I want to know if there is a way to know what the value of the proportionality constant mu (as mentioned in the papers) is after running SIFT/SIFT2
If you’ve run
tcksift, this will be reported as a key-value entry “
sift_mu” in the track file’s header, visible through
tcksift2, you don’t get this since no track file is generated (in the coming update there’s an additional command-line option to write this value to a text file, which can come in handy). The value does however get reported if you run either command with the
-info flag (both before and after filtering in the case of
tcksift, and just once for
tcksift2 since it remains fixed).
So what I’ve done in the past is run
tcksift with the
-nofilter flags: That’ll redo the FOD segmentation and track mapping, print the value of the proportionality coefficient, but won’t actually remove any streamlines.
I worked my way backward, using the
after_target.mif to compute
mu. But this value always turns out to be 1. Why is it so?
after_tdi.mif is pre-scaled by
Track density scaled” nothing but
TD is the same as “
Track density unscaled”? If so, I should be able to get at
mu just by a simple operation.
Correct - if you’ve generated that file already.
If this is indeed the case, the
mu that I get from
after_scatterplot.csv should match with what I get from
after_diff.mif. But this doesn’t happen. Am I missing something here?
Suspect this is a continuation of the point above?
Also, what does the field “
Weight” correspond to?
This was expressed as
PM in the manuscript. I called it a “processing mask” early on and stuck with it, but in retrospect it’s a bad name because the influence of these data is non-binary. Different fixels contribute more or less toward the model on a continuous scale depending on the (estimated from 5TT image) partial volume contamination.