help > Visualize cortical thickness from freesurfer
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May 14, 2021  03:05 AM | Jung Hwan Shin
Visualize cortical thickness from freesurfer
Hi. Thanks for this beautiful program.

I am no trying to display cortical thickness pattern derived and processed with freesurfer (aparc.a2009s atlas- 76 ROI for each hemisphere)

I made a custom annot file and overlayed the result.The result are as follows.

Using Lh.curv and Lh. inflated as background are shown as the attached file. I would like a background template to be somewhere between these two.

Would there be any template that I can use or modify?

Next, I have two annot file seperately for left and right hemisphere. I cannot display annot file for right hemisphere.
Eventhough I load rh.curv or rh.inflated, the overlayed image are only shown in left hemisphere. 
Eventhough I open rh.pial, the overlay window in the program is noted as "lh.curv "

I would like to display results for the right hemisphere only. How can I solve this issue? 

Thank you in advance!

Sincerely.
Attachment: capture.PNG
May 14, 2021  07:05 PM | Chris Rorden
RE: Visualize cortical thickness from freesurfer
1. Surfice is an visualization program. If you want to change the inflation of a background mesh, you should consider adjusting the parameters of the tool used to create the mesh. Therefore, this is a question for the developers of the tool used to make the mesh, e.g. FreeSurfer, BrainStorm, SUMA.
 https://afni.nimh.nih.gov/afni/community/board/read.php?1,162375,162375

2. An issue with the FreeSurfer format images is that the format itself does not report whether the image is Left Hemisphere, Right Hemisphere, or Bilateral. AFNI, FreeSurfer and other tools seem to use naming conventions based on the "lh." and "rh." prefixes. Because there is no documented, consistent way to deal with this, the behavior of Surfice may be a little idiosyncratic. One thing you can try is inserting the command "gl.meshloadbilateral(1)" or "gl.meshloadbilateral(0)" into a script, to enable to disable Surfice's attempt to resolve a bilateral mesh load when a user chooses a FreeSurfer format mesh.  You can see the influence yourself by changing this value in the include script. At the moment, the behavior is very fiddly depending on the naming of your files.




import gl
gl.resetdefaults()
gl.meshloadbilateral(1)
gl.azimuthelevation(70, 15)
gl.meshload('BrainMesh_ICBM152.rh.mz3')
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(1,2,12)
gl.overlayload('motor_4t95vol.nii.gz')
gl.overlayminmax(2,-1,-2)
gl.colorbarvisible(1)
gl.overlaytransparencyonbackground(25)
gl.meshcurv()
gl.shadername('MatCap');
gl.shadermatcap('Cortex3')
gl.hemispheredistance(0.62)
gl.hemispherepry(-35)
gl.azimuthelevation(180,0)
print('Emulate WalnutBrain https://afni.nimh.nih.gov/pub/dist/doc/h...)