Summary of what happened:
I cant run ASLprep using included M0scan images.
I always have the following problem, after two minutes of aslprep running normally.
I configured all the .json files with .tsv files, which are formatted with reference to the bids standard.Also I tried changing the working path and that didn’t solve the problem.
</traits.trait_errors.TraitError: The 'm0scan_mat_files' trait of a _CombineMotionParametersInputSpec instance must be a list of items which are a pathlike object or string representing an existing file or None, but a value of '/wd/aslprep_wf/single_subject_53_wf/asl_preproc_acq_DE_wf/asl_hmc_wf/mcflirt_m0scan/sub-53_acq-DE_asl_reduced_m0scan_mcf.nii.gz.mat/MAT_0000' <class 'str'> was specified.>
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv \
-B $aslprep_wd:/wd \
-B $BidsDir:/BIDS \
-B $aslprep_output:/output \
-B $fs_license:/fs_license \
-B $fs_dir:/fs_dir \
-B $templateflow:$templateflow \
/ibmgpfs/****/****/.singularity/aslprep-0.4.0.simg \
/BIDS /output participant \
--participant_label ${subj} \
-w /wd \
--fs-license-file /fs_license/license.txt \
--output-spaces T1w MNI152NLin6Asym \
--notrack --verbose \
--skip-bids-validation \
--stop-on-first-crash \
--resource-monitor \
--basil \
--ignore sbref fieldmaps \
--use-syn-sdc \
--nthreads $nthreads \
--omp-nthreads $nthreads \
--mem-mb 160000 \
here is part of my .json
"ArterialSpinLabelingType":"PCASL",
"PostLabelingDelay":1.99,
"BackgroundSuppression":"false",
"M0Type":"Included",
"TotalAcquiredPairs":135,
"LabelingDuration":0.7
and _aslcontext.tsv
volume_type
m0scan
label
control
label
control
Version:
aslprep-0.4.0.simg
Environment (Docker, Singularity, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
Relevant log outputs (up to 20 lines):
nipype.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: aslprep_wf.single_subject_53_wf.asl_preproc_acq_DE_wf.asl_hmc_wf.combine_motpars
Interface: aslprep.interfaces.utility.CombineMotionParameters
Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.8/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/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 342, in is_cached
hashed_inputs, hashvalue = self._get_hashval()
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 548, in _get_hashval
self._get_inputs()
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 619, in _get_inputs
self.set_input(key, deepcopy(output_value))
File "/usr/local/miniconda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 312, in set_input
setattr(self.inputs, parameter, deepcopy(val))
File "/usr/local/miniconda/lib/python3.8/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'm0scan_mat_files' trait of a _CombineMotionParametersInputSpec instance must be a list of items which are a pathlike object or string representing an existing file or None, but a value of '/wd/aslprep_wf/single_subject_53_wf/asl_preproc_acq_DE_wf/asl_hmc_wf/mcflirt_m0scan/sub-53_acq-DE_asl_reduced_m0scan_mcf.nii.gz.mat/MAT_0000' <class 'str'> was specified.