I have yet another, likely obvious, question and I apologize if this is answered elsewhere. I ran the below series of functions to apply the HCP-MM1 (Glasser) atlas to the FreeSurfer output. I was able to produce an annotation file that had the labels in the
right locations and mapping.
Yet, when I look at the output HCP-MMP1.mgz and HCP-MMP1+aseg.mgz files in FreeView or 3DSlicer, the old DKT FreeSurfer labels are applied to the brain labels (which are inaccurate). Is there an additional step I need to convert the labels such as using a modified
HCP-MMP1 LUT look up table (such as
linked here)?