k/11.0M [00:00<01:16, 144kB/s]
1%|▏ | 141k/11.0M [00:00<00:39, 276kB/s]
3%|▎ | 298k/11.0M [00:00<00:22, 475kB/s]
6%|▌ | 629k/11.0M [00:01<00:11, 896kB/s]
12%|█▏ | 1.31M/11.0M [00:01<00:05, 1.74MB/s]
24%|██▍ | 2.63M/11.0M [00:01<00:02, 3.33MB/s]
40%|████ | 4.44M/11.0M [00:01<00:01, 5.13MB/s]
56%|█████▌ | 6.20M/11.0M [00:01<00:00, 6.27MB/s]
72%|███████▏ | 7.96M/11.0M [00:02<00:00, 7.05MB/s]
88%|████████▊ | 9.75M/11.0M [00:02<00:00, 7.62MB/s]
100%|██████████| 11.0M/11.0M [00:02<00:00, 4.94MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_des
c-brain_mask.nii.gz
0%| | 0.00/150k [00:00<?, ?B/s]
12%|█▏ | 17.4k/150k [00:00<00:01, 85.9kB/s]
46%|████▋ | 69.6k/150k [00:00<00:00, 187kB/s]
70%|██████▉ | 104k/150k [00:00<00:00, 179kB/s]
100%|██████████| 150k/150k [00:00<00:00, 245kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_re
s-01_T1w.nii.gz
0%| | 0.00/13.7M [00:00<?, ?B/s]
0%| | 17.4k/13.7M [00:00<02:37, 87.0kB/s]
0%| | 54.3k/13.7M [00:00<01:34, 144kB/s]
1%| | 89.1k/13.7M [00:00<01:26, 157kB/s]
1%| | 140k/13.7M [00:00<01:09, 196kB/s]
1%|▏ | 176k/13.7M [00:01<01:11, 190kB/s]
2%|▏ | 211k/13.7M [00:01<01:13, 184kB/s]
2%|▏ | 298k/13.7M [00:01<00:50, 265kB/s]
4%|▎ | 507k/13.7M [00:01<00:25, 512kB/s]
7%|▋ | 925k/13.7M [00:01<00:12, 1.00MB/s]
13%|█▎ | 1.74M/13.7M [00:02<00:06, 1.95MB/s]
25%|██▍ | 3.39M/13.7M [00:02<00:02, 3.87MB/s]
45%|████▌ | 6.20M/13.7M [00:02<00:01, 6.94MB/s]
65%|██████▌ | 8.93M/13.7M [00:02<00:00, 8.96MB/s]
84%|████████▍ | 11.5M/13.7M [00:02<00:00, 10.2MB/s]
100%|██████████| 13.7M/13.7M [00:02<00:00, 4.77MB/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]
11%|█ | 17.4k/160k [00:00<00:01, 88.5kB/s]
33%|███▎ | 52.2k/160k [00:00<00:00, 140kB/s]
55%|█████▍ | 87.0k/160k [00:00<00:00, 157kB/s]
100%|██████████| 160k/160k [00:00<00:00, 269kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_re
s-01_T2w.nii.gz
0%| | 0.00/13.3M [00:00<?, ?B/s]
0%| | 17.4k/13.3M [00:00<02:34, 85.9kB/s]
0%| | 52.2k/13.3M [00:00<01:36, 137kB/s]
1%| | 122k/13.3M [00:00<00:57, 231kB/s]
1%|▏ | 174k/13.3M [00:00<00:54, 242kB/s]
2%|▏ | 244k/13.3M [00:01<00:46, 279kB/s]
3%|▎ | 348k/13.3M [00:01<00:35, 360kB/s]
4%|▎ | 470k/13.3M [00:01<00:29, 439kB/s]
7%|▋ | 870k/13.3M [00:01<00:13, 930kB/s]
12%|█▏ | 1.62M/13.3M [00:01<00:06, 1.80MB/s]
24%|██▍ | 3.16M/13.3M [00:02<00:02, 3.60MB/s]
43%|████▎ | 5.71M/13.3M [00:02<00:01, 6.34MB/s]
63%|██████▎ | 8.32M/13.3M [00:02<00:00, 8.31MB/s]
83%|████████▎ | 11.1M/13.3M [00:02<00:00, 9.89MB/s]
100%|██████████| 13.3M/13.3M [00:02<00:00, 5.00MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz
0%| | 0.00/32.4M [00:00<?, ?B/s]
0%| | 17.4k/32.4M [00:00<06:11, 87.2kB/s]
0%| | 54.3k/32.4M [00:00<03:44, 144kB/s]
0%| | 90.1k/32.4M [00:00<03:21, 160kB/s]
1%| | 185k/32.4M [00:00<01:53, 285kB/s]
1%| | 307k/32.4M [00:01<01:19, 402kB/s]
1%|▏ | 446k/32.4M [00:01<01:03, 501kB/s]
2%|▏ | 760k/32.4M [00:01<00:37, 847kB/s]
5%|▍ | 1.50M/32.4M [00:01<00:17, 1.75MB/s]
9%|▉ | 3.01M/32.4M [00:01<00:08, 3.57MB/s]
15%|█▍ | 4.72M/32.4M [00:02<00:05, 5.11MB/s]
20%|█▉ | 6.40M/32.4M [00:02<00:04, 6.10MB/s]
25%|██▌ | 8.19M/32.4M [00:02<00:03, 6.96MB/s]
31%|███ | 10.0M/32.4M [00:02<00:02, 7.59MB/s]
37%|███▋ | 11.9M/32.4M [00:02<00:02, 8.01MB/s]
42%|████▏ | 13.7M/32.4M [00:03<00:02, 8.32MB/s]
47%|████▋ | 15.2M/32.4M [00:03<00:02, 8.08MB/s]
53%|█████▎ | 17.1M/32.4M [00:03<00:01, 8.45MB/s]
58%|█████▊ | 18.9M/32.4M [00:03<00:01, 8.63MB/s]
64%|██████▍ | 20.6M/32.4M [00:03<00:01, 8.68MB/s]
69%|██████▉ | 22.3M/32.4M [00:04<00:01, 8.58MB/s]
74%|███████▍ | 24.0M/32.4M [00:04<00:00, 8.45MB/s]
80%|████████ | 25.9M/32.4M [00:04<00:00, 8.68MB/s]
86%|████████▌ | 27.7M/32.4M [00:04<00:00, 8.78MB/s]
91%|█████████ | 29.4M/32.4M [00:04<00:00, 8.71MB/s]
97%|█████████▋| 31.3M/32.4M [00:05<00:00, 8.88MB/s]
100%|██████████| 32.4M/32.4M [00:05<00:00, 6.41MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain
_probseg.nii.gz
0%| | 0.00/2.59M [00:00<?, ?B/s]
1%| | 17.4k/2.59M [00:00<00:30, 85.5kB/s]
3%|▎ | 69.6k/2.59M [00:00<00:13, 185kB/s]
5%|▍ | 122k/2.59M [00:00<00:11, 217kB/s]
6%|▌ | 157k/2.59M [00:00<00:12, 198kB/s]
10%|█ | 261k/2.59M [00:01<00:07, 310kB/s]
18%|█▊ | 470k/2.59M [00:01<00:03, 551kB/s]
35%|███▍ | 905k/2.59M [00:01<00:01, 1.06MB/s]
69%|██████▉ | 1.79M/2.59M [00:01<00:00, 2.10MB/s]
100%|██████████| 2.59M/2.59M [00:01<00:00, 1.57MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainC
erebellumExtraction_mask.nii.gz
0%| | 0.00/265k [00:00<?, ?B/s]
7%|▋ | 17.4k/265k [00:00<00:02, 84.3kB/s]
26%|██▋ | 69.6k/265k [00:00<00:01, 184kB/s]
46%|████▌ | 121k/265k [00:00<00:00, 213kB/s]
72%|███████▏ | 191k/265k [00:00<00:00, 264kB/s]
100%|██████████| 265k/265k [00:00<00:00, 321kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-WM_pr
obseg.nii.gz
0%| | 0.00/4.06M [00:00<?, ?B/s]
0%| | 1.02k/4.06M [00:00<13:23, 5.05kB/s]
1%| | 34.8k/4.06M [00:00<00:40, 99.8kB/s]
3%|▎ | 104k/4.06M [00:00<00:18, 210kB/s]
5%|▍ | 191k/4.06M [00:00<00:13, 296kB/s]
8%|▊ | 331k/4.06M [00:01<00:08, 435kB/s]
16%|█▋ | 662k/4.06M [00:01<00:04, 838kB/s]
32%|███▏ | 1.31M/4.06M [00:01<00:01, 1.60MB/s]
64%|██████▍ | 2.59M/4.06M [00:01<00:00, 3.10MB/s]
100%|██████████| 4.06M/4.06M [00:01<00:00, 2.46MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-BS_pr
obseg.nii.gz
0%| | 0.00/447k [00:00<?, ?B/s]
4%|▍ | 17.4k/447k [00:00<00:05, 85.2kB/s]
12%|█▏ | 52.2k/447k [00:00<00:02, 135kB/s]
27%|██▋ | 122k/447k [00:00<00:01, 230kB/s]
62%|██████▏ | 279k/447k [00:00<00:00, 442kB/s]
100%|██████████| 447k/447k [00:00<00:00, 545kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_re
s-02_desc-fMRIPrep_boldref.nii.gz
0%| | 0.00/1.75M [00:00<?, ?B/s]
1%| | 17.4k/1.75M [00:00<00:19, 87.2kB/s]
3%|▎ | 52.2k/1.75M [00:00<00:12, 138kB/s]
7%|▋ | 122k/1.75M [00:00<00:06, 234kB/s]
15%|█▍ | 261k/1.75M [00:00<00:03, 416kB/s]
31%|███ | 540k/1.75M [00:01<00:01, 767kB/s]
64%|██████▎ | 1.11M/1.75M [00:01<00:00, 1.48MB/s]
100%|██████████| 1.75M/1.75M [00:01<00:00, 1.45MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_re
s-02_desc-brain_mask.nii.gz
0%| | 0.00/29.6k [00:00<?, ?B/s]
100%|█████████
█| 29.6k/29.6k [00:00<00:00, 146kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_re
s-01_label-brain_probseg.nii.gz
0%| | 0.00/3.93M [00:00<?, ?B/s]
0%| | 17.4k/3.93M [00:00<00:45, 85.2kB/s]
1%|▏ | 52.2k/3.93M [00:00<00:28, 135kB/s]
4%|▍ | 157k/3.93M [00:00<00:12, 306kB/s]
8%|▊ | 331k/3.93M [00:00<00:06, 521kB/s]
18%|█▊ | 714k/3.93M [00:01<00:03, 1.00MB/s]
37%|███▋ | 1.44M/3.93M [00:01<00:01, 1.88MB/s]
75%|███████▍ | 2.94M/3.93M [00:01<00:00, 3.64MB/s]
100%|██████████| 3.93M/3.93M [00:01<00:00, 2.71MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_re
s-01_desc-carpet_dseg.nii.gz
0%| | 0.00/451k [00:00<?, ?B/s]
4%|▍ | 17.4k/451k [00:00<00:05, 85.4kB/s]
12%|█▏ | 54.3k/451k [00:00<00:02, 142kB/s]
27%|██▋ | 124k/451k [00:00<00:01, 234kB/s]
58%|█████▊ | 263k/451k [00:00<00:00, 412kB/s]
100%|██████████| 451k/451k [00:00<00:00, 553kB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_T1w
.nii.gz
0%| | 0.00/1.41M [00:00<?, ?B/s]
1%| | 17.4k/1.41M [00:00<00:16, 86.1kB/s]
4%|▍ | 54.3k/1.41M [00:00<00:09, 143kB/s]
11%|█ | 159k/1.41M [00:00<00:03, 314kB/s]
24%|██▎ | 333k/1.41M [00:00<00:02, 529kB/s]
51%|█████ | 716k/1.41M [00:01<00:00, 1.02MB/s]
86%|████████▋ | 1.22M/1.41M [00:01<00:00, 1.52MB/s]
100%|██████████| 1.41M/1.41M [00:01<00:00, 1.16MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-02_des
c-brain_mask.nii.gz
0%| | 0.00/28.6k [00:00<?, ?B/s]
65%|██████▍ | 18.4k/28.6k [00:00<00:00, 91.8kB/s]
100%|██████████| 28.6k/28.6k [00:00<00:00, 142kB/s]
When fMRIPrep finishes, the files we care about most for FEAT are:
the HTML report
the preprocessed BOLD file for the run we want
the confounds table for that run
Because we wrote the outputs into ~/trust_example/derivatives/fmriprep, the next steps can keep using the same paths throughout the notebook.
If the HTML report does not open correctly inside Neurodesktop, open it through JupyterLab instead. It is worth checking the report before moving on, because bad preprocessing or bad alignment will usually be easier to catch here than later in the FEAT output.
!find ~/trust_example/derivatives/fmriprep -name "sub-104.html"
!find ~/trust_example/derivatives/fmriprep -name "*run-01*desc-preproc_bold.nii.gz"
!find ~/trust_example/derivatives/fmriprep -name "*run-01*desc-confounds_timeseries.tsv"
/home/jovyan/trust_example/derivatives/fmriprep/sub-104.html
/home/jovyan/trust_example/derivatives/fmriprep/sub-104/func/sub-104_task-trust_run-01_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz
/home/jovyan/trust_example/derivatives/fmriprep/sub-104/func/sub-104_task-trust_run-01_desc-confounds_timeseries.tsv
4. Make a FEAT confounds file#
Here we take the fMRIPrep confounds table for one run and save a FEAT-ready text file.
We keep:
cosine regressors
non-steady-state regressors
6 motion parameters
the first 6 aCompCor components
framewise displacement, if it exists
FEAT wants a plain text file without a header, so we write the output that way.
This is a good example of why notebook workflows can be useful for teaching: you can see exactly which nuisance regressors are being kept, rather than hiding that logic inside a separate script.
confounds_tsv = base_dir / "derivatives" / "fmriprep" / "sub-104" / "func" / "sub-104_task-trust_run-01_desc-confounds_timeseries.tsv"
confounds = pd.read_csv(confounds_tsv, sep=" ")
# Keep a simple but still realistic set of nuisance regressors.
cosine_cols = [c for c in confounds.columns if c.startswith("cosine")]
nss_cols = [c for c in confounds.columns if c.startswith("non_steady_state")]
motion_cols = ["trans_x", "trans_y", "trans_z", "rot_x", "rot_y", "rot_z"]
acompcor_cols = [c for c in confounds.columns if c.startswith("a_comp_cor_")][:6]
fd_cols = ["framewise_displacement"] if "framewise_displacement" in confounds.columns else []
keep_cols = cosine_cols + nss_cols + motion_cols + acompcor_cols + fd_cols
feat_confounds = confounds[keep_cols].fillna(0)
out_dir = base_dir / "derivatives" / "fsl" / "confounds" / "sub-104"
out_dir.mkdir(parents=True, exist_ok=True)
out_file = out_dir / "sub-104_task-trust_run-01_desc-fslConfounds.tsv"
feat_confounds.to_csv(out_file, sep=" ", header=False, index=False)
print(out_file)
print(feat_confounds.shape)
feat_confounds.head()
/home/jovyan/trust_example/derivatives/fsl/confounds/sub-104/sub-104_task-trust_run-01_desc-fslConfounds.tsv
(217, 19)
| cosine00 | cosine01 | cosine02 | cosine03 | cosine04 | non_steady_state_outlier00 | trans_x | trans_y | trans_z | rot_x | rot_y | rot_z | a_comp_cor_00 | a_comp_cor_01 | a_comp_cor_02 | a_comp_cor_03 | a_comp_cor_04 | a_comp_cor_05 | framewise_displacement | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 1.0 | -0.028677 | -0.050250 | 0.041419 | -0.001136 | -0.000077 | -3.280445e-04 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 | 0.000000 |
| 1 | 0.096223 | 0.096215 | 0.096202 | 0.096184 | 0.096161 | 0.0 | -0.020840 | -0.050390 | 0.077573 | -0.000667 | -0.000360 | -1.197739e-07 | 0.092616 | -0.026204 | 0.101412 | -0.034399 | 0.042093 | -0.077511 | 0.098113 |
| 2 | 0.096202 | 0.096133 | 0.096019 | 0.095859 | 0.095653 | 0.0 | -0.016589 | -0.015174 | 0.059022 | -0.000540 | -0.000058 | -2.060158e-04 | -0.018382 | 0.116795 | 0.089136 | -0.041624 | 0.022263 | 0.072593 | 0.089766 |
| 3 | 0.096161 | 0.095971 | 0.095653 | 0.095209 | 0.094639 | 0.0 | -0.009081 | -0.045662 | 0.038655 | -0.000667 | 0.000078 | 2.599182e-08 | -0.086435 | 0.021827 | -0.071150 | 0.036173 | -0.004025 | -0.012221 | 0.081813 |
| 4 | 0.096100 | 0.095727 | 0.095105 | 0.094237 | 0.093125 | 0.0 | -0.012794 | 0.007354 | 0.047157 | -0.000667 | -0.000073 | -2.435978e-08 | -0.049187 | 0.018794 | -0.086241 | 0.033125 | 0.006822 | -0.001962 | 0.072783 |
5. Convert events.tsv to 3-column files#
This step uses BIDSto3col.sh from bidsutils and keeps the logic to one run.
BIDSto3col.sh reads the BIDS events file and writes one 3-column text file per event type.
Each output file has three columns:
onset
duration
weight
Those output files are exactly the kind of timing files FEAT expects for custom EVs, so this is one of the main bridges between a BIDS dataset and an FSL first-level model.
%%bash
set -e
EXAMPLE_DIR="$HOME/trust_example"
sub=104
run=01
events_tsv="$EXAMPLE_DIR/bids/ds003745/sub-${sub}/func/sub-${sub}_task-trust_run-${run}_events.tsv"
out_base="$EXAMPLE_DIR/derivatives/fsl/EVfiles/sub-${sub}/trust/run-${run}"
mkdir -p "$(dirname "$out_base")"
# This creates one 3-column file per event type found in the BIDS events file.
bash "$EXAMPLE_DIR/bidsutils/BIDSto3col/BIDSto3col.sh" "$events_tsv" "$out_base"
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_choice_computer.tx
t'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_choice_friend.txt'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_choice_stranger.tx
t'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_missed_trial.txt'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_outcome_computer_d
efect.txt'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_outcome_computer_r
ecip.txt'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_outcome_friend_def
ect.txt'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_outcome_friend_rec
ip.txt'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_outcome_stranger_d
efect.txt'
Creating '/home/jovyan/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_outcome_stranger_r
ecip.txt'
!ls ~/trust_example/derivatives/fsl/EVfiles/sub-104/trust
!head -n 5 ~/trust_example/derivatives/fsl/EVfiles/sub-104/trust/run-01_choice_computer.txt
run-01_choice_computer.txt run-01_outcome_computer_recip.txt
run-01_choice_friend.txt run-01_outcome_friend_defect.txt
run-01_choice_stranger.txt run-01_outcome_friend_recip.txt
run-01_missed_trial.txt run-01_outcome_stranger_defect.txt
run-01_outcome_computer_defect.txt run-01_outcome_stranger_recip.txt
4.03279 1.860030 1.0
35.3721 1.830190 1.0
90.4619 2.570010 1.0
178.15 2.770810 1.0
212.465 2.416930 1.0
6. Render the FEAT template#
The template file already contains the FEAT model structure.
What changes from subject to subject and run to run are the paths and a few settings.
This is a useful pattern for reproducible work: keep the design mostly fixed, and then fill in the parts that should vary across runs.
Placeholders we replace#
OUTPUT→ where the.featdirectory should be writtenDATA→ the preprocessed BOLD file from fMRIPrepEVDIR→ the prefix used by the EV timing filesMISSED_TRIAL→ path to the optional missed-trial EV fileEV_SHAPE→3if the missed-trial file exists, otherwise10for an empty EVSMOOTH→ smoothing kernel in mmCONFOUNDEVS→ the confounds file we just created
template_text = (base_dir / "templates" / "L1_task-trust_model-01_type-act.fsf").read_text()
for token in ["OUTPUT", "DATA", "EVDIR", "MISSED_TRIAL", "EV_SHAPE", "SMOOTH", "CONFOUNDEVS"]:
print(f"--- lines containing {token} ---")
for line in template_text.splitlines():
if token in line:
print(line)
print()
--- lines containing OUTPUT ---
set fmri(outputdir) "OUTPUT"
--- lines containing DATA ---
set feat_files(1) "DATA"
--- lines containing EVDIR ---
set fmri(custom1) "EVDIR_choice_computer.txt"
set fmri(custom2) "EVDIR_choice_friend.txt"
set fmri(custom3) "EVDIR_choice_stranger.txt"
set fmri(custom4) "EVDIR_outcome_computer_defect.txt"
set fmri(custom5) "EVDIR_outcome_computer_recip.txt"
set fmri(custom6) "EVDIR_outcome_friend_defect.txt"
set fmri(custom7) "EVDIR_outcome_friend_recip.txt"
set fmri(custom8) "EVDIR_outcome_stranger_defect.txt"
set fmri(custom9) "EVDIR_outcome_stranger_recip.txt"
--- lines containing MISSED_TRIAL ---
set fmri(custom10) "MISSED_TRIAL"
--- lines containing EV_SHAPE ---
set fmri(shape10) EV_SHAPE
--- lines containing SMOOTH ---
set fmri(smooth) SMOOTH
--- lines containing CONFOUNDEVS ---
set confoundev_files(1) "CONFOUNDEVS"
The next cell renders a new .fsf file. Each variable is written out explicitly so you can see what is being inserted.
Even if you do not remember every line of FEAT syntax, the important lesson is that the .fsf file is just text. That means you can inspect it, edit it, and generate it systematically.
%%bash
set -e
EXAMPLE_DIR="$HOME/trust_example"
TASK=trust
SMOOTH=6
sub=104
run=01
OUTPUT="$EXAMPLE_DIR/derivatives/fsl/sub-${sub}/L1_task-${TASK}_model-01_type-act_run-${run}_sm-${SMOOTH}"
DATA="$EXAMPLE_DIR/derivatives/fmriprep/sub-${sub}/func/sub-${sub}_task-${TASK}_run-${run}_space-MNI152NLin6Asym_res-2_desc-preproc_bold.nii.gz"
CONFOUNDEVS="$EXAMPLE_DIR/derivatives/fsl/confounds/sub-${sub}/sub-${sub}_task-${TASK}_run-${run}_desc-fslConfounds.tsv"
EVDIR="$EXAMPLE_DIR/derivatives/fsl/EVfiles/sub-${sub}/${TASK}/run-${run}"
MISSED_TRIAL="${EVDIR}_missed_trial.txt"
if [ -e "$MISSED_TRIAL" ]; then
EV_SHAPE=3
else
EV_SHAPE=10
fi
mkdir -p "$(dirname "$OUTPUT")"
sed \
-e "s@OUTPUT@${OUTPUT}@g" \
-e "s@DATA@${DATA}@g" \
-e "s@EVDIR@${EVDIR}@g" \
-e "s@MISSED_TRIAL@${MISSED_TRIAL}@g" \
-e "s@EV_SHAPE@${EV_SHAPE}@g" \
-e "s@SMOOTH@${SMOOTH}@g" \
-e "s@CONFOUNDEVS@${CONFOUNDEVS}@g" \
"$EXAMPLE_DIR/templates/L1_task-trust_model-01_type-act.fsf" \
> "$EXAMPLE_DIR/derivatives/fsl/sub-${sub}/L1_sub-${sub}_task-${TASK}_model-01_run-${run}_act.fsf"
rendered_fsf = base_dir / "derivatives" / "fsl" / "sub-104" / "L1_sub-104_task-trust_model-01_run-01_act.fsf"
print(rendered_fsf)
print()
print(rendered_fsf.read_text()[:4000])
/home/jovyan/trust_example/derivatives/fsl/sub-104/L1_sub-104_task-trust_model-01_run-01_act.fsf
# FEAT version number
set fmri(version) 6.00
# Are we in MELODIC?
set fmri(inmelodic) 0
# Analysis level
# 1 : First-level analysis
# 2 : Higher-level analysis
set fmri(level) 1
# Which stages to run
# 0 : No first-level analysis (registration and/or group stats only)
# 7 : Full first-level analysis
# 1 : Pre-processing
# 2 : Statistics
set fmri(analysis) 7
# Use relative filenames
set fmri(relative_yn) 0
# Balloon help
set fmri(help_yn) 1
# Run Featwatcher
set fmri(featwatcher_yn) 0
# Cleanup first-level standard-space images
set fmri(sscleanup_yn) 0
# Output directory
set fmri(outputdir) "/home/jovyan/trust_example/derivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6"
# TR(s)
set fmri(tr) 2.020000
# Total volumes
set fmri(npts) 217
# Delete volumes
set fmri(ndelete) 0
# Perfusion tag/control order
set fmri(tagfirst) 1
# Number of first-level analyses
set fmri(multiple) 1
# Higher-level input type
# 1 : Inputs are lower-level FEAT directories
# 2 : Inputs are cope images from FEAT directories
set fmri(inputtype) 2
# Carry out pre-stats processing?
set fmri(filtering_yn) 1
# Brain/background threshold, %
set fmri(brain_thresh) 10
# Critical z for design efficiency calculation
set fmri(critical_z) 5.3
# Noise level
set fmri(noise) 0.66
# Noise AR(1)
set fmri(noisear) 0.34
# Motion correction
# 0 : None
# 1 : MCFLIRT
set fmri(mc) 0
# Spin-history (currently obsolete)
set fmri(sh_yn) 0
# B0 fieldmap unwarping?
set fmri(regunwarp_yn) 0
# EPI dwell time (ms)
set fmri(dwell) 0.7
# EPI TE (ms)
set fmri(te) 35
# % Signal loss threshold
set fmri(signallossthresh) 10
# Unwarp direction
set fmri(unwarp_dir) y-
# Slice timing correction
# 0 : None
# 1 : Regular up (0, 1, 2, 3, ...)
# 2 : Regular down
# 3 : Use slice order file
# 4 : Use slice timings file
# 5 : Interleaved (0, 2, 4 ... 1, 3, 5 ... )
set fmri(st) 0
# Slice timings file
set fmri(st_file) ""
# BET brain extraction
set fmri(bet_yn) 1
# Spatial smoothing FWHM (mm)
set fmri(smooth) 6
# Intensity normalization
set fmri(norm_yn) 0
# Perfusion subtraction
set fmri(perfsub_yn) 0
# Highpass temporal filtering
set fmri(temphp_yn) 0
# Lowpass temporal filtering
set fmri(templp_yn) 0
# MELODIC ICA data exploration
set fmri(melodic_yn) 0
# Carry out main stats?
set fmri(stats_yn) 1
# Carry out prewhitening?
set fmri(prewhiten_yn) 1
# Add motion parameters to model
# 0 : No
# 1 : Yes
set fmri(motionevs) 0
set fmri(motionevsbeta) ""
set fmri(scriptevsbeta) ""
# Robust outlier detection in FLAME?
set fmri(robust_yn) 0
# Higher-level modelling
# 3 : Fixed effects
# 0 : Mixed Effects: Simple OLS
# 2 : Mixed Effects: FLAME 1
# 1 : Mixed Effects: FLAME 1+2
set fmri(mixed_yn) 2
# Number of EVs
set fmri(evs_orig) 10
set fmri(evs_real) 10
set fmri(evs_vox) 0
# Number of contrasts
set fmri(ncon_orig) 18
set fmri(ncon_real) 18
# Number of F-tests
set fmri(nftests_orig) 0
set fmri(nftests_real) 0
# Add constant column to design matrix? (obsolete)
set fmri(constcol) 0
# Carry out post-stats steps?
set fmri(poststats_yn) 1
# Pre-threshold masking?
set fmri(threshmask) ""
# Thresholding
# 0 : None
# 1 : Uncorrected
# 2 : Voxel
# 3 : Cluster
set fmri(thresh) 3
# P threshold
set fmri(prob_thresh) 0.05
# Z threshold
set fmri(z_thresh) 2.3
# Z min/max for colour rendering
# 0 : Use actual Z min/max
# 1 : Use preset Z min/max
set fmri(zdisplay) 0
# Z min in colour rendering
set fmri(zmin) 2
# Z max in colour rendering
set fmri(zmax) 8
# Colour rendering type
# 0 : Solid blobs
# 1 : Transparent blobs
set fmri(rendertype) 1
# Background image for higher-level stats overlays
# 1 : Mean highres
# 2 : First highres
# 3 : Mean functional
# 4 : First functional
# 5 : Standard space template
set fmri(bgimage) 1
# Create time series plots
set fmri(tsplot_yn) 1
# Registration to initial structural
set fmri(reginitial_highres_yn) 0
# Search space for registration to initial structural
# 0 : No search
# 90 : Normal search
# 180 : Full search
se
7. Run first-level FEAT#
This command runs FEAT on the rendered design file.
At this point, the main conceptual pieces are in place: preprocessed data, confounds, EV timing files, and a rendered design file. FEAT now uses those pieces to estimate the first-level GLM.
%%bash
set -e
# Run FEAT on the rendered first-level design file.
feat "$HOME/trust_example/derivatives/fsl/sub-104/L1_sub-104_task-trust_model-01_run-01_act.fsf"
To view the FEAT progress and final report, point your web browser at /home/jovyan/trust_example/der
ivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6.feat/report_log.html
8. Fix FEAT registration for fMRIPrep-preprocessed data#
Because the functional image already came out of fMRIPrep in standard space, FEAT’s usual registration outputs are not the right ones to trust here.
The next cell follows the same post-FEAT registration fix used in the original L1stats.sh script.
This is based on the NeuroStars post referenced in that script.
In plain language, this step tells FEAT to treat the input as already being in standard space, so the registration files inside the .feat directory do not point to misleading transforms.
%%bash
set -e
OUTPUT="$HOME/trust_example/derivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6"
# fix registration as per NeuroStars post:
# https://neurostars.org/t/performing-full-glm-analysis-with-fsl-on-the-bold-images-preprocessed-by-fmriprep-without-re-registering-the-data-to-the-mni-space/784/3
mkdir -p ${OUTPUT}.feat/reg
ln -sf $FSLDIR/etc/flirtsch/ident.mat ${OUTPUT}.feat/reg/example_func2standard.mat
ln -sf $FSLDIR/etc/flirtsch/ident.mat ${OUTPUT}.feat/reg/standard2example_func.mat
ln -sf ${OUTPUT}.feat/mean_func.nii.gz ${OUTPUT}.feat/reg/standard.nii.gz
9. Results#
The FEAT output directory should now contain the standard report, design matrix, and statistical maps.
A few files worth checking first are:
report.htmldesign.pngthresh_zstat1.nii.gzthresh_zstat2.nii.gzthresh_zstat10.nii.gz
This is also a good point to slow down and inspect the outputs before interpreting anything. Make sure the design looks sensible, the report opens, and the expected thresholded maps actually exist.
feat_dir = base_dir / "derivatives" / "fsl" / "sub-104" / "L1_task-trust_model-01_type-act_run-01_sm-6.feat"
for rel in [
"report.html",
"design.png",
"thresh_zstat1.nii.gz",
"thresh_zstat2.nii.gz",
"thresh_zstat10.nii.gz",
]:
p = feat_dir / rel
print(f"{p}: {p.exists()}")
/home/jovyan/trust_example/derivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6.feat/report.html: True
/home/jovyan/trust_example/derivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6.feat/design.png: True
/home/jovyan/trust_example/derivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6.feat/thresh_zstat1.nii.gz: True
/home/jovyan/trust_example/derivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6.feat/thresh_zstat2.nii.gz: True
/home/jovyan/trust_example/derivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6.feat/thresh_zstat10.nii.gz: True
design_png = feat_dir / "design.png"
if design_png.exists():
display(Image(filename=str(design_png)))
else:
print("Run FEAT first, then come back to this cell.")
Optional: try a quick NiiVue visualization#
This cell overlays a thresholded FEAT result on the example functional image from the same run.
Here we use thresh_zstat10.nii.gz, which corresponds to reciprocate > defect. In this task, that contrast is roughly reward-related, so even in a single run you may see activation in the ventral striatum and nearby reward-sensitive regions.
A few learning notes:
example_func.nii.gzgives you a background image in the same space as the FEAT results, but it’s a little blurryMNI152_T1_2mm_brain.nii.gzis a T1 background in MNI space and should be better for visualization.thresh_zstat10.nii.gzis already thresholded, so the overlay is easier to interpretif your notebook shows nothing, first confirm that the
.featdirectory exists and thatthresh_zstat10.nii.gzis really there
from pathlib import Path
from IPython.display import display
from ipyniivue import NiiVue
import nibabel as nib
import numpy as np
# FEAT background and contrast map from the same run
# bg = str(feat_dir / "example_func.nii.gz")
bg = "/cvmfs/neurodesk.ardc.edu.au/containers/fsl_6.0.7.16_20250131/fsl_6.0.7.16_20250131.simg/opt/fsl-6.0.7.16/data/standard/MNI152_T1_2mm_brain.nii.gz"
zmap = str(feat_dir / "thresh_zstat10.nii.gz") # reciprocate > defect
print("Background exists:", Path(bg).exists(), bg)
print("Contrast exists:", Path(zmap).exists(), zmap)
if Path(bg).exists() and Path(zmap).exists():
# Load the EPI background and choose a sensible display window
epi = nib.load(bg).get_fdata()
epi_nonzero = epi[epi > 0]
lo = float(np.percentile(epi_nonzero, 2))
hi = float(np.percentile(epi_nonzero, 98))
nv = NiiVue()
nv.load_volumes([
{
"path": bg,
"name": "example_func",
"colormap": "gray",
"opacity": 1.0,
"cal_min": lo,
"cal_max": hi
},
{
"path": zmap,
"name": "reciprocate > defect",
"colormap": "red",
"opacity": 0.45
}
])
display(nv)
else:
print("Run FEAT first, then come back to this cell.")
Background exists: True /cvmfs/neurodesk.ardc.edu.au/containers/fsl_6.0.7.16_20250131/fsl_6.0.7.16_20250131.simg/opt/fsl-6.0.7.16/data/standard/MNI152_T1_2mm_brain.nii.gz
Contrast exists: True /home/jovyan/trust_example/derivatives/fsl/sub-104/L1_task-trust_model-01_type-act_run-01_sm-6.feat/thresh_zstat10.nii.gz
Dependencies in Jupyter/Python#
Using the package watermark to document system environment and software versions used in this notebook, alongside the Neurodesktop version extracted from the
JUPYTER_IMAGEorNEURODESKTOP_VERSIONenvironment variables.
import os
%load_ext watermark
%watermark
%watermark --iversions
neurodesktop_version = (
os.environ.get('JUPYTER_IMAGE', '').split(':')[-1] or
os.environ.get('NEURODESKTOP_VERSION', 'unknown')
)
print(f"Neurodesktop version: {neurodesktop_version}")
Last updated: 2026-07-21T08:06:50.027303+00:00
Python implementation: CPython
Python version : 3.13.14
IPython version : 9.12.0
Compiler : GCC 14.3.0
OS : Linux
Release : 6.8.0-111-generic
Machine : x86_64
Processor : x86_64
CPU cores : 16
Architecture: 64bit
IPython : 9.12.0
ipyniivue: 2.4.4
nibabel : 5.4.2
numpy : 2.5.1
pandas : 2.3.3
Neurodesktop version: 2026-07-11