Summary of what happened:
First time qsiprep/recon user here. For this reason I’m not sure this belongs here or as a git issue…so I start here. I am running more or less default qsiprep (1.0.1) with apptainer. It completes without error, and all output seems ok (at least according to what I’ve seen on readthedocs/here). I then try to run qsirecon (1.1.0) with the hbcd recon (using an abcd dwi & fm). However it keeps throwing an error related to the template.
Command used (and if a helper script was used, a link to the helper script or the command generated):
apptainer run --no-mount hostfs --cleanenv --containall -B ${bidsDir},${work},${subjdir},${TEMPLATEFL
OW_HOME} --env "TEMPLATEFLOW_HOME=$TEMPLATEFLOW_HOME" --env "SUBJECTS_DIR=$subjdir" qsiprep-1.0.1.sif
${bidsDir} ${bidsDir}/derivatives/dwi/qsiprep participant --output-resolution 1.7 --fs-license-file
${fsLicense} --nprocs 190 --omp-nthreads 20 --participant-label sub-1115 --skip-bids-validation -w ${
work} --anatomical-template MNI152NLin2009cAsym
apptainer run --no-mount hostfs --cleanenv --containall -B ${bidsDir},${work},${subjdir} qsirecon-1.1
.0.sif ${bidsDir}/derivatives/dwi/qsiprep ${bidsDir}/derivatives/dwi/qsirecon participant --fs-licens
e-file ${fsLicense} --nprocs 190 --participant-label sub-1115 -w ${work} --recon-spec hbcd_scalar_map
s --fs-subjects-dir ${subjdir} --output-resolution 1.7 --input-type qsiprep --debug all -vvv
Version:
qsirecon: 1.0.1
qsiprep: 1.1.0
Environment (Docker, Singularity / Apptainer, custom installation):
singularity/apptainer
Data formatted according to a validatable standard? Please provide the output of the validator:
I skip bids validation for now
Relevant log outputs (up to 20 lines):
250626-23:45:19,922 nipype.workflow INFO:
Found 1 high-res anatomicals to process
Traceback (most recent call last):
File "/opt/conda/envs/qsiprep/bin/qsirecon", line 8, in <module>
sys.exit(main())
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/cli/run.py", line 84, in main
retval = build_workflow(str(config_file), {})
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/cli/workflow.py", line 133, in
build_workflow
retval["workflow"] = init_qsirecon_wf()
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/base.py", line 44, in
init_qsirecon_wf
single_subject_wf = init_single_subject_recon_wf(subject_id=subject_id)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/base.py", line 246, i
n init_single_subject_recon_wf
dwi_anat_wfs[dwi_file], dwi_available_anatomical_data = init_dwi_recon_anatomical_workflow(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/qsirecon/workflows/recon/anatomical.py",
line 406, in init_dwi_recon_anatomical_workflow
GetTemplate(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 56
7, in __init__
super().__init__(
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 20
4, in __init__
self.inputs.trait_set(**inputs)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/traits/has_traits.py", line 1520, in tra
it_set
setattr(self, name, value)
File "/opt/conda/envs/qsiprep/lib/python3.10/site-packages/traits/base_trait_handler.py", line 74,
in error
raise TraitError(
traits.trait_errors.TraitError: The 'template_name' trait of a _GetTemplateInputSpec instance must be
a string, but a value of None <class 'NoneType'> was specified.
Screenshots / relevant information:
I have tried with several other (built-in) recon options, but they all give the same error. My apologies if I’m missing something very simple here.
