[Mrtrix-discussion] RE: Mrtrix-discussion Digest, Vol 33, Issue 9

[Robert Smith]

Gabriel

When placing your exclusion regions, bear in mind that a streamline only
has to enter that region *at any point along its length* to be excluded
from the output. Therefore, you ideally want to draw these regions such
that they do not interfere with your pathway of interest whatsoever, but
all of the spurious tracks that you do wish to remove enter at least one of
them, even if it is only for a short section of their length.

An alternative to excluding these spurious pathways during tracking would
be to perform your tracking using inclusion regions only, and later
sub-divide the track data using the filter_tracks program I distributed
earlier this year. This program uses the same -include / -exclude syntax as
streamtrack, but applies this logic to an existing track file, rather than
the streamlines as they are generated. This may be preferable to
iteratively tracking and then refining your regions of interest, and has
the added benefit of being able to see exactly which streamlines are being
included / excluded by comparing the track files before and after filtering
(if one of your exclusion regions interferes with your pathway of interest
during tracking, you may not be made aware of it). You can find this
program within the discussion
archives<http://www.nitrc.org/pipermail/mrtrix-discussion/2011-September/000269.html>
.

Happy tracking!
Rob

--

Robert Smith
Melbourne Brain Centre
245 Burgundy Street
Heidelberg VIC 3084
Telephone: (+61 3) 9035 7128
Fax: (+61 3) 9035 7301
Email:  r.smith at brain.org.au
www.florey.edu.au <http://www.fni.edu.au>        www.brain.org.au



On Sat, Nov 26, 2011 at 12:05 AM, Gabriel Gonzalez Escamilla <ggonesc at upo.es
> wrote:

> Thank you so much Rob, now everything works just fine.
>
> I have i little doubt about the tracking, when I do it, some regions have
> spurious tracks, so as you said I will include some exclude ROIs but, my
> doubt is, the track I don't want are in regions belonging other tracts that
> i will track latter, should I use a mask of each tract as excluding region,
> or just some parts of them??'
>
>
> El 25/11/11, *Robert Smith * <r.smith at brain.org.au> escribió:
>
> Gabriel
>
> From that error message, it looks like you're running either MRtrix 0.2.8
> or 0.2.9. The files I provided were from the subversion repository (which
> contains the most up-to-date code), but it would seem that there's an
> incompatibility between this code and the numbered releases.
>
> The attached files (again to replace those in
> src/dwi/tractography/tracker/) should compile on either 0.2.8 or 0.2.9.
> They will fix the issue with the -stop command, without modifying the
> tracking in any other way.
>
> Rob
>
> --
>
> Robert Smith
> Melbourne Brain Centre
> 245 Burgundy Street
> Heidelberg VIC 3084
> Telephone: (+61 3) 9035 7128
> Fax: (+61 3) 9035 7301
> Email:  r.smith at brain.org.au <r.smith at brain.org.au>
> www.florey.edu.au <http://www.fni.edu.au>        www.brain.org.au
>
>
>
>
> On Fri, Nov 25, 2011 at 8:23 PM, Gabriel Gonzalez Escamilla <
> ggonesc at upo.es <ggonesc at upo.es>> wrote:
>
>> Dear Robert,
>> I was trying to compile again the MRtrix, but it gave an error message:
>>
>> ERROR: [CC] cmd/streamtrack.o
>>
>> g++ -c wall -march=native -fPIC -fno-strict-aliasing
>> -DGL_GLEXT_PROTOTYPES -DUSE_TR1 -03 -pthread -I/user/include/glibmm-2.4
>> -I/user/lib/glibmm-2.4/include -I/user/include/sigc++-2.0
>> -I/user/lib/sigc++-2.0/include -I/user/include/glib-2.0
>> -I/user/lib/glib-2.0/include -Ilib -Isrc cmd/streamtrack.cpp -o
>> cmd/streamtrack.o
>>
>> failed with ourtput:
>>
>> cmd/streamtrack.cpp: In member function ´void
>> Threader::execute(MR::DWITractography::Tracker::Base*)´:
>> cmd/streamtrack.cpp.270: error: no matching function for call to
>> MR::DWI::Tractography::Tracker::Base::new_seed(const MR::Point&)´
>> src/dwi/tractography/tracker/base.h:65: note: candidates are: void
>> MR::DWI::Tractography::Tracker::Base::new_seed(const MR::Point&, float)
>>
>>
>> Do you have any idea of what's happening?
>>
>> Best Regards,
>> Gabriel
>>
>
>
> --
> --------------------------
> PhD. student Gabriel González-Escamilla
> Laboratory of Functional Neuroscience
> Department of Physiology, Anatomy, and Cell Biology
> University Pablo de Olavide
> Ctra. de Utrera, Km.1
> 41013 - Seville
> - Spain -
>
> Email: ggonesc at upo.es
> http://www.upo.es/neuroaging/es/
>
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