help > ch2better.nii template visualization
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Aug 5, 2019  02:08 PM | Joanna Sierpowska - Donders Centre for Cognition / Radboud University
ch2better.nii template visualization
Hello, 

Context : I wish to visuzalize my FSL Probtrackx results (in nifti) on a ch2better.nii template in a way, that both white and gray matter structures are visible underneath, but when I'm using Surf Ice I can only see the mesh showing gray matter surfaces and my results are only shown on these, cortical areas. Anything below the cortex is empty. 

Question: Is it possible to visualize any MNI template in their full form using Surf Ice? 



Thank you in advance for reaction, 

Best regards, 


Joanna
Aug 7, 2019  06:08 AM | Chris Rorden
RE: ch2better.nii template visualization
My own inclination would be to visualize these using MRIcroGL (see attached image where the output of probtrackx is loaded as an overlay and the glass-brain overlay is used). In my own work, I tend to turn the output of bedpostx into streamlines that can be visualized as Tracks in Surfice (similar to running the "Track" demo from the Scripting/Pascal menu item). 

If you really do want to visualize these with Surfice, you will need to choose a single surface intensity for your probtrackx output with the Advanced/ConvertVoxelwiseVolumeToMesh option and view these. You would then use the "XRay" feature to make the cortex translucent so you can see the fiber bundle beneath:

BEGIN
RESETDEFAULTS;
COLORBARVISIBLE(false);
MESHLOAD('cortex_mesh.obj');
OVERLAYLOAD('fiber_mesh.obj');
SHADERXRAY(1.0, 0.2);
END.
Attachment: mricrogl_glass.jpg