Hi, I’m trying to run ASLPrep but it keeps failing to identify the m0 file, even though I’ve ensured the ‘IntendedFor’ file points to it. My m0 is separate, and I even added ‘M0Type = Separate’, but I keep receiving the same error.
Command used (and if a helper script was used, a link to the helper script or the command generated): command used to run it
apptainer run --cleanenv \
-B $PWD:/data \
-B $HOME/aslprep_out:/out \
$HOME/aslprep/aslprep-25.1.0.sif \
/data /out participant \
--participant-label 4028 \
--fs-license-file /home/cic/murrub/aslprep/license.txt \
--skip_bids_validation #used this later thinking it might help
Version:
25.1.0
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer
Data formatted according to a validatable standard? Please provide the output of the validator:
BIDS Validated
Relevant log outputs (up to 20 lines):
Running ASLPrep version 25.1.0
License NOTICE ##################################################
ASLPrep 25.1.0
Copyright 2023 The PennLINC Team and the NiPreps Developers.
This product is primarily developed by the PennLINC team,
but it is also a part of the NiPreps community.
This product includes software developed by
the NiPreps Community (https://nipreps.org/).
Portions of this software were developed 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 software may be distributed through an add-on package called
"Docker Wrapper" that is under the BSD 3-clause License.
#################################################################
251125-23:04:24,50 nipype.workflow IMPORTANT:
Building ASLPrep's workflow:
* BIDS dataset path: /data.
* Participant list: ['4028'].
* Run identifier: 20251125-230416_76be52db-d863-42c5-b1ba-90511e7b1c98.
* Output spaces: MNI152NLin2009cAsym:res-native.
* Pre-run FreeSurfer's SUBJECTS_DIR: /out/sourcedata/freesurfer.
251125-23:04:24,219 nipype.workflow INFO:
ANAT Stage 1: Adding template workflow
251125-23:04:24,528 nipype.workflow INFO:
ANAT Stage 2: Preparing brain extraction workflow
251125-23:04:24,581 nipype.workflow INFO:
ANAT Stage 3: Preparing segmentation workflow
251125-23:04:24,583 nipype.workflow INFO:
ANAT Stage 4: Preparing normalization workflow for ['MNI152NLin2009cAsym']
251125-23:04:24,590 nipype.workflow INFO:
ANAT Stage 5: Preparing surface reconstruction workflow
251125-23:04:24,600 nipype.workflow INFO:
ANAT Stage 6: Preparing mask refinement workflow
251125-23:04:24,601 nipype.workflow INFO:
ANAT Stage 7: Creating T2w template
251125-23:04:24,604 nipype.workflow INFO:
ANAT Stage 8: Creating GIFTI surfaces for ['white', 'pial', 'midthickness', 'sphere_reg', 'sphere']
251125-23:04:24,613 nipype.workflow INFO:
ANAT Stage 8: Creating GIFTI metrics for ['thickness', 'sulc']
251125-23:04:24,616 nipype.workflow INFO:
ANAT Stage 8a: Creating cortical ribbon mask
251125-23:04:24,618 nipype.workflow INFO:
ANAT Stage 9: Creating fsLR registration sphere
251125-23:04:24,620 nipype.workflow INFO:
ANAT Stage 10: MSM-Sulc disabled
251125-23:04:24,620 nipype.workflow INFO:
ANAT Stage 11: Creating cortical surface mask
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/envs/aslprep/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/opt/conda/envs/aslprep/lib/python3.11/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/cli/workflow.py", line 101, in build_workflow
retval['workflow'] = init_aslprep_wf()
^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 69, in init_aslprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 798, in init_single_subject_wf
asl_wf = init_asl_wf(
^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/asl/base.py", line 211, in init_asl_wf
run_data = collect_run_data(layout, asl_file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/utils/bids.py", line 106, in collect_run_data
raise FileNotFoundError(f'M0 file for {asl_file} not found.')
FileNotFoundError: M0 file for /data/sub-4028/ses-01/perf/sub-4028_ses-01_asl.nii.gz not found.
