anat-fast-track crashing, io_spec missing fields?
bpinsard opened this issue · comments
Describe the bug
Running fmriprep with anat fast-track on 23.1.4 repronim image I get the following error.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/utility/wrappers.py", line 142, in _run_interface
out = function_handle(**args)
TypeError: _select_surfaces() missing 1 required positional argument: 'spherical_registrations'
Tracking where that value should be set I get to
smriprep/smriprep/utils/bids.py
Line 126 in 97a4098
which uses https://github.com/nipreps/smriprep/blob/master/smriprep/data/io_spec.json to list the files from smriprep output.
It seems that
sphere_reg_fsLR
is missing in that file to properly pass the spheres to fmriprep cifti workflows.
This is likely not covered by fmriprep tests if anat-fast-track is never combined with cifti outputs.
Exact command line executed
Are you positive that the input dataset is BIDS-compliant?
- I have used the online BIDS-Validator
- I have run a local installation of the BIDS-Validator (please, note the version of the validator here).
- I let sMRIPrep check it for me (in other words, I didn't set the
--skip-bids-validation
argument). - No, I haven't checked myself AND used the
--skip-bids-validation
argument.
sMRIPrep feedback information
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Installation type (please complete the following information):
- "Bare-metal"
- Singularity
- Docker
Additional context
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