Summary of what happened:
Trying to run XCP on a single scan preprocessed with fMRIprep 23.2.0. Running into an error about a missing “brain_mask_trans” file in the work directory. I have not seen this file name before and cannot find much about it online. I previously ran XCP 0.7.? on this dataset with no issues.
Command used (and if a helper script was used, a link to the helper script or the command generated):
+ export FREESURFER_HOME=/Users/ahalab/Documents
+ FREESURFER_HOME=/Users/ahalab/Documents
+ export HOME_DIR=/Volumes/Seagate/
+ HOME_DIR=/Volumes/Seagate/
+ for SES in '{1..1}'
+ for RUN in '{1..1}'
+ docker run --rm -it -v /Volumes/Seagate/BIDS/derivatives:/fmriprep:ro -v /Volumes/Seagate/work_xcp:/work:rw -v /Volumes/Seagate/BIDS/derivatives/xcp_d:/out:rw -v /Users/ahalab/Documents/license.txt:/out/fs_license:rw -v /Volumes/Seagate/BIDS/bids_filters/bids_filter_ses1_run1.json:/out/bids_filter.json:rw pennlinc/xcp_d:latest /fmriprep /out participant -w /work --fs-license-file /out/fs_license --mem-gb 15 --low-mem --bids-filter-file /out/bids_filter.json --participant_label AEON101 --mode abcd --smoothing 6 --combine-runs n --create-matrices all --motion-filter-type lp --band-stop-min 6 --file-format nifti --warp-surfaces-native2std n --min-time 0 --abcc-qc n
Version:
0.10.1
Environment (Docker, Singularity / Apptainer, custom installation):
Docker
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS valid
Relevant log outputs (up to 20 lines):
2024-12-11 14:21:42,110 [ INFO] Loading atlas: 4S756Parcels
241211-14:21:42,110 nipype.workflow INFO:
Loading atlas: 4S856Parcels
2024-12-11 14:21:42,110 [ INFO] Loading atlas: 4S856Parcels
241211-14:21:42,110 nipype.workflow INFO:
Loading atlas: 4S956Parcels
2024-12-11 14:21:42,110 [ INFO] Loading atlas: 4S956Parcels
241211-14:21:42,209 nipype.interface INFO:
stderr 2024-12-11T14:21:42.209365:Illegal instruction
2024-12-11 14:21:42,209 [ INFO] stderr 2024-12-11T14:21:42.209365:Illegal instruction
Process Process-2:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.10/site-packages/nibabel/loadsave.py", line 101, in load
stat_result = os.stat(filename)
FileNotFoundError: [Errno 2] No such file or directory: '/work/sub_AEON101_wf/sub-AEON101_ses-001_space-MNI152NLin2009cAsym_desc-brain_mask_trans.nii.gz'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/usr/local/miniconda/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/cli/workflow.py", line 100, in build_workflow
retval['workflow'] = init_xcpd_wf()
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/base.py", line 81, in init_xcpd_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/workflows/base.py", line 376, in init_single_subject_wf
warp_brainmask_results = warp_brainmask.run(
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/interfaces/ants.py", line 216, in _run_interface
runtime = super()._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.10/site-packages/niworkflows/interfaces/fixes.py", line 68, in _run_interface
_copyxform(
File "/usr/local/miniconda/lib/python3.10/site-packages/niworkflows/utils/images.py", line 79, in _copyxform
resampled = nb.load(out_image, mmap=False)
File "/usr/local/miniconda/lib/python3.10/site-packages/nibabel/loadsave.py", line 103, in load
raise FileNotFoundError(f"No such file or no access: '{filename}'")
FileNotFoundError: No such file or no access: '/work/sub_AEON101_wf/sub-AEON101_ses-001_space-MNI152NLin2009cAsym_desc-brain_mask_trans.nii.gz'
Screenshots / relevant information:
I’m running this on an external hard drive. I want to use abcd or hcbd mode so that I can retain the original TR indices of a complete time series and discard interpolated volumes manually. The censored output of linc mode won’t give me what I need for subsequent analysis. However, I tried running linc and hbcd mode and got the same error. I also copied a limited portion of my BIDS directory onto my internal HD and got the same error.
. I ran fMRIprep on a different laptop with an Intel chip. I can try fMRIprep on this laptop if it’s helpful. I’ll see if I can just run it on my Intel laptop, which I was trying to avoid. If the testing isn’t too involved I’m happy to help and try to run it here.