meegpype.workflows.anat.fs_individual_atlas module🔗

meegpype.workflows.anat.fs_individual_atlas.generate_fname(atlas_name, subject_id, subjects_dir, data_dir)🔗
meegpype.workflows.anat.fs_individual_atlas.generate_fs_individual_labelling_workflow(name='freesurfer_labelling_workflow', base_dir=None)🔗

Build the FreeSurfer labelling workflow using an atlas classifier.

The cortex of each hemisphere is labelled with the atlas GCS classifier (mris_ca_label), and the resulting annotations are combined with the aseg segmentation into a volumetric segmentation (mri_aparc2aseg).

The annotations are written to subjects_dir/subject_id/label/{lh,rh}.<atlas_name>.annot.

Workflow Graph
../_images/meegpype-workflows-anat-fs_individual_atlas-1.png

(Source code, png, svg, pdf)

Parameters:

  • name (str) – Name of the workflow.

  • base_dir (str, optional) – Working directory of the workflow.

Inputs:

  • subject_id – FreeSurfer subject identifier.

  • subjects_dir – FreeSurfer subjects directory.

  • atlas_name – Name of the atlas to be used for labelling. Must be one of the atlases listed in meegpype.data.freesurfer.classifiers.ATLAS.

  • data_dir – Path to the data directory containing the classifiers (classifiers/{lh,rh}.<atlas_name>.gcs) and the lookup tables (LUTs/<atlas_name>_LUT.txt).

Outputs:

  • volume – Path to the volumetric segmentation (<subject_id>_space-fsnative_atlas-<atlas>[_seg-<seg>][_scale-<scale>]_dseg.nii).

  • lh_aseg – Path to the left hemisphere annotation, renamed with BIDS-like entities (<subject_id>_hemi-L_space-fsnative_atlas-<atlas>[_seg-<seg>][_scale-<scale>]_dseg.annot).

  • rh_aseg – Path to the right hemisphere annotation, renamed with BIDS-like entities (<subject_id>_hemi-R_space-fsnative_atlas-<atlas>[_seg-<seg>][_scale-<scale>]_dseg.annot).

  • atlas_name – Name of the atlas used for labelling.

  • lut – Path to the lookup table file.

  • subject_id – FreeSurfer subject identifier.

  • subjects_dir – FreeSurfer subjects directory.