Extracting DTI indices of segmented nuclei from FSL atlas


Dear MRTrix experts,

Thank you for the effort and time in developing MRTrix.

I am currently trying to extract the DTI indexes (AFD, FA, etc.) of my ROIs, which are segmented nuclei from FSL atlas.

However, I encountered this issue of dimension mismatch between my ROIs and DTI values. I attained the DTI values with tensor2metric.

Question 1

I noted the reply in a post on the MRTrix forum: Extracting ROIs for fixel-based analysis

I understand that DTI indexes are stored as fixel while my segmented nuclei are 3D images in voxel, hence the dimension mismatch. I also understand that to overcome this issue, I can first convert my 3D images into fixel by using voxel2fixel.

However, I have difficulties attempting the voxel2fixel successfully. The function is:

voxel2fixel [ options ] image_in fixel_directory_in fixel_directory_out fixel_data_out

May I have your help on what should I input for the four arguments of this function? What do they mean separately? I noted that there are only few posts about the actual example on running this function.

Question 2

May I know if there is another way in attaining the DTI indexes from my segmented nuclei?

Thank you for your time.

Best regards