Finally, I understand that the “count” line in tckinfo output gives the number of streamlines that have not been rejected by the exclusion criteria and have been accepted by the inclusion criteria, however I am not complete sure about what “total count” means.
It’s kind of legacy to a certain extent. In MRtrix 0.2, back when the command for generating streamlines was the only command that produced track data as output, “count” was the number of tracks in the file, and “total_count” was the number of streamlines that were generated (but not all of which were written to file). That’s still the case with tckgen, but obviously we now have many more commands that write track data. What I’ve tried to do throughout the various commands is have “total_count” reflect the number of streamlines present in the track file that was the input to the command that produced that track file.
Does the seed image of tckgen must be from the subcortical tissue type? I read that it is possible to seed from a subcortical structure, but I am giving a seed mask of the thalamus that was manually drawn and for that reason does not correspond 100% to the subcortical tissue as it is classified in the 5ttseg image.
Seeds will be drawn within the seeding mask you have defined, and cross-checked against the 5TT image to ensure that each individually is a “biologically valid” seed point. So if your mask contains a little bit of white matter, or omits a little bit of the thalamus, it just means that some streamlines may be seeded within the white matter near the thalamus, and some areas of the thalamus might not be seeded in. This is completely fine as far as the tracking code is concerned; it’s up to you to determine whether or not this is problematic from the standpoint of your experiment. Note however that this is pretty much inevitable, given that a seed mask is constrained to be binary whereas the 5TT segmentation includes partial volume fractions.
Is it possible that if a seed is located within my mask and outside subcortical tissue (as defined in 5ttseg), and a streamline keeps on going trough my mask and enters the subcortical tissue (as defined in 5ttseg), terminates due to criterion 5 (from ACT paper)?
Yes. Imagine two streamline points that are right next to one another, but one is just inside the SGM and the other is just outside it (i.e. in the surrounding white matter). The tracking will by default be bidirectional in both cases, and the same anatomical priors apply. The only potential difference in behaviour between the two is that if the streamline seeded within the SGM fails to exit the SGM in either direction, it will be thrown out, as all streamlines must be inside the WM at some point along their length.
Also, regarding SIFT2, I have been following the pipeline: … Am I correct to use this metric to compare the same pathway obtained in different hemispheres?
Yes, that’s the usual pipeline. The only other requirement is that bias field correction is necessary (otherwise, if the image intensities in one hemisphere were half that of the other, then the quantified “connectivity” would be halved as well).
I saw that I can also tckmap using both -precise and -tck_weights_in, where each voxel represents a volume. Therefore if I use mrcalc to sum just the non-zero voxels, am I going to get the fiber volume of the entire pathway?
Yes; although you could have taken the sum of (product of streamline weight and streamline length) and gotten the same result.
Is this a metric that can be used for “connectivity”?
You can; but we specifically advocate that fibre cross-sectional area is a better measure of “connectivity” than volume, as the latter scales directly with pathway length even though it has little effect on connection “bandwidth”, which is probably the best analogue of “connectivity” we can invoke. There’s some relevalt discussion here, as well as in the Fixel-Based Analysis paper in the justification of the FC metric.
