Cannot run nibabies. Missing dependencies: c3d_affine_tool #460
Description
What happened?
When running Nibabies with Apptainer, I seem to be running into this error that sometimes appears and sometimes doesn't, where Nibabies exits after complaining that there's a missing command called 'c3d_affine_tool'.
What command did you use?
#!/bin/bash
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
sub=$1
ses=$2
[ -z $sub ] && echo "usage: ./run_nibabies.sh <sub> [<ses>]" && exit 1 || shift
[ -z $ses ] || shift
workdir=/export/scratch1/bmsc-5mo/work/$sub/nibabies
rm -rf $workdir
mkdir -p $workdir/home
apptainer run --nv --cleanenv --no-home \
-B /export/scratch1/bmsc-5mo:/input \
-B /export/scratch1/bmsc-5mo/derivatives/nibabies:/output \
-B $workdir:/work \
-B ${FREESURFER_LICENSE}:/opt/freesurfer/license.txt:ro \
-B ${SCRIPT_DIR}/filter_files:/filter_files \
-B /export/scratch1/bmsc-5mo/derivatives/bibsnet:/bibsnet \
-H ${HOME}:/work/home \
/data/sylvester/data1/software/apptainer/images/nibabies-25.0.1.sif \
/input /output participant -v \
--participant-label $sub \
$([ -z $ses ] && echo '' || echo "--session-id $ses") \
-w /work \
--fs-license-file /opt/freesurfer/license.txt \
--derivatives /bibsnet \
--surface-recon-method None \
--norm-csf \
--output-spaces fsLR MNIInfant:cohort-7 MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 T2w \
$([ -f ${SCRIPT_DIR}/filter_files/sub-${sub}.json ] && echo "--bids-filter-file /filter_files/sub-${sub}.json") \
$([[ $# -gt 0 ]] && echo $@)What version of NiBabies are you using?
25.0.1
Relevant log output
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator@1.14.10
(node:3067583) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
1: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)
Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.
2: [WARN] The Name field of dataset_description.json is present but empty of visible characters. (code: 115 - EMPTY_DATASET_NAME)
Please visit https://neurostars.org/search?q=EMPTY_DATASET_NAME for existing conversations about this issue.
3: [WARN] The recommended file /README is very small. Please consider expanding it with additional information about the dataset. (code: 213 - README_FILE_SMALL)
./README
Please visit https://neurostars.org/search?q=README_FILE_SMALL for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
113 Files, 1.22GB MRI
1 - Subject
2 - Sessions
If you have any questions, please post on https://neurostars.org/tags/bids.
250514-14:04:44,479 nipype.workflow WARNING:
Previous output generated by version 0+unknown found.
250514-14:04:44,479 nipype.workflow IMPORTANT:
Running nibabies version 25.0.1:
* BIDS dataset path: /input.
* Participant list: [['BMSCP010V20', '01'], ['BMSCP010V20', '02']].
* Run identifier: 20250514-140431_113b58e6-75c9-412d-b061-a13675198bf1.
* Output spaces: fsLR MNIInfant:cohort-7:res-native MNI152NLin6Asym:res-2 MNI152NLin2009cAsym:res-2 T2w.
* Derivatives: {'bibsnet': PosixPath('/bibsnet')}.
* Pre-run FreeSurfer's SUBJECTS_DIR: /output/sourcedata/freesurfer.
250514-14:04:45,477 nipype.workflow INFO:
ANAT: Using T1w as the reference anatomical
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-7/tpl-MNIInfant_cohort-7_res-1_T1w.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 12.1M/12.1M [00:00<00:00, 41.6MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-7/tpl-MNIInfant_cohort-7_res-1_desc-brain_mask.nii.gz
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 120k/120k [00:00<00:00, 2.17MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNIInfant/cohort-7/tpl-MNIInfant_cohort-7_res-1_T2w.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 12.0M/12.0M [00:00<00:00, 41.0MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_T1w.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 11.0M/11.0M [00:00<00:00, 37.5MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin6Asym/tpl-MNI152NLin6Asym_res-01_desc-brain_mask.nii.gz
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 150k/150k [00:00<00:00, 2.63MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 13.7M/13.7M [00:00<00:00, 47.9MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-brain_mask.nii.gz
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 160k/160k [00:00<00:00, 2.99MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T2w.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 13.3M/13.3M [00:00<00:00, 48.1MB/s]
250514-14:04:49,167 nipype.workflow INFO:
ANAT Stage 1: Adding T1w template workflow
250514-14:04:49,172 nipype.workflow INFO:
ANAT Stage 1: Adding T2w template workflow
250514-14:04:49,176 nipype.workflow INFO:
ANAT Found T1w brain mask
250514-14:04:49,176 nipype.workflow INFO:
ANAT Skipping skull-strip, INU-correction only
250514-14:04:49,185 nipype.workflow INFO:
ANAT Found T2w brain mask
250514-14:04:49,185 nipype.workflow INFO:
ANAT Skipping skull-strip, INU-correction only
250514-14:04:49,187 nipype.workflow INFO:
ANAT Coregistering anatomicals
250514-14:04:49,196 nipype.workflow INFO:
ANAT Found precomputed anatomical segmentation
250514-14:04:49,196 nipype.workflow INFO:
ANAT Stage 4: Tissue segmentation
250514-14:04:49,198 nipype.workflow INFO:
ANAT Segmentation: Using existing segmentation
250514-14:04:49,205 nipype.workflow INFO:
ANAT Stage 5a: Preparing normalization workflow for ['MNIInfant:cohort-7', 'MNI152NLin6Asym', 'MNI152NLin2009cAsym']
250514-14:04:49,214 nipype.workflow INFO:
ANAT Skipping Stages 6+
250514-14:04:50,67 nipype.workflow INFO:
B0 field inhomogeneity map will be estimated with the following 10 estimator(s): [<EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>, <EstimatorType.PEPOLAR: 2>].
250514-14:04:51,95 nipype.workflow INFO:
Setting-up fieldmap "auto_00001" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-01_dir-AP_run-02_epi.nii.gz, sub-BMSCP010V20_ses-01_dir-PA_run-02_epi.nii.gz>
250514-14:04:51,166 nipype.workflow INFO:
Setting-up fieldmap "auto_00002" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-01_dir-AP_run-04_epi.nii.gz, sub-BMSCP010V20_ses-01_dir-PA_run-04_epi.nii.gz>
250514-14:04:51,242 nipype.workflow INFO:
Setting-up fieldmap "auto_00003" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-01_dir-AP_run-06_epi.nii.gz, sub-BMSCP010V20_ses-01_dir-PA_run-06_epi.nii.gz>
250514-14:04:51,311 nipype.workflow INFO:
Setting-up fieldmap "auto_00004" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-01_dir-AP_run-08_epi.nii.gz, sub-BMSCP010V20_ses-01_dir-PA_run-08_epi.nii.gz>
250514-14:04:51,380 nipype.workflow INFO:
Setting-up fieldmap "auto_00005" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-01_dir-AP_run-10_epi.nii.gz, sub-BMSCP010V20_ses-01_dir-PA_run-10_epi.nii.gz>
250514-14:04:51,449 nipype.workflow INFO:
Setting-up fieldmap "auto_00007" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-02_dir-AP_run-02_epi.nii.gz, sub-BMSCP010V20_ses-02_dir-PA_run-02_epi.nii.gz>
250514-14:04:51,518 nipype.workflow INFO:
Setting-up fieldmap "auto_00008" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-02_dir-AP_run-04_epi.nii.gz, sub-BMSCP010V20_ses-02_dir-PA_run-04_epi.nii.gz>
250514-14:04:51,588 nipype.workflow INFO:
Setting-up fieldmap "auto_00009" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-02_dir-AP_run-06_epi.nii.gz, sub-BMSCP010V20_ses-02_dir-PA_run-06_epi.nii.gz>
250514-14:04:51,657 nipype.workflow INFO:
Setting-up fieldmap "auto_00010" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-02_dir-AP_run-08_epi.nii.gz, sub-BMSCP010V20_ses-02_dir-PA_run-08_epi.nii.gz>
250514-14:04:51,726 nipype.workflow INFO:
Setting-up fieldmap "auto_00011" (EstimatorType.PEPOLAR) with <sub-BMSCP010V20_ses-02_dir-AP_run-10_epi.nii.gz, sub-BMSCP010V20_ses-02_dir-PA_run-10_epi.nii.gz>
250514-14:04:52,414 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-01_bold.nii.gz.
250514-14:04:52,769 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:52,778 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:52,786 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 1.75M/1.75M [00:00<00:00, 9.49MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 29.6k/29.6k [00:00<00:00, 1.06MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_label-brain_probseg.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3.93M/3.93M [00:00<00:00, 20.2MB/s]
250514-14:04:53,832 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:53,846 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:04:54,93 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-02_bold.nii.gz.
250514-14:04:54,145 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:54,151 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:54,154 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:54,201 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:54,207 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.388s.
250514-14:04:54,853 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-03_bold.nii.gz.
250514-14:04:54,905 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:54,910 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:54,914 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:54,960 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:54,966 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:04:55,195 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-04_bold.nii.gz.
250514-14:04:55,245 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:55,251 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:55,255 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:55,301 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:55,308 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:04:55,979 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-05_bold.nii.gz.
250514-14:04:56,31 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:56,37 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:56,41 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:56,90 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:56,96 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:04:56,322 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-01_bold.nii.gz.
250514-14:04:56,372 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:56,378 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:56,382 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:56,427 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:56,434 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:04:56,660 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-02_bold.nii.gz.
250514-14:04:56,710 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:56,715 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:56,719 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:57,12 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:57,19 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:04:57,468 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-03_bold.nii.gz.
250514-14:04:57,519 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:57,524 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:57,528 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:57,575 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:57,581 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:04:57,808 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-04_bold.nii.gz.
250514-14:04:57,860 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:57,865 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:57,869 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:57,914 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:57,921 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.388s.
250514-14:04:58,149 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-05_bold.nii.gz.
250514-14:04:58,200 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:04:58,206 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:04:58,209 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:04:58,255 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:04:58,262 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:04:59,329 nipype.workflow INFO:
ANAT: Using T1w as the reference anatomical
250514-14:04:59,509 nipype.workflow INFO:
ANAT Stage 1: Adding T1w template workflow
250514-14:04:59,512 nipype.workflow INFO:
ANAT Stage 1: Adding T2w template workflow
250514-14:04:59,516 nipype.workflow INFO:
ANAT T2w mask will be transformed into T1w space
250514-14:04:59,520 nipype.workflow INFO:
ANAT Atlas-based brain mask will be calculated on the T2w
Downloading https://templateflow.s3.amazonaws.com/tpl-UNCInfant/cohort-1/tpl-UNCInfant_cohort-1_T1w.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 3.55M/3.55M [00:00<00:00, 16.3MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-UNCInfant/cohort-1/tpl-UNCInfant_cohort-1_label-brain_probseg.nii.gz
100%|████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 602k/602k [00:00<00:00, 4.82MB/s]
Downloading https://templateflow.s3.amazonaws.com/tpl-UNCInfant/cohort-1/tpl-UNCInfant_cohort-1_label-BrainCerebellumExtraction_mask.nii.gz
100%|██████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 95.4k/95.4k [00:00<00:00, 1.96MB/s]
250514-14:05:00,793 nipype.workflow INFO:
ANAT Coregistering anatomicals
250514-14:05:00,820 nipype.workflow INFO:
ANAT Stage 4: Tissue segmentation
250514-14:05:00,834 nipype.workflow INFO:
ANAT Stage 5a: Preparing normalization workflow for ['MNIInfant:cohort-7', 'MNI152NLin6Asym', 'MNI152NLin2009cAsym']
250514-14:05:00,849 nipype.workflow INFO:
ANAT Skipping Stages 6+
250514-14:05:01,892 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-01_bold.nii.gz.
250514-14:05:01,943 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:01,949 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:01,953 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:01,986 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:01,993 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:02,173 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-02_bold.nii.gz.
250514-14:05:02,223 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:02,229 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:02,234 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:02,266 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:02,273 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.388s.
250514-14:05:02,454 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-03_bold.nii.gz.
250514-14:05:02,504 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:02,509 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:02,514 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:02,547 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:02,553 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:02,734 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-04_bold.nii.gz.
250514-14:05:02,783 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:02,789 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:02,794 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:02,826 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:02,833 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:03,13 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-01_task-rest_run-05_bold.nii.gz.
250514-14:05:03,64 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:03,69 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:03,74 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:03,108 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:03,114 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:03,881 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-01_bold.nii.gz.
250514-14:05:03,931 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:03,936 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:03,940 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:03,976 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:03,983 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:04,166 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-02_bold.nii.gz.
250514-14:05:04,216 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:04,221 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:04,225 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:04,259 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:04,266 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:04,448 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-03_bold.nii.gz.
250514-14:05:04,497 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:04,503 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:04,507 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:04,541 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:04,547 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:04,729 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-04_bold.nii.gz.
250514-14:05:04,779 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:04,784 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:04,788 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:04,823 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:04,830 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.388s.
250514-14:05:05,12 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-05_bold.nii.gz.
250514-14:05:05,61 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:05,67 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:05,71 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:05,105 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:05,112 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:04,784 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:04,788 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:04,823 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:04,830 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.388s.
250514-14:05:05,12 nipype.workflow INFO:
No single-band-reference found for sub-BMSCP010V20_ses-02_task-rest_run-05_bold.nii.gz.
250514-14:05:05,61 nipype.workflow INFO:
Stage 1: Adding HMC boldref workflow
250514-14:05:05,67 nipype.workflow INFO:
Stage 2: Adding motion correction workflow
250514-14:05:05,71 nipype.workflow INFO:
Stage 3: Adding coregistration boldref workflow
250514-14:05:05,105 nipype.workflow WARNING:
T2w intermediate for FSL is not implemented, registering with T1w instead.
250514-14:05:05,112 nipype.workflow IMPORTANT:
BOLD series will be slice-timing corrected to an offset of 0.389s.
250514-14:05:05,409 nipype.workflow CRITICAL:
Cannot run nibabies. Missing dependencies:
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)
* c3d_affine_tool (Interface: C3dAffineTool)Add any additional information or context about the problem here.
I'm mounting a path called /filter_files, which should contain a BIDS filter file for each subject in the dataset; the ${SCRIPT_DIR} variable will consistently store the directory containing this script, which also contains the source directory mounted as /filter_files.