Dear experts,

I have several masks of different regions (binarized masks created with the JHU atlas in FSL) on top of which I'd like to project my statistical map. I would like the maps to be translucent, without affecting the statistical map. So, the statistical map should still have 0 opacity, while the masks underneath are translucent. 

I tried the following script:

BEGIN
RESETDEFAULTS;
MESHLOAD('BrainMesh_ICBM152_smoothed.mz3');
SHADERLIGHTAZIMUTHELEVATION(1, 25);
SHADERXRAY(1, 0.3);

OVERLAYLOAD('D:\FSL\shared\Studies\pipeline_data\H1c\bold\processing\2ndLevelFeat\Group.gfeat\atlas_masks\bin.thr.INS_LR.nii.gz');
OVERLAYCOLORNAME(1, 'Bronze-Gold')
OVERLAYTRANSLUCENT(1, true);
OVERLAYLOAD('D:\FSL\shared\Studies\pipeline_data\H1c\bold\processing\2ndLevelFeat\Group.gfeat\atlas_masks\bin.thr.ACC_LR.nii.gz');
OVERLAYCOLORNAME(2, 'Violet [r+b]')
OVERLAYTRANSLUCENT(2, true);
OVERLAYLOAD('D:\FSL\shared\Studies\pipeline_data\H1c\bold\processing\2ndLevelFeat\Group.gfeat\atlas_masks\bin.thr.S1_BA2_LR.nii.gz');
OVERLAYCOLORNAME(3, 'Cyan [g+b]')
OVERLAYTRANSLUCENT(3, true);
OVERLAYLOAD('D:\FSL\shared\Studies\pipeline_data\H1c\bold\processing\2ndLevelFeat\Group.gfeat\atlas_masks\bin.thr.S2_OP1_LR.nii.gz');
OVERLAYCOLORNAME(4, 'Blue-Green')
OVERLAYTRANSLUCENT(4, true);
OVERLAYLOAD('D:\FSL\shared\Studies\pipeline_data\H1c\bold\processing\2ndLevelFeat\Group.gfeat\atlas_masks\bin.thr.Tha_LR.nii.gz');
OVERLAYCOLORNAME(5, 'Blue')
OVERLAYTRANSLUCENT(5, true);
OVERLAYLOAD('D:\FSL\shared\Studies\pipeline_data\H1c\bold\processing\2ndLevelFeat\Group.gfeat\cope1.feat\thresh_zstat1.nii.gz');
OVERLAYCOLORNAME(6, 'Red-Yellow')
OVERLAYMINMAX(6, 3.1, 5);

COLORBARVISIBLE(false);
OVERLAYTRANSPARENCYONBACKGROUND(0);

END.

This gives me almost what I want, but the overlapping regions between statistical map and masks are still blurred into each other. 

Is it possible to put the masks in the background in a way that the statistical map has it's native color coding, and not that the color of the mask is mixing with the statistical map? 

Thanks in advance and I hope to hear from you soon.

Kind regards,

Jurjen Heij

You can not get the result you desire with the Surfice surface painting. It is attempting to reveal how different regions overlap. What I would suggest you do is use the Advanced/ConvertVoxelwiseVolumeToMesh option to convert your thresholded statistics to a mesh. This can then be shown as a separate volume floating above the surface of the cortex.

import gl
gl.resetdefaults()
#opacity adjusts whether overlays are translucent (0)
opacity = 30
pth = '/Users/rorden/Downloads/sf/'
gl.azimuthelevation(70, 15)
gl.meshload('BrainMesh_ICBM152_smoothed.mz3')
gl.overlayload(pth+'bin.thr.ACC_LR.nii.gz')
gl.overlaycolorname(1, 'Violet [r+b]')
gl.overlayminmax(1,0.5,0.5)
gl.overlayopacity(1, opacity)
gl.overlayload(pth+'bin.thr.S2_OP1_LR.nii.gz')
gl.overlaycolorname(2, 'Violet [r+b]')
gl.overlayminmax(2,0.5,0.5)
gl.overlayopacity(2, opacity)
gl.overlayload(pth+'bin.thr.INS_LR.nii.gz')
gl.overlaycolorname(3, 'Bronze-Gold')
gl.overlayminmax(3,0.5,0.5)
gl.overlayopacity(3, opacity)
gl.overlayload(pth+'bin.thr.Tha_LR.nii.gz')
gl.overlaycolorname(4, 'Blue')
gl.overlayminmax(4,0.5,0.5)
gl.overlayopacity(4, opacity)
gl.overlayload(pth+'bin.thr.S1_BA2_LR.nii.gz')
gl.overlaycolorname(5, 'Cyan [g+b]')
gl.overlayminmax(5,0.5,0.5)
gl.overlayopacity(5, opacity)
gl.overlayload(pth+'thresh_zstat1_2.mz3')
gl.overlaycolorname(6, 'Red')
gl.meshcurv()