Hi folks,
thanks for putting together and maintaining MRTrix.
I am trying to use tckgen using iFOD2 with ACT to get some tractography data.
I am trying to seed a particular region of the whole-brain GMWMI, and I have created the corresponding GMWMI mask. I would like to get a fixed number of successful streamlines.
My general call looks like this
tckgen \
-algorithm ifod2 \
-act "${5ttgen_fname}" \
-backtrack \
-seed_grid_per_voxel "${gmwmi_fname}" ${grid_size} \
-nthreads ${n_threads} \
-minlength ${min_length} \
-maxlength ${max_length} \
-select ${strml_count} \
${fod_fname} \
${tractogram_fname}
where strml_count is 500k.
For an attempt I have done with the whole brain GMWMI, the resulting tractogram contains a little over 6M streamlines (so selected is over 6M). For another attempt I have done with the particular GMWMI region, I get 134k streamlines selected.
My understanding would be that -seed_grid_per_voxel fully determines how many seeds are going to be generated. I would have expected tckgen to return a tractogram with exactly the desired streamline count as long as the successful tracking attempts exceed that value. From my first attempt, this seems not to be the case.
I see that if I use -seed_gmwmi instead of -seed_grid_per_voxel I do get 500k streamlines selected in either case, which matches my expectations.
So I am wondering whether the behavior about the number of selected streamlines cannot be achieved with -seed_grid_per_voxel.
Also, I am wondering whether specifying -crop_at_gmwmi means that all resulting streamlines will have at least one vertex in the GMWMI. That is, if I later do a tckedit where the inclusion mask is my GMWMI, whether I should get the exact same tractogram given at the input. I assume that the cropping will happen at the WMGMI that the 5ttgen image contains.
I am for sure missing very fundamental things here.
Thank you.