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Aug 30, 2018  03:08 PM | Hugo Botha
Custom Atlas Files

The ability to show atlas based results looks great. However, how can I go from an atlas nifty file (where each region is defined by an integer from 1-42) to a mz3 file so that I can use the atlasstat function? I tried to convert it in SurfIce but it made a .obj file of each region, instead of a labelled/indexed mesh file. I also tried playing around with MRICroS.

Thanks so much (and thanks Chris for a great tool)

Aug 31, 2018  09:08 AM | Chris Rorden
RE: Custom Atlas Files
I am attaching a small Matlab file that will help convert a NIfTI atlas to MZ3 format. It uses the Matlab code from MRIcroS to create the MZ3 files. It might need minor modifications. Last I checked, Matlab's reducepatch function had a bug that could create gaps in manifold meshes. The attached code has a basic kludge for this issue, but if you invest the time I am sure you can develop a better solution (and if you do, please share it).
Sep 6, 2018  06:09 AM | Hugo Botha
RE: Custom Atlas Files
Thanks so much! It converts and combined the atlas nii file nicely. Doesn't seem to work with the atlasstat function but that appears to be due to the RGBA data not being included in the mz3 that's put out? I think we can tweak it from here, will share whatever improvements we implement