I am (very) new with MRtrix and would like to delineate the arcuate fasciculus in 20 stroke patients, preferably in some sort of common space (MNI or group template), and then extract subject-specific FA-values for this tract. I’ve performed all the necessary preprocessing steps and first started with a whole-brain deterministic tractography with the following command:
tckgen -algorithm Tensor_Det -angle 40 -minlength 20 -maxlength 400 -step 1 -cutoff 0.2 input.nii output.tck -seed_image brainmask.nii -fslgrad bvec bval
I have also calculated the FA (colored) maps for every subject with dwi2tensor and tensor2metric. I started with subject-specific delineations but am looking for something less time consuming.
Thank you very much for your input.