Summary of what happened:
Hi! I’m working on processing data using the mrtrix_multishell_msmt_ACT-hsvs recon workflow in QSIRecon. The pipeline begins the anatomical workflow, but crashes on node ds_fs_5tt_hsvs with this error: “ValueError: Could not build path with entities {‘subject’: ‘123’, ‘suffix’: ‘dseg’, ‘datatype’: ‘anat’, ‘extension’: ‘mif.gz’, ‘space’: ‘fsnative’, ‘desc’: ‘hsvs’}.” I’m wondering if this could be because the FreeSurfer outputs aren’t in BIDS format? All other data are, but FS data are in default output format. Thanks so much for any insight or troubleshooting suggestions!
Command used (and if a helper script was used, a link to the helper script or the command generated):
apptainer run \
--containall --writable-tmpfs \
-B ${basedir} -B ${workdir} \
qsirecon-0.23.2.sif ${indir} ${outdir} participant --participant-label ${sub} \
--fs-license-file ${hbndir}/license.txt --freesurfer-input ${fsdir} --debug all \
-w ${workdir} --recon-spec mrtrix_multishell_msmt_ACT-hsvs --stop-on-first-crash -v -v
Version:
QSIRecon 0.23.2
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer on cluster compute system
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):
241206-12:26:54,171 nipype.workflow INFO:
***********************************
241206-12:26:54,171 nipype.workflow ERROR:
could not run node: qsirecon_0_23_wf.123_mrtrix_multishell_msmt_hsvs.recon_anatomical_wf.ds_fs_5tt_hsvs
241206-12:26:54,171 nipype.workflow INFO:
***********************************
241206-12:26:54,194 nipype.workflow CRITICAL:
QSIRecon failed: Exception raised while executing Node ds_fs_5tt_hsvs.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/niworkflows/interfaces/bids.py", line 632, in _run_interface
raise ValueError(f"Could not build path with entities {out_entities}.")
ValueError: Could not build path with entities {'subject': '123', 'suffix': 'dseg', 'datatype': 'anat', 'extension': 'mif.gz', 'space': 'fsnative', 'desc': 'hsvs'}.