Hello all in AFNI-land,

I am trying to get some labels from a Freesurfer annotation file into SUMA dsets. If I use the standard version of Freesurfer, everything works fine. I actually want the labels from the development version of Freesurfer, however, and that is not working so well.

My general procedure is to use FSread_annot to convert the annotation file to SUMA format, and SurfToSurf to convert the dset to the standard mesh (see actual commands below). In the standard version of Freesurfer, this leads to labels that are in the right place on both the individual's standard mesh and a group average standard mesh. Using the development version, the labels look ok on the individual's standard mesh, but not the group average standard mesh (anterior shift on average in the lh, inferior shift in the rh).

This leads me to wonder if there may be some issue with MapIcosohedron and the dev version of Freesurfer- is there any reason that those two should not play nice together? Any suggestions for better diagnosing or working around this problem?

Thanks,
Katherine



Commands:
FSread_annot -input ${hemi}.aparc.annot -roi_1D ${hemi}.aparc.annot.1D

SurfToSurf \
-prefix ${hemi}.aparc.annot.std.1D \
-i_fs ../SUMA/stdmesh/MapIco_${hemi}_std.inflated.asc \
-i_fs ../SUMA/${hemi}.inflated.asc \
-output_params Data NearestNode \
-data ../label/${hemi}.aparc.annot.1D[1]