nipreps / smriprep

Structural MRI PREProcessing (sMRIPrep) workflows for NIPreps (NeuroImaging PREProcessing tools)

Home Page:https://nipreps.github.io/smriprep

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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

def collect_derivatives(

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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