Hi MRTrix team,
I am building my analysis pipeline and am curious your thoughts on my approach. My data are b=0,1000,2000.
I would like to implement ACT via 5ttgen. I initially attempted 5ttgen fsl, which worked for a non-lesioned brain, but was not accurate when run on a brain with a large lesion. I then found 5ttgen hsvs, which uses the freesurfer outputs I have already computed. I added the flag -white_stem to classify the brainstem as white matter. However, in the description of -white_stem, it states that **“**streamlines will not be permitted to terminate within this region”.
The pathways I’m interested in terminate in the brainstem. Could you please confirm that if this option is selected, I would not be able to denote the pathway terminus regions as within the brainstem?
If I cannot, do you have alternative solutions to using 5ttgen?
I appreciate the help!
My best,
Adam