Tracts out of included regions


I used the following code to generate tracts starting from Caudate and terminate in SMA:

tckgen ../Temporary_files/ss_wm.mif SMA_Paracentral_right.tck -seed_image rcaudate.nii.mgz.nii.gz -include rparacentral.nii.mgz.nii.gz -stop -act ../Temporary_files/5ttseg.mif -select 10000 -force

However in the final image there are also some tracts that are not terminated in the specified ROI (in this picture the tracts of both right and left hemisphere are shown which were calculated separately):

What can be the problem exactly?

I’m guessing this might be the same issue as in this post: you need to also specify the -seed_unidirectional option to ensure streamlines propagate only one way from the seed, rather than the default bidirectional behaviour.

Thank you very much. Yes that was the problem. I solved it.

Alternatively, since you’re using ACT, and the regions appear to be defined based on cortical segmentation, you can use -seed_gmwmi. That will automatically enforce unidirectional seeding when from the cortex, and may well give more homogeneous seeding in this instance also.