Using fmriprep 23.1.4 with –anat-derivatives after doing anat-only, but now running into issues:
Its looking for the file: /dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID001804/ses-20/fmap/sub-SID001804_ses-20_acq-mb8_dir-ap_epi.nii.gz, but I don’t have such a file, I have instead:
sub-SID001804_ses-20_acq-mb8_dir-ap_run-01_epi.nii.gz
sub-SID001804_ses-20_acq-mb8_dir-ap_run-02_epi.nii.gz
(The participant got up in the middle of the session to go to the bathroom, so two fieldmaps were taken).
The fmriprep command was as follows:
singularity run
–cleanenv
-B {MAINDIR}:{MAINDIR}
-B {BIDSDIR},{BIDSDIR},{PREPROCDIR},{SCRATCHDIR},{OUTDIR} \ -B /optnfs/freesurfer:/optnfs/freesurfer {IMAGE}
{BIDSDIR} {OUTDIR} participant
–participant_label {SUBJ} \ --ignore slicetiming \ --resource-monitor \ --bold2t1w-dof 9 \ --dummy-scans 6 \ --notrack \ --nprocs 32 \ --omp-nthreads 5 \ --nthreads 32 \ --mem_mb 280000 \ --fs-license-file /optnfs/freesurfer/6.0.0/license.txt \ --cifti-output 91k \ --output-spaces T1w MNI152NLin2009cAsym fsnative fsaverage6 \ --skull-strip-fixed-seed \ -w {WORKDIR}
–random-seed 42
–stop-on-first-crash
–force-syn
–use-syn-sdc
–force-bbr
–anat-derivatives {OUTDIR}/sub-{SUBJ}/anat
–skip_bids_validation
–bids-database-dir ${BIDSDIR}/1080_wasabi_BIDSLayout
230929-21:51:12,742 nipype.workflow WARNING:
Attempted to access pre-existing anatomical derivatives at </dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/derivatives/fmriprep/sub-SID001804/anat>, however not all expectations of fMRIPrep were met (for participant , spaces <MNI152NLin2009cAsym, MNI152NLin6Asym>, reconall ).
Process Process-2:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/multiprocessing/process.py”, line 314, in _bootstrap
self.run()
File “/opt/conda/envs/fmriprep/lib/python3.10/multiprocessing/process.py”, line 108, in run
self._target(*self._args, **self._kwargs)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/workflow.py”, line 115, in build_workflow
retval[“workflow”] = init_fmriprep_wf()
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/workflows/base.py”, line 93, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/workflows/base.py”, line 396, in init_single_subject_wf
fmap_estimators = find_estimators(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/sdcflows/utils/wrangler.py”, line 392, in find_estimators
fmapfile = fm.FieldmapFile(fmap.path, metadata=fmap.get_metadata())
File “”, line 11, in init
__attr_validator_path(self, __attr_path, self.path)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/sdcflows/fieldmaps.py”, line 203, in check_path
raise FileNotFoundError(
FileNotFoundError: File path </dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID001804/ses-20/fmap/sub-SID001804_ses-20_acq-mb8_dir-ap_epi.nii.gz> does not exist, is a broken link, or it is not a file