Displaying NIfTI data with SurfaceViewer

[ZviBaratz]

Hi all,

Thank you for all your incredible work!
I am hoping to use the SurfaceViewer in our lab's website, and I was wondering whether there's some sort of recommended procedure for producing .obj files from NIfTI files. I realize the process of converting a 3D matrix to a surface is involved, but I was hoping some of you may have a readily available solution that produces good results.

If I succeed in creating/adapting a simple solution for this, I would be more than happy to contribute the implementation to the codebase, or at least add a short guide to the docs.

Thank you very much in any case and all the best,
Zvi

[lblewis]

For surface extraction, you can use our lab's pipeline, CIVET:

http://mcin.ca/technology/civet

or FreeSurfer: https://surfer.nmr.mgh.harvard.edu

Both are available on CBRAIN: http://mcin.ca/technology/cbrain

FreeSurfer accepts .nii input. CIVET requires .mnc input, but you can use the tool nii2mnc (also on CBRAIN) before submitting.

Surface output filetypes of CIVET (.obj) and FreeSurfer (binary lh.white or .asc lh.white.asc) are all viewable in SurfaceViewer.