Filling Annot Files Into a Volume

This page describes a 2-step process to fill values from an "annot" file to a volume.

Step 1 : Creating a Cortical Ribbon

You need a cortical ribbon in order to create an accurate mask of the ribbon. If the files lh.ribbon.mgz and rh.ribbon.mgz don't already exist in your <subject>/mri directory, then you can create them using mris_volmask. For instance, if your subject's name is bert, you can run

mris_volmask --save_ribbon bert

Step 2 : Filling the Cortical Ribbon

Once the ribbon files have been created, you can fill the ribbon with values from the desired annot file, using mri_aparc2aseg. The annot files will have to be in the subject's label directory. If your annot files are lh.myAnnot.annot and rh.myAnnot.annot, then you can run the following command to fill them

mri_aparc2aseg --ribbon --s bert --annot myAnnot --o bert/mri/myAnnot.mgz