i am working with some slightly problematic data that is stored solely as the SH coefficients in 4D matrix in matlab format (sh_mat = 120x120x100x15 matrix) and i am trying to convert it to .mif using the write_mrtrix command. the data has a transform associated with it
M = -2 0 0 122 0 -2 0 122 0 0 -2 102 0 0 0 1 fod.data = sh_mat; fod.transform = M;
write_mrtrix(fod, 'outfod.mif') gives the wrong orientation in the corpus callosum (obv they’re all wrong but it’s noticeable in the CC). you can also see it in the projections to the cortex.
I’ve tried a bunch of different ways to flip the orientations but nothing’s worked, any suggestions on this would be great.