Extract DKT Parcellation volume from Freesurfer

AFNI Message Board
1

Dear AFNI experts,

I notice that the most recent Freesurfer version also provides DKT parcellation results (https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation). Is there any way that @SUMA_Make_Spec_FS can extract and create this parcellation volume as well (something like aparc.a2009s_aseg_rank.nii but for DKT atlas labelling)? Or any other AFNI scripts can do this? Thanks!

Best,
Qiuhai

2

You could try something like this (following the example inside the @SUMA_MakeSpecFS script). Right now the 2009 parcellation is given priority over the DKT parcellation. We’ll consider adding that in the future to the output, but in the meantime, I think this should work.


#!/bin/tcsh
set suma_dir = mysumadir       # usually a directory called SUMA
set fslabel_dir = myFSlabeldir  # this is a parallel directory to your existing SUMA output directory called "label"
set hands = (lh rh)

cd $fslabel_dir
# make the annotation labels on the original FreeSurfer surfaces for each hemisphere
foreach hand ( $hands )
  FSread_annot -input ${hand}.aparc.DKTatlas40.annot -roi_1D $suma_dir/${hand}.aparc.DKTatlas40.annot.1D.roi \
  -dset  $suma_dir/${hand}.aparc.DKTatlas40.annot.niml.dset -cmap_1D $suma_dir/${hand}.aparc.DKTatlas40.annot.1D.cmap \
  -FScmap aparc.annot.DKTatlas40.ctab
end

cd $suma_dir
# transform labels to standard meshes
foreach hand ( $hands )
   MapIcosahedron -spec $suma_dir/FS_${hand}.spec -ld 60 -NN_dset_map $suma_dir/${hand}.aparc.DKTatlas40.annot.niml.dset \
    -morph $suma_dir/${hand}.sphere.reg.gii -prefix std.60.DKT.{$hand}.
end
3

Hi Daniel,

Thank you for your help! I would give it a try.

Best,
Qiuhai