Dear All,
I’ve tried running fMRIprep but run into a trait error right at the start. I’m not sure what that means. I have checked and all the data is in valid BIDS format and I am using the latest fMRIprep release (1.0.9).
The command I used was:
fmriprep /data/group/edu/faces/bids_root/ /data/group/edu/faces/derivatives/ participant -w /data/group/edu/faces/work/ --participant_label sub-01 -t faces --output-space {T1w} --write-graph --stop-on-first-crash
The error message:
180411-17:09:26,764 workflow IMPORTANT:
Running fMRIPREP version 1.0.9:
* BIDS dataset path: /data/group/edu/faces/bids_root.
* Participant list: ['01'].
* Run identifier: 20180411-170926_2d465c5c-b0d5-4ab2-b637-c1451b3d6ddb.
/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/grabbit/core.py:410: UserWarning: No valid root directory found for domain 'derivatives'. Falling back on the Layout's root directory. If this isn't the intended behavior, make sure the config file for this domain includes a 'root' key.
"'root' key." % config['name'])
180411-17:09:28,677 workflow IMPORTANT:
Creating bold processing workflow for "/data/group/edu/faces/bids_root/sub-01/func/sub-01_task-faces_bold.nii.gz" (0.02 GB / 180 TRs). Memory resampled/largemem=0.07/0.10 GB.
180411-17:09:29,216 workflow IMPORTANT:
Slice-timing correction will be included.
180411-17:09:29,244 workflow WARNING:
SDC: no fieldmaps found or they were ignored (/data/group/edu/faces/bids_root/sub-01/func/sub-01_task-faces_bold.nii.gz).
180411-17:09:48,552 workflow WARNING:
Error while checking node hash, forcing re-run. Although this error may not prevent the workflow from running, it could indicate a major problem. Please report a new issue at https://github.com/nipy/nipype/issues adding the following information:
Node: fmriprep_wf.single_subject_01_wf.summary
Interface: fmriprep.interfaces.reports.SubjectSummary
Traceback:
Traceback (most recent call last):
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 341, in _local_hash_check
cached, updated = self.procs[jobid].is_cached()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 310, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 504, in _get_hashval
self._get_inputs()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 547, in _get_inputs
self.set_input(key, deepcopy(output_value))
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 292, in set_input
setattr(self.inputs, parameter, deepcopy(val))
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/traits/trait_types.py", line 2338, in validate
self.error( object, name, value )
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/traits/trait_handlers.py", line 172, in error
value )
traits.trait_errors.TraitError: The 'bold' trait of a SubjectSummaryInputSpec instance must be a list of items which are any value, but a value of '/data/group/edu/faces/bids_root/sub-01/func/sub-01_task-faces_bold.nii.gz' <class 'str'> was specified.
Error setting node input:
Node: summary
input: bold
results_file: /data/group/edu/faces/work/fmriprep_wf/single_subject_01_wf/bidssrc/result_bidssrc.pklz
value: /data/group/edu/faces/bids_root/sub-01/func/sub-01_task-faces_bold.nii.gz
Traceback (most recent call last):
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 339, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 424, in run
cached, updated = self.is_cached()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 310, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 504, in _get_hashval
self._get_inputs()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 547, in _get_inputs
self.set_input(key, deepcopy(output_value))
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 292, in set_input
setattr(self.inputs, parameter, deepcopy(val))
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/traits/trait_types.py", line 2338, in validate
self.error( object, name, value )
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/traits/trait_handlers.py", line 172, in error
value )
traits.trait_errors.TraitError: The 'bold' trait of a SubjectSummaryInputSpec instance must be a list of items which are any value, but a value of '/data/group/edu/faces/bids_root/sub-01/func/sub-01_task-faces_bold.nii.gz' <class 'str'> was specified.
Error setting node input:
Node: summary
input: bold
results_file: /data/group/edu/faces/work/fmriprep_wf/single_subject_01_wf/bidssrc/result_bidssrc.pklz
value: /data/group/edu/faces/bids_root/sub-01/func/sub-01_task-faces_bold.nii.gz
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/software/system/fmriprep/1.0.9/bin/fmriprep", line 11, in <module>
sys.exit(main())
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/fmriprep/cli/run.py", line 274, in main
fmriprep_wf.run(**plugin_settings)
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/workflows.py", line 602, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 190, in run
self._send_procs_to_workers(updatehash=updatehash, graph=graph)
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 347, in _send_procs_to_workers
'traceback': traceback
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/base.py", line 227, in _clean_queue
raise RuntimeError("".join(result['traceback']))
RuntimeError: Traceback (most recent call last):
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/plugins/multiproc.py", line 339, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 424, in run
cached, updated = self.is_cached()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 310, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 504, in _get_hashval
self._get_inputs()
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 547, in _get_inputs
self.set_input(key, deepcopy(output_value))
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/niworkflows/nipype/pipeline/engine/nodes.py", line 292, in set_input
setattr(self.inputs, parameter, deepcopy(val))
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/traits/trait_types.py", line 2338, in validate
self.error( object, name, value )
File "/cns_zfs/system/u1604/fmriprep/1.0.9/lib/python3.6/site-packages/traits/trait_handlers.py", line 172, in error
value )
traits.trait_errors.TraitError: The 'bold' trait of a SubjectSummaryInputSpec instance must be a list of items which are any value, but a value of '/data/group/edu/faces/bids_root/sub-01/func/sub-01_task-faces_bold.nii.gz' <class 'str'> was specified.
Error setting node input:
Node: summary
input: bold
results_file: /data/group/edu/faces/work/fmriprep_wf/single_subject_01_wf/bidssrc/result_bidssrc.pklz
value: /data/group/edu/faces/bids_root/sub-01/func/sub-01_task-faces_bold.nii.gz
Does anyone know what is causing this? And what can I do to fix it?
Many thanks,
Jenni