Hello!

Is there a way to view a medial layout of the brain surface? The only views I can find are lateral left/right, posterior, anterior, superior and inferior. 

Thank you!
Kaitlin

If your brain mesh shows a single hemisphere, set the azimuth to look at the medial surface

import gl
gl.resetdefaults()
gl.azimuthelevation(270, 15)
gl.meshload('BrainMesh_ICBM152Right.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()

If your brain mesh shows both hemispheres, apply a clip plane to hide one hemisphere. You can paste the code below into the 'Scripting' panel on the right side, and choose Scripting/Run to see the sample image. Typically, one can not define a perfect clip plane between the two hemisphere due to asymmetries (Yakovlevian torque)


import gl
gl.resetdefaults()
gl.meshload('mni152_2009')
gl.overlayload('motor_4t95mesh.mz3')
gl.clipazimuthelevation(0.5, 270, 0)
gl.shaderxray(1.0, 0.3)
gl.azimuthelevation(270, 15)

A final option is to use MRIcroGL instead of Surfice, if you have a voxel-based representation of your data


import gl
gl.resetdefaults()
#open background image
gl.loadimage('spm152')
#open overlay: show positive regions
gl.overlayload('spmMotor')
gl.minmax(1, 4, 4)
gl.opacity(1,50)
gl.clipazimuthelevation(0.5, 270, 0)

Originally posted by Chris Rorden: Dear pro. Chris, do you know how to file these hollows, to achieve a flat medial view of brain like the figure attached.

You can convert voxelwise data to a mesh by using the "Advanced" menu item "Convert voxelwise volume to a mesh", so you could use a tool like MRIcroGL to crop a bilateral image to show one one hemisphere. Alternatively, you could use a tool like FreeSurfer to convert a brain image to a hemispheric mesh.