help > Overlay with .gii file
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Jul 11, 2018  05:07 AM | epapp - University of Trento, Department of Psychology and Cognitive Sciences
Overlay with .gii file
Dear Surf-Ice experts,
sorry for the question, but I'm naive to the topic. I would like to add as overlay a .gii file (cortical thickness), obtained by a contrast from CAT12-SPM toolboxes. However, the software returns this error: "GIFTI overlay has a different number of vertices than the background mesh (1 vs 81924)". Is there a way to add this type of file to the template?
Thank you in advance,
Best,

Edoardo
Nov 5, 2018  08:11 AM | Chris Rorden
RE: Overlay with .gii file
The issue is that CAT12 generates the mesh in GIfTI format (e.g. "lh.central.cr.gii"),but the corresponding thickness file (e.g. "lh.thickness.cr") is saved in FreeSurfer CURV format, but does not attach the ".curv" extension. The next release of Surfice will be better at automatically detecting these mis-named files, but for the moment you can append the ".curv" extension to your thickness file. You can then open the GIfTI file you want (e.g. "lh.central.cr.gii", "lh.sphere.cr.gii") and then use Overlays/AddOverlays to add the thickness file. You will probably want to change the color map (e.g. to ACTC) and the range (e.g. to 0..6mm).
Attachment: thickness.jpg
Jan 30, 2019  05:01 PM | nvogt
RE: Overlay with .gii file
Hi Chris,

I was hoping you could provide some clarification about if it's possible to overlay CAT12 spm T-stat giftis in Surfice (or other statistical maps).

I've tried loading CAT12 32k template surface giftis ("spm/toolbox/cat12/templates_surfaces_32k/mesh.central.freesurfer.gii) and the spmT_0001.gii (from the two-sample T test contrast that I've run) as an overlay. It will load the mesh.central.freesurfer.gi, but it won't load the statistical map (it doesn't even give any errors, just nothing happens).

I'm not very familiar with the gifti format, but when I open the spmT file with a text editor, it's pointing to an external file spmT_0001.dat in the same directory. Is Surfice having a problem loading this data in? The gifti files in your example on the wiki have the data embedded in the actual file. Is there a way to combine the CAT12 .gii and .dat files so Surfice knows how to load it? Thanks in advance!!
Jan 31, 2019  01:01 PM | Chris Rorden
RE: Overlay with .gii file
Thanks for pointing this out. The upcoming release of Surfice will support GIfTI files that use external data.