Summary of what happened:
I am trying out the custom confound regressor strategy (which only uses fMRIprep regressors) with the latest release candidate. I ran into a problem that I didn’t have with the previous version 0.8.3 (it all ran through with the older version with the default -p)
Command used (and if a helper script was used, a link to the helper script or the command generated):
apptainer run --cleanenv xcp-d_v0.10.0rc1.sif input_dir output_dir participant
–participant_label 01
–mode linc
–nuisance-regressors output_dir/custom.yaml
–dummy-scans 4
–fs-license-file /project/mri/license.txt
Version:
0.10.0rc1
Relevant log outputs (up to 20 lines):
2024-10-10 20:25:15,493 [ WARNING] WARNING: `sentry_sdk.Hub` is deprecated and will be removed in a future major release. Please consult our 1.x to 2.x migration guide for details on how to migrate `Hub` usage to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x
2024-10-10 20:25:15,733 [ WARNING] Framewise displacement-based scrubbing is disabled. The following parameters will have no effect:
--min-time
2024-10-10 20:25:26,902 [ WARNING] WARNING: sentry_sdk.configure_scope is deprecated and will be removed in the next major version. Please consult our migration guide to learn how to migrate to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x#scope-configuring
2024-10-10 20:25:39,324 [ WARNING] WARNING: `sentry_sdk.Hub` is deprecated and will be removed in a future major release. Please consult our 1.x to 2.x migration guide for details on how to migrate `Hub` usage to the new API: https://docs.sentry.io/platforms/python/migration/1.x-to-2.x
241010-20:25:41,509 nipype.workflow IMPORTANT:
Running XCP-D version 0.10.0rc1
2024-10-10 20:25:41,509 [IMPORTANT] Running XCP-D version 0.10.0rc1
241010-20:25:41,512 nipype.workflow WARNING:
Previous output generated by version 0+unknown found.
2024-10-10 20:25:41,512 [ WARNING] Previous output generated by version 0+unknown found.
241010-20:25:45,253 nipype.workflow IMPORTANT:
Building XCP-D's workflow:
* Preprocessing derivatives path: /xdisk/jandrewshanna/yuhua/ACHV/MRIS/derivatives.
* Participant list: ['74'].
* Run identifier: 20241010-202511_2a158dae-8a8c-4cb3-9a40-b13d6df5e31c.
* Searching for derivatives and atlases: {'xcpdatlases': PosixPath('/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases'), 'xcpd4s': PosixPath('/AtlasPack')}.
2024-10-10 20:25:45,253 [IMPORTANT] Building XCP-D's workflow:
* Preprocessing derivatives path: /xdisk/jandrewshanna/yuhua/ACHV/MRIS/derivatives.
* Participant list: ['74'].
* Run identifier: 20241010-202511_2a158dae-8a8c-4cb3-9a40-b13d6df5e31c.
* Searching for derivatives and atlases: {'xcpdatlases': PosixPath('/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/data/atlases'), 'xcpd4s': PosixPath('/AtlasPack')}.
Process Process-2:
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 127, in init_single_subject_wf
subj_data = collect_data(
File "/usr/local/miniconda/lib/python3.10/site-packages/xcp_d/utils/bids.py", line 209, in collect_data
raise FileNotFoundError(
FileNotFoundError: No BOLD data found in allowed spaces (fsLR).
Query: {'datatype': 'func', 'desc': ['preproc', None], 'suffix': 'bold', 'extension': '.dtseries.nii', 'space': 'fsLR'}
Found files: