I have a set of diffusion weighted MRI data that was collected with 64 directions at 3 shells, namely, b1000 b2000 and b3000. There are 3 age groups and within each age group there are 3 cognitive groups.
I have processed to the point where I have fixel maps of each individual brain in template space. I have processed using the MRtrix cfestats command but I would like to (if possible) get “mean fixel maps” of the “average” of each of my 9 groups (3 age groups with 3 cognitive groups within each age group). Is that possible? How would I go about doing so? I’ve looked all over the documentation about it and cant find an answer.
Fixels are usually stored as directories containing image files that define the location (index) and direction of fixels as well as fixels data files (Fixel image (directory) format — MRtrix 3.0 documentation). As long as your subject fixels share index and directions, you can use voxel-wise operations using
mrcalc to perform operations on the fixel value files. So, you’d need to map subject fixels to a common reference fixel image (see Fibre density and cross-section - Multi-tissue CSD — MRtrix 3.0 documentation).
You can compute the mean across specific fixel value files with:
mrmath path/to/fixel_values_subj1.mif path/to/fixel_values_subj2.mif path/to/fixel_values_subj3.mif mean path/to/groupmean.mif.
Depending on your filenames on linux/macOS you could use standard globbing patterns (see Wildcards) to identify files of interest.