Creating and displaying a surface file (*.gii)

SPM can create and show surfaces. This is an example using the SUIT template. Display a 3D surface is called “rendering”.

From SPM Menu GUI: Batch, SPM menu, Tools, Rendering, Surface Extraction
Find a nifti file that has masked brain (or whatever structure you want)
- “Masked” means the outside, non-brain voxels are 0 or a value that is lower that the brain
- SUIT example: …\toolbox\suit\atlas\SUIT.nii (snapshot on right)
- The surface *.gii file will be created in the same folder as the *.nii file, so copy that latter if you want the *.gii to be created somewhere else.
- You can also do a combination (gray and white for example)
Input Images, select the file(s)
Under Surfaces, click New: Surface
For expression leave as is (“i1”)
- If you have gray and white files, the expression would be i1 + i2 (sum two images)
For Surface isovalues, put a number that will exclude non-brain. For a mask, the default 0.5 makes sense. For a T1 ranging from 0--300, a value of 10 might work better
Run (green “Play” button)

SUIT Example (…\suit\atlas\SUIT.nii) - black = 0, gray voxels range from >0 to ~300 (view with histogram)

From SPM Menu GUI: Batch, SPM menu, Tools, Rendering, Surface Extraction
Under Objects, click “New: Object”
For Surface File, select the *.gii file
Run; this will display in the SPM Graphics window. You can click-and-drag to rotate the 3D view
Change the surface settings (under Surface File”) to change 3D characteristics
The surface file can also be used in CSPM’s 3D visualization