help > Merging Surfaces and Projecting Annotations
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Aug 25, 2017  08:08 AM | Thomas DeRamus - TReNDs
Merging Surfaces and Projecting Annotations

I apologize if this is a newbie issue but I haven't found anything in the wiki describing it how to deal with it.
I'm tying to merge a smaller version of the Yeo2011 atlas annotation file from Freesurfer into a single gifti that I can overlay onto a gifti image with both Freesurfer hemispheres.

I can merge the two hemispheres pretty easily with:

mris_convert --combinesurfs lh.pial rh.pial Bothhemi.gii

And I can convert the annotation files to giis pretty easily with:
mris_convert --annot lh.ReducedYeo2011.annot lh.pial lh.ReducedYeo2011.gii

But I can't then merge the separate annot files and project it onto the merged surface gifti. Either because it can't read the annot.gii or when it does it just projects it onto one hemisphere as a single value.

Would anyone know how to do this conversion?

Or alternatively, would it be easier to project a nii with the ROIs I'm interested in onto a surface with both hemispheres and then adjust accordingly? If so, how would I go about that? I would prefer not to do that since I'm using SurfIceOld (my GPU apparently has issues with SurfIce and MRICroGL is the windows download now).

Annots attached.
Dec 5, 2017  05:12 AM | Chris Rorden
RE: Merging Surfaces and Projecting Annotations
Since mris_convert is a part of the FreeSurfer tools, I would suggest you ask this question on the FreeSurfer forum