[STORY] Port Freesurfer ApplyVolTransform Nipype interface to Pydra

[tclose]

Metadata

Epic: #17
Feature: #79
Feature Release: 1

Description

As a user, I want to be able to use Pydra interfaces for selected Freesurfer commands, so I can reimplement sMRIPrep in Pydra

Acceptance Criteria

Port the following Freesurfer Nipype interfaces to Pydra with appropriate tests

• ApplyVolTransform()

Notes

This interface should go in the https://github.com/nipype/pydra-freesurfer repository in modules named recon.py and utils.py in https://github.com/nipype/pydra-freesurfer/tree/master/pydra/tasks/freesurfer.

There is a script for porting from the Nipype interface to Pydra in the "port-converter" branch of that repository (https://github.com/nipype/pydra-freesurfer/tree/port-converter). @Mahdieh-dst should be able to help you get set up to use it

Please refer to https://github.com/nipype/pydra-dcm2niix/blob/main/pydra/tasks/dcm2niix/utils.py for the latest style to use while defining the interface and the Pydra docs: https://pydra.readthedocs.io/en/latest/input_spec.html & https://pydra.readthedocs.io/en/latest/output_spec.html for more information (although the docs are a little light)

[ablachair]

The script generates the new interface.
The doctest currently fails because the Input ported fields spec

1. requires "target_file", "tal" and "fs_target"
2. declares these fields mutually exclusive (xor)

We might need to override input specs manually in this issue
And create a new issue to fix the porting script accordingly