Support MCRIBS derivatives

[tsalo]

Closes #840 and relates to #976.

Changes proposed in this pull request

• Create interface, xcp_d.interfaces.bids.CollectRegistrationFiles, to collect FreeSurfer or MCRIBs sphere and transform files for anatomical workflow.
• Remove xcp_d.utils.bids.get_freesurfer_sphere, as the functionality is now in CollectRegistrationFiles.
• Heavily refactor xcp_d.utils.bids.get_freesurfer_dir to support MCRIBS on top of FreeSurfer.

[codecov]

Codecov Report

Attention: Patch coverage is 85.45455% with 8 lines in your changes missing coverage. Please review.

Project coverage is 82.45%. Comparing base (673efa3) to head (9752361).
Report is 138 commits behind head on main.

Files with missing lines	Patch %	Lines
xcp_d/interfaces/bids.py	79.41%	5 Missing and 2 partials ⚠️
xcp_d/workflows/anatomical.py	87.50%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #1029      +/-   ##
==========================================
- Coverage   82.51%   82.45%   -0.07%     
==========================================
  Files          48       48              
  Lines        5846     5871      +25     
  Branches      786      787       +1     
==========================================
+ Hits         4824     4841      +17     
- Misses        826      832       +6     
- Partials      196      198       +2     

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[tsalo]

@madisoth I think this should work. Would you be willing to try it out on some Nibabies+MCRIBS data?

[madisoth]

I got an error in CollectingRegistrationFiles ingressing NiBabies 24.0.0a1 MCRIBS derivatives; changing it to this fixed it for me:

class CollectRegistrationFiles(SimpleInterface):
    """Collect registration files for fsnative-to-fsLR transformation."""

    input_spec = _CollectRegistrationFilesInputSpec
    output_spec = _CollectRegistrationFilesOutputSpec

    def _run_interface(self, runtime):
        import os

        from pkg_resources import resource_filename as pkgrf
        from templateflow.api import get as get_template

        hemisphere = self.inputs.hemisphere
        hstr = f"{hemisphere.lower()}h"
        participant_id = self.inputs.participant_id
        if not participant_id.startswith("sub-"):
            participant_id = f"sub-{participant_id}"

        # Find the subject's sphere in the segmentation derivatives.
        # TODO: Collect from the preprocessing derivatives if they're a compliant version.
        # Namely, fMRIPrep >= 23.1.2, Nibabies >= 24.0.0a1.
        self._results["subject_sphere"] = os.path.join(
            self.inputs.segmentation_dir,
            participant_id,
            "surf",
            f"{hstr}.sphere.reg",
        )

        # NOTE: Why do we need the fsaverage mesh?
        # TODO: Replace with appropriate files.
        if self.inputs.software == "FreeSurfer":
            # Find the subject's sphere in the FreeSurfer derivatives.
            # TODO: Collect from the preprocessing derivatives if they're a compliant version.
            # Namely, fMRIPrep >= 23.1.2, Nibabies >= 24.0.0a1.
            self._results["subject_sphere"] = os.path.join(
                self.inputs.segmentation_dir,
                participant_id,
                "surf",
                f"{hstr}.sphere.reg",
            )
            # Load the fsaverage-164k sphere
            # FreeSurfer: tpl-fsaverage_hemi-?_den-164k_sphere.surf.gii
            self._results["source_sphere"] = str(
                get_template(
                    template="fsaverage",
                    space=None,
                    hemi=hemisphere,
                    density="164k",
                    desc=None,
                    suffix="sphere",
                )
            )
            # NOTE: Can we upload these to templateflow?
            # FreeSurfer: fs_?/fs_?-to-fs_LR_fsaverage.?_LR.spherical_std.164k_fs_?.surf.gii
            self._results["sphere_to_sphere"] = pkgrf(
                "xcp_d",
                (
                    f"data/standard_mesh_atlases/fs_{hemisphere}/"
                    f"fs_{hemisphere}-to-fs_LR_fsaverage.{hemisphere}_LR.spherical_std."
                    f"164k_fs_{hemisphere}.surf.gii"
                ),
            )
            # FreeSurfer: tpl-fsLR_hemi-?_den-32k_sphere.surf.gii
            self._results["target_sphere"] = str(
                get_template(
                    template="fsLR",
                    space=None,
                    hemi=hemisphere,
                    density="32k",
                    desc=None,
                    suffix="sphere",
                )
            )

        elif self.inputs.software == "MCRIBS":
            # Find the subject's sphere in the MCRIBS derivatives.
            # TODO: Collect from the preprocessing derivatives if they're a compliant version.
            # Namely, fMRIPrep >= 23.1.2, Nibabies >= 24.0.0a1.
            self._results["subject_sphere"] = os.path.join(
                self.inputs.segmentation_dir,
                participant_id,
                "freesurfer",
                participant_id,
                "surf",
                f"{hstr}.sphere.reg2",
            )
            # MCRIBS: tpl-fsaverage_hemi-?_den-41k_desc-reg_sphere.surf.gii
            self._results["source_sphere"] = os.path.join(
                self.inputs.segmentation_dir,
                "templates_fsLR",
                f"tpl-fsaverage_hemi-{hemisphere}_den-41k_desc-reg_sphere.surf.gii",
            )
            # MCRIBS: tpl-dHCP_space-fsaverage_hemi-?_den-41k_desc-reg_sphere.surf.gii
            self._results["sphere_to_sphere"] = os.path.join(
                self.inputs.segmentation_dir,
                "templates_fsLR",
                f"tpl-dHCP_space-fsaverage_hemi-{hemisphere}_den-41k_desc-reg_sphere.surf.gii",
            )
            # MCRIBS: tpl-dHCP_space-fsLR_hemi-?_den-32k_desc-week42_sphere.surf.gii
            self._results["target_sphere"] = os.path.join(
                self.inputs.segmentation_dir,
                "templates_fsLR",
                f"tpl-dHCP_space-fsLR_hemi-{hemisphere}_den-32k_desc-week42_sphere.surf.gii",
            )

        return runtime