Summary of what happened:
I keep getting this error during the resample_skulled_to_reference node:
traits.trait_errors.TraitError: The ‘output_image’ trait of an ApplyTransformsOutputSpec instance must be a pathlike object or string representing an existing file, but a value of ‘/tmp/work/qsiprep_wf/single_subject_001_wf/anat_preproc_wf/pad_anat_reference_wf/resample_skulled_to_reference/sub-001_T1w_lps_trans.nii.gz’ <class ‘str’> was specified.
Additional error output is below. I’ve tried with two datasets collected on two different scanners with the same result. Is this a possible bug? I attached a json (as a txt) for one of my scans and the crash log.
sub-cima_acq-16mm_dir-RL_run-1_dwi.txt (3.0 KB)
crash-20240413-145358-root-resample_skulled_to_reference-741a0ab4-047b-40c5-9d9f-514649894042.txt (3.6 KB)
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run --rm -it -v /Users/joseph.orr/Documents/Orr_Diffusion_PILOT/bids/:/data:ro -v /Users/joseph.orr/Documents/Orr_Diffusion_PILOT/derivatives:/out pennbbl/qsiprep:0.20.0 /data /out participant --output-resolution 1.2 --participant-label sub-001 --fs-license-file /out/license.txt
Version:
qsiprep v 0.20.0
Environment (Docker, Singularity / Apptainer, custom installation):
docker
Data formatted according to a validatable standard? Please provide the output of the validator:
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
bids-validator@1.8.4
1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
35 Files, 848MB MRI
2 - Subjects
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
Relevant log outputs (up to 20 lines):
Node resample_skulled_to_reference failed to run on host 4144e338150b.
240413-14:29:34,478 nipype.workflow ERROR:
Saving crash info to /out/qsiprep/sub-001/log/20240413-142855_eb85b3fc-3b95-4052-ba28-5381892b482e/crash-20240413-142934-root-resample_skulled_to_reference-ca69d006-c0cb-4cc4-a4e3-fc6b7d656063.txt
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node resample_skulled_to_reference.
Cmdline:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input /tmp/work/qsiprep_wf/single_subject_001_wf/anat_preproc_wf/anat_template_wf/anat_conform/mapflow/_anat_conform0/sub-001_T1w_lps.nii.gz --interpolation BSpline --output sub-001_T1w_lps_trans.nii.gz --reference-image /tmp/work/qsiprep_wf/single_subject_001_wf/anat_preproc_wf/pad_anat_reference_wf/prepare_synthstrip_reference/sub-001_T1w_lps_resample_autobox_SynthStripGrid.nii --transform identity
Stdout:
Stderr:
Illegal instruction
Traceback:
Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 453, in aggregate_outputs
setattr(outputs, key, val)
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 'output_image' trait of an ApplyTransformsOutputSpec instance must be a pathlike object or string representing an existing file, but a value of '/tmp/work/qsiprep_wf/single_subject_001_wf/anat_preproc_wf/pad_anat_reference_wf/resample_skulled_to_reference/sub-001_T1w_lps_trans.nii.gz' <class 'str'> was specified.