Summary of what happened:
When I attempt to run the qsiprep-0.20.0 singularity image, it quickly crashes due to the following ‘TraitError’ error.
This seems very similar to this issue, which according to this thread was resolved with 0.20.0, but I’m still running into problems:
https://github.com/PennLINC/qsiprep/issues/648
I also have tried qsiprep-latest (i.e. qsiprep-0.20.1.dev0+geda84d5.d20240112), but I run into the same exact issue.
Please let me know if there’s any additional info you need.
Thanks,
Shane
Command used (and if a helper script was used, a link to the helper script or the command generated):
Here is the call I make to run the qsiprep singularity container:
singularity run --cleanenv \
-B $BIDS_DIR,$derivatives_DIR,$Work_DIR,${fsLicense}:${fsLicense} \
$qsiprep \
$BIDS_DIR $derivatives_DIR participant \
--participant_label ${SUBJECTS} \
--output-resolution 1.3 \
--work-dir /${Work_DIR} \
--fs-license-file ${fsLicense} \
--stop_on_first_crash
Version:
0.20.0
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity 3.7.0-1.el7
Data formatted according to a validatable standard? Please provide the output of the validator:
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/plugins/base.py", line 376, in _local_hash_check
cached, updated = self.procs[jobid].is_cached()
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 342, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 548, in _get_hashval
self._get_inputs()
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 590, in _get_inputs
outputs = _load_resultfile(results_fname).outputs
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/utils.py", line 293, in load_resultfile
result = loadpkl(results_file)
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/utils/filemanip.py", line 666, in loadpkl
raise e
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/utils/filemanip.py", line 643, in loadpkl
unpkl = pickle.loads(pkl_contents)
File "/usr/local/miniconda/lib/python3.10/site-packages/traits/has_traits.py", line 1410, in __setstate__
self.trait_set(trait_change_notify=trait_change_notify, **state)
File "/usr/local/miniconda/lib/python3.10/site-packages/traits/has_traits.py", line 1520, in trait_set
setattr(self, name, value)
File "/usr/local/miniconda/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 "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/base/traits_extension.py", line 135, in validate
self.error(objekt, name, str(value))
File "/usr/local/miniconda/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'template_file' trait of a _GetTemplateOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/usr/local/miniconda/lib/python3.8/site-packages/qsiprep/data/mni_1mm_t1w_lps.nii.gz' <class 'str'> was specified.