So I have loaded my .mif files into Matlab using read_mrtrix.m. I was wondering: how do I get the position or voxel location (as would appear in mrview), from the i,j,k location of the matrix data? There might be an easy answer that I’m missing (hopefully so!). Thank you for the help.

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The only difference is that in MatLab, indexing starts from 1, whereas it starts from 0 in MRtrix. So the voxel at position `[ 1 2 3 ]`

in MRView should be at `im.data(2,3,4)`

in MatLab.

I found the problem - I was looking at the voxel coordinates in mrtrix of the mif ROI overlaid on another image, so the voxel coords I were getting were in the other image’s space.