Hi Chris,

I tried plot three binary nii images on surface, and had an issue when ploting using lh.inflated.
The question is: the brain areas were displayed normally when i used e.g., BrainMesh_ICBM152_smoothed.rh.mz3
but it didn't when using lh.inflated (see attached screenshot), with only part of activation appeared.
Could you give me some advice why and how to make it right? Thanks!

Here is the code I used (Cond1.nii, Cond2.nii, and Cond3.nii were binary images):

import gl
gl.resetdefaults()
gl.meshloadbilateral('lh.inflated')

gl.overlayload('/Volumes/T7/Cond1.nii')
gl.overlaycolorname(1, 'red')
gl.overlayminmax(1,0.1,1)
gl.overlayload('/Volumes/T7/Cond2.nii')
gl.overlaycolorname(2, 'green')
gl.overlayminmax(1,0.1,1)
gl.overlayload('/Volumes/T7/Cond3.nii')
gl.overlaycolorname(3, 'blue')
gl.overlayminmax(1,0.1,1)
gl.azimuthelevation(80, 50)
gl.colorbarvisible(0)
gl.shadername('MatCap')
gl.shadermatcap('Porcelain')
gl.hemispheredistance(0.65)
gl.hemispherepry(-85)
gl.azimuthelevation(360,0)

When you load a NIfTI image onto a mesh, Surfice assumes they have the same spatial mapping. The FreeSurfer inflated images no longer have any correspondence to MNI space. Indeed, the inflated left and right hemisphere are no longer left or right (each is dilated so the X-coordinates extend both left and right of the origin. You will need to use a FreeSurfer too to help you:
  https://imaging.mrc-cbu.cam.ac.uk/meg/AnalyzingData/MNE_SPM2Freesurfer

Thanks Chris! That make sense, very helpful!

Hi Chris,

A follow-up on this question.

I was able to convert an image from MNI152 to fsaverage.
Then I was able to display it using freeview

freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.inflated:overlay=MNI2fsaverage_ALE.nii:color='178,190,181':overlay_custom=val:overlay_color='clearlower':all='true' -view 'left'

However, when I tried to display this overlay on lh.inflated on Surf Ice, it doesn't show me anything as it showed in Freeview.
I'm puzzled and could you give me some advice? The overlay nii file was attached.

Thanks,
Chuanji