create full flat map from subject surface

AFNI Message Board
1

Hello AFNI team,

I have a question to create full flat maps from subject surface. I’ve created the subject surface using FreeSurfer (recon-all -all -subjid xxx) and then created the spec files (@SUMA_Make_Spec_FS -NIFTI -sid xxx). Under the SUMA folder, I’ve got SmoothWm, Inflated, Pial, Spherical spec files. At this point, I would like to create the full flat maps (e.g. full.flat.patch.3d.gii from suma_TT_N27). Is this something SUMA can handle it or should I need to generate full flat maps from FreeSurfer…?

Thank you!
Taek

2

Hi Taek-

You’ll need to make the cuts on the inflated maps in Freesurfer. You can follow the tutorials on any of these sites:

  1. https://openwetware.org/wiki/Beauchamp:FreeSurfer
  2. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferOccipitalFlattenedPatch
  3. https://www.youtube.com/watch?v=-qko5wa2cTc

The first one includes the commands in AFNI to use. To view that, you can add the lines into the .spec files that AFNI will use. I have a vague recollection that if you name the cut and flattened surfaces correctly, @SUMA_Make_Spec_FS will automatically do this, but I’m not finding it in my notes at the moment.