Hi, I installed the newest fmriprep (v20.0.1rc) in my servers for getting processed data in fsLR-32k space as cifti output. I found this version no long contained fsLR in --output-space but allowed CIFTI output when using --cifti-output and will compliant with HCP grayordinate space (cortex in fsLR, subcortical in MNI152NLin6Asym). (Issue 1887)
However, after running command only with --cifti-output: fmriprep test_fmriprep test_fmriprep_output participant -w work -cifti-output , I got one another error as
Process Process-2:
Traceback (most recent call last):
File “/usr/local/neurosoft/miniconda3/lib/python3.6/multiprocessing/process.py”, line 258, in _bootstrap
self.run()
File “/usr/local/neurosoft/miniconda3/lib/python3.6/multiprocessing/process.py”, line 93, in run
self._target(*self._args, **self._kwargs)
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 676, in build_workflow
work_dir=str(work_dir),
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/fmriprep/workflows/base.py”, line 267, in init_fmriprep_wf
use_syn=use_syn,
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/fmriprep/workflows/base.py”, line 623, in init_single_subject_wf
use_syn=use_syn,
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/fmriprep/workflows/bold/base.py”, line 945, in init_func_preproc_wf
repetition_time=metadata[‘RepetitionTime’])
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/fmriprep/workflows/bold/resampling.py”, line 744, in init_bold_grayords_wf
for hemi in ‘LR’
File “/nfs/s2/userhome/huangtaicheng/.local/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py”, line 425, in validate
value = super(MultiObject, self).validate(objekt, name, newvalue)
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/traits/trait_types.py”, line 2573, in validate
return TraitListObject(self, object, name, value)
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2474, in init
raise excp
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2466, in init
value = [validate(object, name, val) for val in value]
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 2466, in
value = [validate(object, name, val) for val in value]
File “/nfs/s2/userhome/huangtaicheng/.local/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py”, line 329, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
File “/nfs/s2/userhome/huangtaicheng/.local/lib/python3.6/site-packages/nipype/interfaces/base/traits_extension.py”, line 134, in validate
self.error(objekt, name, str(value))
File “/usr/local/neurosoft/miniconda3/lib/python3.6/site-packages/traits/trait_handlers.py”, line 236, in error
object, name, self.full_info(object, name, value), value
traits.trait_errors.TraitError: Each element of the ‘current_sphere’ trait of a DynamicTraitedSpec instance must be a pathlike object or string representing an existing file, but a value of ‘[]’ <class ‘str’> was specified.
I guess this problem is due to configurations of fsLR template in my servers. I have set TEMPLATEFLOW_HOME in my servers but it looks useless.
Could someone give me some suggestions on this problem? Or if any lower versions of fmriprep could generate processed data in fsLR-32k space as cifti output, it would also be a great help to me.
Thanks for help in advance,
Taicheng