[Mrtrix-discussion] Bidirectional tracks and include region (follow up to Question on fiber tracking)

[Donald Tournier]

Hi Chris,

With the -stop option, inclusion regions and bidirectional tracks in
> streamtrack, do tracks get accepted if tracks in both directions hit the
> inclusion region or are they accepted if only one direction hits the
> inclusion region?
>

Only one direction needs to hit the inclusion ROI for the whole track to be
accepted. The -stop option simply ensures the track does not propagate any
further as soon as it's included, so you don't need to worry about where
else it might go if it were to propagate through the inclusion ROI and out
of the other side.



> Also, is there a way of finding out where the tracks are ultimately
> seeded from if using bidirectional tracks?
>

Unfortunately not... It would be easy to modify the code to output this
information into a separate file if required. Basically, you'd need to
modify cmd/streamtrack.cpp, and add:

- one line at 276 to store the seed point:
       Point seed (tracker->position());

- modify line 287 to accept the seed point as an additional argument:
     append (tck, (!tracker->track_excluded() && tracker->track_included()
&& tck->size() > min_size), seed);

- modify the append() declaration at line 223 to accept the seed point as an
argument:
   void append (std::vector<Point>*& tck, bool accept, const Point& seed)

- get append() to output the positions at line 229 if the track is accepted:
  std::cout << seed[0] << " " << seed[1] << " " << seed[2] << "\n";

This will spit out the seed positions to standard output, so you'd need to
redirect the output of streamtrack to a file:
$ streamtrack blah blah > seeds.txt

There's ways to make it prettier with options etc, but as a first rough cut
that should do it...

Cheers,

Donald.



> Thank you in advance,
>
> Chris Adamson.
>
> --
> Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons.,
> Monash)
> Research Officer
> Developmental Imaging, Critical Care and Neurosciences
>
> Murdoch Childrens Research Institute
> The Royal Children’s Hospital
> Flemington Road Parkville Victoria 3052 Australia
> T 9345 4306
> M XXXX XXX XXX
> E chris.adamson at mcri.edu.au
> www.mcri.edu.au
>
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-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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