ENH: Custom atlas support

[sebastientourbier]

Brainstorming on how to make CMP3 handling custom cortical parcellation atlases.

Possible inputs

• Custom BIDS derivative directory with parcellation in native space - (*_atlas-<atlas_name>_dseg.nii.gz and *_atlas-<atlas_name>_dseg.tsv) i.e.:

   /path/to/my_custom_atlas_derivatives/
       |__ atlas-AAL2_dseg.tsv
       |__ sub-01/
       |      |__ sub-01_atlas-AAL2_dseg.nii.gz
       |__ sub-02/
       |      |__ sub-02_atlas-AAL2_dseg.nii.gz
       |__ ...
  
  

  following the BIDS specs as described in https://bids-specification.readthedocs.io/en/stable/05-derivatives/03-imaging.html#common-image-derived-labels.

• Freesurfer .annot files like:

  • Yeo functional atlas - https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation)
  • HCP MMP 1.0 (Glasser) atlas - https://figshare.com/articles/dataset/HCP-MMP1_0_projected_on_fsaverage/3498446

• Freesurfer .gcs (like the brainnetome atlas - https://atlas.brainnetome.org/)

Resources

• List of cortical atlas parcellations - https://www.lead-dbs.org/helpsupport/knowledge-base/atlasesresources/cortical-atlas-parcellations-mni-space/

[sebastientourbier]

• New config traits
  • Segmentation stage
    • Add Custom option for segmentation_tool
    • custom_bids_derivatives that specifyies the BIDS derivatives directory where WM tissue and brain masks are located
    • pybids_config a path to a JSON file that specifies the pybids query to get the WM mask (like label-WM)
  • Parcellation stage
    • Add Custom Parcellation option for parcellation_scheme
    • custom_bids_derivatives that specifyies the BIDS derivatives directory where parcellation(s) is(are) located
    • pybids_config a path to a JSON file that specifies the pybids query to get the atlas (like atlas=Desikan)
    • parcellation_name the name of the atlas used in the output parcellation filename of the anatomical pipeline.