Hi, all. I’m getting this error when trying to run fmriprep on a few functional scans, a structural scan, and a couple of field maps.
Running fMRIPREP version 20.2.1:
* BIDS dataset path: /proj/mnhallqlab/studies/NeuroMAP/bids_just_064.
* Participant list: ['064'].
* Run identifier: 20210616-201633_7ac7dba1-476b-4ca6-bb6c-b93b4f77db77.
* Output spaces: MNI152NLin2009cAsym:res-native.
* Pre-run FreeSurfer's SUBJECTS_DIR: /proj/mnhallqlab/studies/NeuroMAP/MR_Proc/UNC/freesurfer.
210616-20:16:53,518 nipype.workflow INFO:
Using single-band reference file(s) sub-064_task-restPost_run-01_sbref.nii.gz.
210616-20:16:55,523 nipype.workflow IMPORTANT:
Slice-timing correction will be included.
Process Process-2:
Traceback (most recent call last):
File "/proj/mnhallqlab/sw/python-3.8.3/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/proj/mnhallqlab/sw/python-3.8.3/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/fmriprep/cli/workflow.py", line 82, in build_workflow
retval["workflow"] = init_fmriprep_wf()
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/fmriprep/workflows/base.py", line 64, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/fmriprep/workflows/base.py", line 304, in init_single_subject_wf
func_preproc_wf = init_func_preproc_wf(bold_file)
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/fmriprep/workflows/bold/base.py", line 814, in init_func_preproc_wf
carpetplot_wf = init_carpetplot_wf(
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/fmriprep/workflows/bold/confounds.py", line 471, in init_carpetplot_wf
resample_parc = pe.Node(ApplyTransforms(
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/nipype/interfaces/ants/base.py", line 75, in __init__
super(ANTSCommand, self).__init__(**inputs)
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 710, in __init__
super(CommandLine, self).__init__(**inputs)
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 191, in __init__
self.inputs.trait_set(**inputs)
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/traits/has_traits.py", line 1368, in trait_set
setattr(self, name, value)
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/proj/mnhallqlab/lab_resources/fmriprep_python/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'input_image' trait of a _FixTraitApplyTransformsInputSpec instance
must be a pathlike object or string representing an existing file, but a value of '[]' <class 'str'> was
specified.
I recently moved to a new university/HPC, and am getting this error while trying to run fmriprep for the first time at the new location; the script I’m running worked fine at the old location.
Any thoughts? Thanks!