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

[Dorian P.]

Thank you Robert. I hadn't realized the flags can be used multiple times.

Best wishes.
Dorian
On Jul 22, 2014 10:47 PM, "Robert Smith" <robert.smith at florey.edu.au> wrote:

> 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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