fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
240822-12:47:25,980 nipype.workflow ERROR:
Node summary failed to run on host hos70297.
240822-12:47:25,991 nipype.workflow ERROR:
Saving crash info to /data/derivatives/hcph-fmriprep/sub-001/log/20240822-124208_5483f5a8-f287-4bb8-8b23-ef751ac483b3/crash-20240822-124725-oesteban-summary-669e3d14-97b8-467e-9b12-2998f1508fb7.txt
Traceback (most recent call last):
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
self.procs[jobid].run(updatehash=updatehash)
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 497, in run
self._get_hashval()
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 548, in _get_hashval
self._get_inputs()
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 619, in _get_inputs
self.set_input(key, deepcopy(output_value))
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/nipype/pipeline/engine/nodes.py", line 312, in set_input
setattr(self.inputs, parameter, deepcopy(val))
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/nipype/interfaces/base/traits_extension.py", line 424, in validate
value = super(MultiObject, self).validate(objekt, name, newvalue)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/traits/trait_types.py", line 2699, in validate
return TraitListObject(self, object, name, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/traits/trait_list_object.py", line 582, in __init__
super().__init__(
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/traits/trait_list_object.py", line 213, in __init__
super().__init__(self.item_validator(item) for item in iterable)
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/traits/trait_list_object.py", line 213, in <genexpr>
super().__init__(self.item_validator(item) for item in iterable)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/traits/trait_list_object.py", line 865, in _item_validator
return trait_validator(object, self.name, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/traits/trait_handlers.py", line 873, in validate
return self.slow_validate(object, name, value)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/traits/trait_handlers.py", line 881, in slow_validate
self.error(object, name, value)
File "/home/oesteban/.miniconda3/envs/fmriprep/lib/python3.11/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: Each element of the 'bold' trait of a SubjectSummaryInputSpec instance must be a pathlike object or string representing an existing file or a list of items which are a pathlike object or string representing an existing file, but a value o
f ['/data/datasets/hcph/sub-001/ses-pilot20103060/func/sub-001_ses-pilot20103060_task-rest_dir-LR_echo-1_part-mag_bold.nii.gz', '/data/datasets/hcph/sub-001/ses-pilot20103060/func/sub-001_ses-pilot20103060_task-rest_dir-LR_echo-2_part-mag_bold.nii.gz', '/data/datasets/h
cph/sub-001/ses-pilot20103060/func/sub-001_ses-pilot20103060_task-rest_dir-LR_echo-3_part-mag_bold.nii.gz'] <class 'list'> was specified.
Error setting node input:
Node: summary
input: bold
results_file: /home/oesteban/tmp/hcph-fmriprep/work/fmriprep_24_1_wf/sub_001_wf/bidssrc/result_bidssrc.pklz
value: [['/data/datasets/hcph/sub-001/ses-001/func/sub-001_ses-001_task-bht_dir-LR_echo-1_part-mag_bold.nii.gz', '/data/datasets/hcph/sub-001/ses-001/func/sub-001_ses-001_task-bht_dir-LR_echo-2_part-mag_bold.nii.gz', '/data/datasets/hcph/sub-001/ses-001/func/sub-001_ses
-001_task-bht_dir-LR_echo-3_part-mag_bold.nii.gz', '/data/datasets/hcph/sub-001/ses-001/func/sub-001_ses-001_task-bht_dir-LR_echo-4_part-mag_bold.nii.gz'], ['/data/datasets/hcph/sub-001/ses-001/func/sub-001_ses-001_task-qct_dir-LR_echo-1_part-mag_bold.nii.gz', '/data/da
tasets/hcph/sub-001/ses-001/func/sub-001_ses-001_task-qct_dir-LR_echo-2_part-mag_bold.nii.gz', '/data/datasets/hcph/sub-001/ses-001/func/sub-001_ses-001_task-qct_dir-LR_echo-3_part-mag_bold.nii.gz', '/data/datasets/hcph/sub-001/ses-001/func/sub-001_ses-001_task-qct_dir-
LR_echo-4_part-mag_bold.nii.gz'], ...
...
...
When creating this crashfile, the results file corresponding
to the node could not be found.
Additional information / screenshots
Datalad without fetched files. Can submit full log output.
What happened?
It seems that the workflow tries to execute the BOLD summary in
--anat-onlymode.This is generally okay, but in my case, I have a datalad dataset where the bold data has not been downloaded yet and therefore, this node fails.
What command did you use?
What version of fMRIPrep are you running?
master
How are you running fMRIPrep?
Local installation ("bare-metal")
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
No
Please copy and paste any relevant log output.
Additional information / screenshots
Datalad without fetched files. Can submit full log output.