I would like to generate the corticospinal tract from the diffusion data, I try with some commands but it does not work.
I would be happy if any of you help me
Hello @zeraiiabderrazek Can you please post the command that you are using for the generation of CST tracks.
And the end results you are getting from it.
I’m sorry for the delay about your question. I tried with this command “tckedit -include -0.6,-16.5,-16.0,3 2M.tck CST.tck” .but I am not satisfied with the result, besides I am looking for an optimal solution.here is the result I found that seems a bit bizzare
@zeraiiabderrazek you can try using tckgen command which should look something like this …
tckgen dwi_data.mif -seed_image roi.mif -mask mask.mif -cutoff 0.1 -select 200k output.tck
Your ROI seed looks a bit strange. Typically for the CST, a seed is placed from axial along the posterior limb of the internal capsule (PLIC) and another in the brainstem. See Figure 66 #1 and #2 (the purple parts) here http://jeromemallershandbookofstructuralbrainmrianalysis.yolasite.com/resources/Jeromes_Structural_MRI_analysis_handbook_April2017_Part2.pdf?sm_au=i0HJ6F1J7kMwjqWrML8tvK34L00HF