[Mrtrix-discussion] Comparing methods: filtering full brain tracts vs. seeding specific tracts

[Robert Smith]

Dorian

Both the -include and -exclude options in filter_tracks can be used
multiple times in the one command invocation, just as they can in
streamtrack. So if you have two ROIs, and want to select only those
streamlines that go through *both* of the ROIs (essentially a boolean AND
operation), your usage should look something like:
filter_tracks in.tck out.tck -include ROI1.mif -include ROI2.mif

>From your text I am guessing that you have combined your two ROIs into a
single image using mradd, then passed this image to filter_tracks using
-include? In this scenario, any streamline that enters *any* part of the
ROI passed to filter_tracks will be included (essentially a boolean OR
operation): the command does not consider whether or not an individual ROI
image contains discrete 'blobs', it just tests to see if the streamline
intersects the ROI at any point along its length. This is most likely why
your result contains unwanted streamlines: some of them traverse one
endpoint of the optic tract but not the other.

Hopefully that clarifies the issue
Rob


--

*Robert Smith, Ph.D*
Research Officer, Imaging Division

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7128
Fax: +61 3 9035 7301
www.florey.edu.au


On Wed, Jul 23, 2014 at 4:11 AM, Dorian P. <alb.net at gmail.com> wrote:

>  Hi all,
>
>  I am currently using MRtrix2 (yeah, I know is the old version) to do
> tractography of the optic tract. I have success when using a seed (+ an
> include roi + an exclude roi). However, when trying to select this pathway
> from full brain tractography it does not work for me. The command
> filter_tracks accepts only an include roi and an exclude roi. I  collapsed
> my previous seed and include roi to obtain a new include roi for the full
> brian filter. Yet, the result is not at all similar to the seed-based
> tractography, with a lot of pathways not related to the optic tract.
>
>  Is there a way to use better the filter_tracks, i.e., to have more than
> one include roi, such tracts are selected that pass both in roi1 AND in
> roi2. The help of filter_tracks states "-include: Tracks that enter ALL
>  such inclusion ROI will be included.". So doesn't seem to consider
> separate portions of rois to get the tracks that connect them.
>
>  P.s. I am using Windows.
>
>  Thank you
> Dorian
> TJU
>
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