Using ACT in tracts that go through subcortical GM structures

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… is it possible to edit the code to get rid of rule 6 …

It would certainly be possible. I didn’t want to have command-line options toggling such things as it would introduce unnecessary code branching that can really slow down modern processors. But I’d need to re-acquaint myself with the code and experiment to get such a change working; I’m not convinced it’s going to be a simple one- or two-liner.

I would instead advocate re-thinking how to approach the experiment. My naive biological expectation is that the individual neuronal axons constituting this pathway do not individually “pass though” the thalamus: instead, there are fibers that come from the cerebellum and synapse in the thalamus, and then there are other fibers that project from the thalamus to the cortex. Why not try to reconstruct this pathway in a similar fashion:

  1. Reconstruct one half of the pathway only, using tckgen / tckedit.

  2. Generate a spatial map of streamline endpoint density, using tckmap -ends_only.

  3. Mask the output of step 2 to include only the streamlines terminations within the thalamus.

  4. Reconstruct the other half of the pathway, providing the output of step 3 to the -seed_rejection option in tckgen, and additionally using -seed_unidirectional.
    This instructs tckgen to place streamline seeds in the same locations as where the streamlines from step 1 terminated, but will importantly place more seeds in those locations where there were more streamlines from step 1 terminating.
    While not described in the ACT manuscript, the current implementation does permit seeding of streamlines within sub-cortical grey matter structures, with the requirement that such a streamline must still traverse the WM at some point along its length (i.e. no within-SGM-only streamlines are permitted).

The difference between this approach, and disabling ACT criterion 6, is that you will not have individual streamlines that go from cerebellum to cortex through the thalamus. You will instead (approximately) have streamline pairs: one from cerebellum to thalamus and one from thalamus to cortex, that originate from (approximately) the same location in the thalamus. The tangent direction of these streamlines at their endpoints within the thalamus will not necessarily be collinear, whereas an individual streamline passing through the thalamus would necessarily have a continuous, slowly-varying tangent.

@jdtournier’s suggestions are also entirely valid.

… note you’re providing two seeding options. I’m not sure how the command will handle this…

Even though it’s “interface” seeding, -seed_gmwmi still requires an image volume as input, and thus has a reportable 3D volume (integral in this case since it can contain floating-point values). So when you provide tckgen with two seeds, what happens is: For each individual streamline to be seeded, one of the two provided seed sources is chosen at random based on their relative volumes, with seed sources of larger volume being more likely to be chosen each time. So once you’ve generated a large number of streamlines, the proportion of generated streamlines (not necessarily the number of selected streamlines) that originated from having seeded in each seed source image should approximately match the relative 3D volumes of those seed sources.

Note however that there are certain seed sources that are expressly forbidden from being combined with one another in a single tckgen invocation… this applies particularly to the -seed_grid_per_voxel and seed_random_per_voxel options. I also can’t guarantee that tckgen will perform exactly in an unambiguously expected manner for all conceivable combinations of multiple input seeds; but I hope that the logic I put in place is robust against such malicious intent.

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