I renamed some T1 files because they were not consistent with our current naming scheme, but for some reason this is leading to crashes when I attempt to rerun fmriprep 23.1.4 with the --anat-only flag.
singularity run
–cleanenv
-B {MAINDIR}:{MAINDIR}
-B {BIDSDIR},{PREPROCDIR},{SCRATCHDIR} \ -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 8 \ --nthreads 12 \ --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
–skip_bids_validation
–anat-only
–bids-database-dir ${BIDSDIR}/1080_wasabi_BIDSLayout
exception calling callback for <Future at 0x2b714de0c820 state=finished raised FileNotFoundError>
concurrent.futures.process._RemoteTraceback:
“”"
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 67, in run_node
result[“result”] = node.run(updatehash=updatehash)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 497, in run
self._get_hashval()
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 548, in _get_hashval
self._get_inputs()
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 619, in _get_inputs
self.set_input(key, deepcopy(output_value))
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 312, in set_input
setattr(self.inputs, parameter, deepcopy(val))
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py”, line 424, in validate
value = super(MultiObject, self).validate(objekt, name, newvalue)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/trait_types.py”, line 2699, in validate
return TraitListObject(self, object, name, value)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/trait_list_object.py”, line 582, in init
super().init(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/trait_list_object.py”, line 213, in init
super().init(self.item_validator(item) for item in iterable)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/trait_list_object.py”, line 213, in
super().init(self.item_validator(item) for item in iterable)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/trait_list_object.py”, line 865, in _item_validator
return trait_validator(object, self.name, value)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py”, line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py”, line 135, in validate
self.error(objekt, name, str(value))
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/traits/base_trait_handler.py”, line 74, in error
raise TraitError(
traits.trait_errors.TraitError: Each element of the ‘t1w_list’ trait of a _TemplateDimensionsInputSpec instance must be a pathlike object or string representing an existing file, but a value of ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-21/anat/sub-SID000002_ses-21_acq-MPRAGEXp3X08mm_run-06_T1w.nii.gz’ <class ‘str’> was specified.Error setting node input:
Node: anat_ref_dimensions
input: t1w_list
results_file: /scratch/f003z4j/fmriprep-work/work-SID000002/fmriprep_23_1_wf/single_subject_SID000002_wf/bidssrc/result_bidssrc.pklz
value: [‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-01/anat/sub-SID000002_ses-01_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-01/anat/sub-SID000002_ses-01_acq-MPRAGEXp3X08mm_run-02_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-06/anat/sub-SID000002_ses-06_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-06/anat/sub-SID000002_ses-06_acq-MPRAGEXp3X08mm_run-02_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-08/anat/sub-SID000002_ses-08_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-08/anat/sub-SID000002_ses-08_acq-MPRAGEXp3X08mm_run-02_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-10/anat/sub-SID000002_ses-10_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-10/anat/sub-SID000002_ses-10_acq-MPRAGEXp3X08mm_run-02_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-15/anat/sub-SID000002_ses-15_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-15/anat/sub-SID000002_ses-15_acq-MPRAGEXp3X08mm_run-02_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-17/anat/sub-SID000002_ses-17_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-18/anat/sub-SID000002_ses-18_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-18/anat/sub-SID000002_ses-18_acq-MPRAGEXp3X08mm_run-02_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-19/anat/sub-SID000002_ses-19_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-20/anat/sub-SID000002_ses-20_acq-MPRAGEXp3X08mm_run-01_T1w.nii.gz’, ‘/dartfs-hpc/rc/lab/C/CANlab/labdata/data/WASABI/1080_wasabi/sub-SID000002/ses-21/anat/sub-SID000002_ses-21_acq-MPRAGEXp3X08mm_run-06_T1w.nii.gz’]During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/process.py”, line 246, in _process_worker
r = call_item.fn(*call_item.args, **call_item.kwargs)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 70, in run_node
result[“result”] = node.result
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py”, line 223, in result
return _load_resultfile(
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py”, line 291, in load_resultfile
raise FileNotFoundError(results_file)
FileNotFoundError: /scratch/f003z4j/fmriprep-work/work-SID000002/fmriprep_23_1_wf/single_subject_SID000002_wf/anat_preproc_wf/anat_template_wf/anat_ref_dimensions/result_anat_ref_dimensions.pklz
“”"The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File “/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/_base.py”, line 342, in _invoke_callbacks
callback(self)
File “/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py”, line 159, in _async_callback
result = args.result()
File “/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/_base.py”, line 451, in result
return self.__get_result()
File “/opt/conda/envs/fmriprep/lib/python3.10/concurrent/futures/_base.py”, line 403, in __get_result
raise self._exception
FileNotFoundError: /scratch/f003z4j/fmriprep-work/work-SID000002/fmriprep_23_1_wf/single_subject_SID000002_wf/anat_preproc_wf/anat_template_wf/anat_ref_dimensions/result_anat_ref_dimensions.pklz