help > Show all four sagittal images at once (medial LH, RH, and lateral LH, RH)
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Dec 10, 2020  12:12 AM | Jamal Williams - Princeton University
Show all four sagittal images at once (medial LH, RH, and lateral LH, RH)
I'm trying to get something like the plot below. Unfortunately in MRIcro GL I can't get a view like this. Furthermore, how does one remove substructures (e.g. cerebellum, brainstem, etc.) like the plots below. Any help would be greatly appreciated!

Image
Dec 10, 2020  12:12 PM | Chris Rorden
RE: Show all four sagittal images at once (medial LH, RH, and lateral LH, RH)
With MRIcroGL you could create two renderings. Choose a template without a cerebellum if you do not want it...

import gl
gl.resetdefaults()
gl.backcolor(255, 255, 255)
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
#open overlay: show negative regions
gl.overlayload('spmMotor')
gl.minmax(2, -4, -4)
gl.colorname (2,"3blue")
gl.colorbarposition(0)
#"a"xial, "c"oronal and "s"agittal "r"enderings
gl.clipazimuthelevation(0.5, 90, 0)
gl.mosaic("S R 0; S R -0");
gl.savebmp("LH.png")
gl.clipazimuthelevation(0.5, 270, 0)
gl.mosaic("S R 0; S R -0");
gl.savebmp("RH.png")
Attachment: MRIcroGL.png
Dec 11, 2020  01:12 PM | Chris Rorden
RE: Show all four sagittal images at once (medial LH, RH, and lateral LH, RH)
It appears like the image you want to mimic is based on a triangle-based mesh-renderer like Surfice, not a voxel-based volume renderer like MRIcroGL. Assuming your statistical maps are aligned to one of the popular mesh templates, you can create a similar image with surfice. This example script should work with the sample images that come with Surfice


import gl
gl.resetdefaults()
gl.meshloadbilateral(0)
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.azimuthelevation(90, 0)
gl.savebmp('RH.png')
gl.azimuthelevation(270, 0)
gl.savebmp('RH2.png')
#show left hemisphere
gl.meshload('BrainMesh_ICBM152.lh.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.azimuthelevation(270, 0)
gl.savebmp('LH.png')
gl.azimuthelevation(90, 0)
gl.savebmp('LH2.png')
Attachment: surfice.jpg