CST tckgen

Hello Mrtrixers
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
cordially

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.

Thanks,
Nayan

hello @nayan_wadhwani
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 :grin::grin:

@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

Jerome