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.
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.