Open tclose opened 2 years ago
Epic: #17 Feature: #79 Feature Release: 1
As a user, I want to be able to use Pydra interfaces for selected Freesurfer commands, so I can reimplement sMRIPrep in Pydra
Port the following Freesurfer Nipype interface to Pydra with appropriate tests
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.
recon.py
utils.py
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)
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 interface to Pydra with appropriate tests
Notes
This interface should go in the https://github.com/nipype/pydra-freesurfer repository in modules named
recon.pyandutils.pyin 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)