Seed points only at the mask edges


Hello all,

After looking at the seed points within the mask (ROI: hippocampus) by tckgen, I realized that only the voxels in vicinity to the white matter were selected as seed points.

(red: mask, violet: seed points)

Is there a way to seed fibers from any voxel of the mask and not only from those at the periphery of the ROI?

Thank you in advance,


Hi Nick,

Could it be there’s a second mask not (completely) including your region of interest? For example a white matter mask.
Maybe you can copy paste here the command you’re using.

Kind regards



Hi Thibo,

In fact, I added the hippocampus to the white matter, but it didn’t change anything.

Here is the command that I’m using for tractography:

tckgen -nthreads 4 -algorithm iFOD2 -number x -maxlength y -minlength z -downsample 6 -act 5TT.nii.gz -backtrack -force -seed_image hippo_mask.nii WM_fod.nii.gz tracto.tck



I suspect that this is because the hippocampus is by default labelled as “cortical” grey matter (really more pragmatically described as “non-penetrable grey matter”), meaning that ACT does not permit streamlines to be within that region (whether due to candidate seed points being within that region or due to streamlines projecting toward that region).

If you were to use the -sgm_amyg_hipp option in 5ttgen, then the hippocampi and amygdalae would be explicitly segmented and labelled as “sub-cortical” (“penetrable”) grey matter, meaning that streamlines can both be seeded within those regions, and when streamlines enter such regions from the white matter, the streamlines can project into those structures, rather than being terminated immediately at the tissue interface.

I’ve never been sure what best to do here: While these two structures would ideally be treated the same way as other non-cortex grey matter nuclei, doing so with the 5ttgen fsl script in particular can lead to some unintended consequences due to the way in which intensity-based and surface-based segmentations are combined.