Tckgen -seed N-ary mask

Good day,

I’ve created a single nifti image with 9 spherical ROIS (N-ary image).
Each of the sphere has a different value.
1st sphere =1 , second sphere = 2 and so on…

Is there an option in the `tckgen -seed_image image command to enable tracking from sphere1 to sphere2 within that single nifti file?

Thank you very much for your help.

Hi Julien,

No, currently tckgen considers any input ROIs in a boolean manner only. So it would simply seed from any voxel with a non-zero value.

So you could either:

  • Write a script that would loop over spherical ROI pairs, generating and using two ROI images corresponding to two of the spherical regions of interest at a time;

  • Do all of the tracking in a single go, and use “tck2connectome -assignment_all_voxels -out_assignments” followed by connectome2tck to produce one track file for every possible pair of regions that contains all streamlines that traverse both of those regions.


Many thanks for your answer.