I’d like to extract the mean AFD-value for a region of interest. My ROI is not a specific tract, but a spherical region (it’ s a mask I created in FSL). I conducted the fixel-based analysis in MRtrix to obtain the afd.mif file. However, I can’t find a way to extract only those AFD-values (i.e. the mean) which lie within the mask. I usually do such analyses in MATLAB, but the dimensions of the afd.mif and my ROI.nii file naturally don’t match, even after converting the ROI.nii to ROI.mif. Can you help me out here?
PS: Sorry, I think I should have been clearer before: Of course, what I really aim for in the end, is to obtain the mean AFD of any fibre population that crosses my ROI, but only within the borders of my ROI.