I am currently working on a pipeline for fixel-based analysis of the corticospinal tract of stroke patients using the following guide:
I have performed nearly all preprocessing steps, but I’m not sure why the analysis has to be performed in template space. I am interested in the fiber density and cross section of the individual corticospinal tract (as identified with CSD tractography) and how this changes over time. I feel like I am losing subject specific information when I identify the corticospinal tract in the fod template, especially because different subjects have different lesion locations and sizes.
So would it be possible for me to calculate the FD of the individual corticospinal tract in subject space? To obtain information on the cross section of the fiber bundles I could calculate this from the template warp and transform this back to the subject space.
Any input on this idea?
Thank you in advance,