[Mrtrix-discussion] filter_tracks

[Robert Smith]

Hi Ilaria,

If you combine the two ROIs into a single image, then filter_tracks will
treat that singular image as a single ROI, and
hence operate on any track that touches any highlighted voxel in that image.
This is why any track touching *either* of the two ROIs is being removed.

In order to perform your desired operation (remove all tracks that touch
both ROIs), you want to use the following:

filter_tracks in.tck -include ROI1.mif -include ROI2.mif -invert out.tck

By providing the two ROIs separately to filter_tracks using separate
-include options, you are specifying that you are
interested only in tracks that touch both ROIs. The -invert option then
specifies that those streamlines elected by the
ROIs are to be *excluded* from the output, rather than being the only
streamlines included in the output.

Cheers
Rob


--

*Robert Smith, Ph.D*
Senior 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

*MRtrix3*: Advanced tools for the analysis of diffusion MRI data
Website <http://www.mrtrix.org/> - Blog <http://www.mrtrix.org/blog/> -
Repository <https://github.com/MRtrix3/mrtrix3> - Community forum
<http://community.mrtrix.org/>

On Mon, Jun 12, 2017 at 4:18 AM, Ilaria Sani <isani01 at mail.rockefeller.edu>
wrote:

> Dear All,
>
> I'm using Mrtrix 0.2
>
> I would like to remove some specific tracks from my connectome.
> Specifically all the tracks between two ROIs.
>
> The closest thing I found is filter_tracks.
> The ROI I’m using is the combination of the two ROIs.
> However filter_tracks removes all the streamlines touching one OR the
> other ROI.
>
> Is there a way to select only the streamlines touching both?
> Alternatively, is there any other tool that removes tracks between two
> ROIs from the connectome?
>
> Thanks!!
>
> Ilaria
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>
>
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