ASLPrep crashes when using sMRIPrep derivatives #573
Description
Summary
I am attempting to run ASLPrep (v. 25.0.0rc1; latest tag pulled from Dockerhub yesterday) with sMRIPrep outputs (unstable tag from Dockerhub pulled yesterday). I have two sessions of data that were collected on the same day but different scanners.
I ran sMRIPrep as follows:
export APPTAINERENV_TEMPLATEFLOW_HOME=/opt/templateflow
apptainer run --containall \
-B $PWD/nifti:/data:ro \
-B $PWD/derivatives/smriprep_latest:/output \
-B /groups/adamraikes/license.txt:/license.txt \
-B /groups/adamraikes/templateflow:/opt/templateflow \
-B /tmp:/tmp \
/groups/adamraikes/singularity_images/smriprep_unstable.sif \
/data /output participant \
--participant-label 106 \
--sub-anatomical-reference sessionwise \
--output-spaces MNI152NLin6Asym:res-native MNI152NLin2009cAsym:res-1 fsaverage:den-10k \
--fs-license-file /license.txt \
--cifti-output 170k \
-w /output/scratch
Everything outputs, no issues. Here's the call for ASLPrep
apptainer run --containall \
-B $PWD/derivatives/smriprep_latest:/smriprep \
-B /groups/adamraikes/templateflow:/opt/templateflow \
-B $PWD/nifti:/data:ro \
-B $PWD/derivatives/aslprep:/output \
-B /tmp:/tmp \
-B /groups/adamraikes/license.txt:/license.txt \
/groups/adamraikes/singularity_images/aslprep_latest.sif \
/data /output participant \
--participant-label 106 \
--fs-license-file /license.txt \
--level full \
-w /output/scratch \
--derivatives smriprep=/smriprep \
--output-spaces MNI152NLin2009cAsym:res-1 \
--cifti-output 170k
Which yields:
250814-10:02:22,595 nipype.workflow IMPORTANT:
Running ASLPrep version 25.0.0rc1
License NOTICE ##################################################
ASLPrep 25.0.0rc1
Copyright 2023 The PennLINC Team and the NiPreps Developers.
This product is primarily developed by the PennLINC team,
but it is also a part of the NiPreps community.
This product includes software developed by
the NiPreps Community (https://nipreps.org/).
Portions of this software were developed at the Department of
Psychology at Stanford University, Stanford, CA, US.
This software is also distributed as a Docker container image.
The bootstrapping file for the image ("Dockerfile") is licensed
under the MIT License.
This software may be distributed through an add-on package called
"Docker Wrapper" that is under the BSD 3-clause License.
#################################################################
250814-10:02:23,110 nipype.workflow IMPORTANT:
Building ASLPrep's workflow:
* BIDS dataset path: /data.
* Participant list: ['106'].
* Run identifier: 20250814-100207_117153e0-e4da-4027-ba0e-bdd36d7d8ef5.
* Output spaces: MNI152NLin2009cAsym:res-1.
* Searching for derivatives: {'smriprep': PosixPath('/smriprep')}.
* Pre-run FreeSurfer's SUBJECTS_DIR: /output/sourcedata/freesurfer.
250814-10:02:30,69 nipype.workflow INFO:
ANAT Found preprocessed T1w - skipping Stage 1
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/interfaces/base/traits_extension.py", line 129, in validate
value = Path(value) # Use pathlib's validation
^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/pathlib.py", line 871, in __new__
self = cls._from_parts(args)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/pathlib.py", line 509, in _from_parts
drv, root, parts = self._parse_args(args)
^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/pathlib.py", line 493, in _parse_args
a = os.fspath(a)
^^^^^^^^^^^^
TypeError: expected str, bytes or os.PathLike object, not list
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/opt/conda/envs/aslprep/lib/python3.11/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/opt/conda/envs/aslprep/lib/python3.11/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/cli/workflow.py", line 101, in build_workflow
retval['workflow'] = init_aslprep_wf()
^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 69, in init_aslprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/aslprep/workflows/base.py", line 277, in init_single_subject_wf
anat_fit_wf = init_anat_fit_wf(
^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/niworkflows/engine/splicer.py", line 21, in _tag
node = func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/smriprep/workflows/anatomical.py", line 818, in init_anat_fit_wf
anat_validate.inputs.in_file = precomputed['t1w_preproc']
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/interfaces/base/traits_extension.py", line 330, in validate
value = super(File, self).validate(objekt, name, value, return_pathlike=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/nipype/interfaces/base/traits_extension.py", line 131, in validate
self.error(objekt, name, str(value))
File "/opt/conda/envs/aslprep/lib/python3.11/site-packages/traits/base_trait_handler.py", line 74, in error
raise TraitError(
traits.trait_errors.TraitError: The 'in_file' trait of a _ValidateImageInputSpec instance must be a pathlike object or string representing an existing file, but a value of "['/smriprep/smriprep/sub-106/ses-CIMA/anat/sub-106_ses-CIMA_run-001_desc-preproc_T1w.nii.gz', '/smriprep/smriprep/sub-106/ses-SKYRA/anat/sub-106_ses-SKYRA_run-001_desc-preproc_T1w.nii.gz']" <class 'str'> was specified.
I tried using a BIDS filter (perhaps I didn't specify it correctly) but got the same error.