meegpype.workflows.anat.fs_template_atlas module🔗

meegpype.workflows.anat.fs_template_atlas.generate_fname(atlas_name, subject_id, classifier_data_dir)🔗
meegpype.workflows.anat.fs_template_atlas.generate_fs_template_labelling_workflow(name='freesurfer_labelling_workflow', base_dir=None)🔗

Build the FreeSurfer labelling workflow using an fsaverage atlas.

The atlas annotations defined on fsaverage are projected onto the subject surfaces (mri_surf2surf), and combined with the aseg segmentation into a volumetric segmentation (mri_aparc2aseg).

Workflow Graph
../_images/meegpype-workflows-anat-fs_template_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.

  • classifier_data_dir – Path to the data directory containing the fsaverage annotations (fsaverage/label/{lh,rh}.<atlas_name>.annot).

Outputs:

  • volume – Path to the volumetric segmentation (sub-<subject_id>_seg-<atlas_name>_space-fsnative_dseg.nii).

  • lh_aseg – Path to the left hemisphere annotation projected onto the subject.

  • rh_aseg – Path to the right hemisphere annotation projected onto the subject.

  • atlas_name – Name of the atlas used for labelling.

  • subject_id – FreeSurfer subject identifier.

  • subjects_dir – FreeSurfer subjects directory.