Creation of a FreeSurfer atlas from a volumetric atlas

[MatthieuJoulot]

FreeSurfer is a very convenient tool. However, it is limited regarding the diversity of atlases it provides. Therefore, we have investigated the methods to convert existing atlases to the FreeSurfer format.
These are the steps gathered to convert a volumetric atlas to the the FreeSurfer format.

FreeSurfer’s atlas format is .gcs as in gaussian classifier surface (atlas). We need this file to easily project the results of recon-all to an atlas with Clinica.

To make this FreeSurfer atlas, you need:
• A subject list a manually labeled brains (Mindboggle 101)
• An atlas file
• A colortable for the atlas

1. Write an .annot file:
   a. Apply CBIG registration fusion to register the atlas to MNI space, using the algorithm from ThomasYeoLab
   b. Generate the fsaverage file using the same toolbox
   c. Using the fsaverage file that was generated write an .annot file using read_annotation.m and write_annotation.m
2. Have all the subjects in your subject list go through recon-all
3. Then you can run mris_ca_train using the colortable, the subject list, the annot files, and the sphere.reg produced by recon-all to make a .gcs version of the atlas for each part of the brain

https://surfer.nmr.mgh.harvard.edu/fswiki/mris_ca_train

faskowit/multiAtlasTT#8

https://github.com/faskowit/multiAtlasTT

https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/registration/Wu2017_RegistrationFusion/bin/standalone_scripts_for_MNI_fsaverage_projection

https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

https://github.com/freesurfer/freesurfer/blob/dev/matlab/write_annotation.m

https://mindboggle.info/data.html