SUMA: activation representation using surface

charujing123 · May 11, 2018, 2:13am

Hi AFNI experts
I want to show my activation results using surface based representation, just as attached file.
I downloaded suma_TT_N27, unfortunately, I donot know how to do next. Activation map was Talairach coordinates. AND, how to represent subcortical regions, such as striatum?
Thanks.

TIM图片20180511021712.png

dglen · May 11, 2018, 2:24pm

See the help for 3dVol2Surf or the surface-based analysis section in afni_proc.py’s help. The SUMA class handouts should also be useful.

charujing123 · May 11, 2018, 6:02pm

Hi Glen
Thanks. Another question is whether the program represent striatum onto surface automatically?
Best.
Rujing

dglen · May 13, 2018, 3:36am

Not automatically, but you can use various atlases for different parts of the striatum. Use the atlases to map the region onto the surface with 3dVol2surf, or generate new surfaces for those regions with IsoSurface.

charujing123 · May 15, 2018, 1:40am

Hi Glen,
Thanks.
Can you send me an example of atlas for the striatum? Then, i can try to map the region onto the surface. Or, it there any spec file that contain striatum segment?
Best
Rujing

dglen · May 15, 2018, 5:52pm

The striatum is composed of different regions across different atlases. Attached is an example of the Eickhoff-Zilles Macrolabel atlas. Quick surfaces can be created with the IsoSurface program.

IsoSurface -isorois+dsets -o TT_ml.gii -input TT_caez_ml_18+tlrc. -Tsmooth 0.3 30
suma -onestate -i Caudategii Putamen.gii Pallidum.gii

Map data to the surface with 3dVol2surf or just by having suma talk to afni (‘t’ key in suma to talk with afni started with -niml option). You can also use the Vol2surf plugin to try different options.

charujing123 · May 16, 2018, 12:58am

Hi Glen,
Thanks.
It’s working. It didnot change the surface, when I press “.” or “,”. Why? suma -onestate -i Caudategii Putamen.gii Pallidum.gii -sv TT_N27+tlrc
Best.

dglen · May 16, 2018, 3:18pm

The comma and period keys change among surface states. Since there is only state, there is nothing to switch among.

charujing123 · May 17, 2018, 2:24am

Hi Glen
Got it. Thanks.
Best
Rujing

charujing123 · May 17, 2018, 9:30am

Hi Glen
If activation was in MNI space, can i use MNI_N27_both.spec and MNIa_caez_N27+tlrc to map the activation onto surface? If so, can i use MNIa_caez_ml_18+tlrc to create surcortical area, then I can map striatum onto surfaces?
Thanks.
Best.

dglen · May 17, 2018, 12:25pm

You can use MNI space atlases and surfaces together but not MNIa or MNI_ANAT space atlases. Those are in a shifted space used by the Eickhoff-Zilles atlases. Find the MNI space version of those atlases from that group here:

https://afni.nimh.nih.gov/pub/dist/atlases/MNIatlases.tgz

charujing123 · May 18, 2018, 1:48am

Hi Glen
Thanks. I see.
Best.
Rujing