My question relates to analyzing the ODF peaks extracted from the FOD using sh2peaks.
I would like to get the “main” direction for each voxel, or more specifically get a mask of the voxels where the “main” direction is left to right.
from reading here, I got the feeling the easiest way for me to to do this would be to convert the peak file to a nifti file and use python for the rest, but while using nibabel.load gets me all the correct metadata and data shape, the data itself consists of nans.
Is there a reason for that, or a simpler way to do what I am trying to do?
To be clear, I’m using dti2fod, sh2peaks and then mrconvert to pick only the first peak and convert to nifti.