I want to do FBA but I want to restrict my FBA to fixels located in the region of a specific pathway
If you are specifically trying to constrain FBA to a particular pathway, this could be done using the
-mask option in
fixelcfestats. Since the fixel-fixel connectivity matrix is constrained to only consider pairs of fixels within this mask, and data smoothing is performed based on this connectivity matrix, use of this option will prevent smoothing from introducing values from outside your pathway of interest into the analysis. So this may be a more direct solution to your issue than attempting to restrict the trajectories or extent of the streamlines used to determine this connectivity.
Ideal is to crop the streamline once it enters the ROI on both sides.
An alternative but imperfect approach, if you really want to manipulate the streamlines in this way, is:
Perform whole-brain tracking on the template as per whole-brain FBA.
Add the two ROIs, and then take the inverse of this mask (using
mrcalc 1.0 - -sub).
Use this as the
-mask option in
tckedit. This will crop out any streamline vertices within your two ROIs. Note that as a result, any streamline that passes entirely through one or both of these ROIs will be broken into multiple streamlines in the output track file.
Dilate each of your ROIs by one voxel.
tckedit again, providing the two dilated ROIs as separate inputs via the
-include option. This will select only streamlines that intersect both of the dilated ROIs. Mostly, this will be streamlines that traversed both ROIs, but only the segment in between the two ROIs will be preserved due to the prior masking step. This may however additionally select some streamlines that pass adjacent to one of the ROIs due to the requisite dilation step; these would need to be cleaned up manually, or you could use e.g. the
tckedit -minlength option.
As you are suggesting ACT, I am wondering, is ACT compatible with other features, such as -include, -exclude and -seed_image?
Yes, ACT operates more-or-less independently of such features. The exception is if you draw such regions entirely within cortical grey matter, then things may not behave as one may expect intuitively; though this will change in the future. But using ACT here would be a bush-mechanic’s fix, and would suffer from a similar problem to the
-stop option described below.
Or maybe the -stop parameter is what I am looking for. Do you think that the following could achieve my goal?
-stop option in
tckgen will terminate a streamline as soon as it intersects the last include region that it encounters. So if you want the streamlines to end as soon as they enter a region, rather than as soon as they exit a region, then this approach can work; however streamlines will still fully traverse and even exit any
-include region if there is at least one other
-include region that it has not yet encountered. So this may or may not be adequate for what you’re trying to do, since each streamline would only be constrained from passing through one of the two ROIs, depending on the direction of propagation. But this could potentially be “solved” using the
tckedit streamline cropping technique described above.