I just updated my MRtrix to the new release, and I just found that the options in tckgen -initcutoff and -number are no longer available. I think the new names are -select and -seed_cutoff. Am I correct?
That sounds correct. These changes to the
tckgen interface happened as part of our first release candidate for 3.0. The changelog for the
tckgen changes specifically reads as follows:
The interface and behaviour of this command with respect to streamlines seeding and selection for inclusion in the output track file have been altered to clarify the logic. Of particular interest for users will be the renaming of these two crucial command-line options:
-number is now accessed through -select.
-maxnum no longer exists, but its approximately equivalent replacement is -seeds.
Previously, -maxnum influenced the maximum number of streamlines that would be generated, irrespective of the desired number of streamlines to be written to the output file. In practise however it tended to be used / interpreted as setting the number of streamline seeds, which is subtly different (some seed positions might not be suitable for generating tracks, e.g. if below threshold or outside the brain mask).
Therefore, the new behaviour is to explicitly control the number of streamline seeds using the -seeds option; and for each seed point attempted, the algorithm will perform a more exhaustive search for an appropriate initial tracking direction.
In addition, the command’s progress message will dynamically report the number of streamline seeds, the number of streamlines actually generated from those seed points, and the number of streamlines selected and written to the output file (previously only the latter two were reported).
The -info option can still be used to report more detailed statistics on how the tracking performed (with respect to e.g. why generated streamlines aren’t being selected and written to the output file).
For more info on other changes that happened during RC1 and the more recent RC2 (both of which would affect you, if you just updated now and witnessed those
tckgen changes) can be found here: