[Mrtrix-discussion] filter_tracks

Tue Jun 13 13:50:09 PDT 2017

Sorry Rob,  I made a mistake…
My problem is that:

filter_tracks is doing an OR operation rather than AND, when I use two combined ROIs.

+

I don’t get any filtering when I use   -include roi1    -include roi2

Is that working for you?
Am I doing something wrong/different?

Thanks,
Ilaria

From: mrtrix-discussion-bounces at www.nitrc.org [mailto:mrtrix-discussion-bounces at www.nitrc.org] On Behalf Of Ilaria Sani
Sent: Tuesday, June 13, 2017 3:21 PM
To: Robert Smith <robert.smith at florey.edu.au>
Cc: mrtrix-discussion at www.nitrc.org
Subject: Re: [Mrtrix-discussion] filter_tracks

Hi Rob,

I’m using the syntax suggested in filter_tracks documentation:
filter_tracks [ options ] input output

that is:
filter_tracks    -invert     -include    my-combined-rois    my-input-connectome    output.tck
This is working, but it’s doing an AND operation rather than OR.

I also tried to use –include twice, once for each roi.
I don’t get any error, but no filtering is happening.
For example, if my input connectome has 500k streamlines, the filtered output connectome will have 500k streamlines too.
Here is my syntax:
filter_tracks    my-intput-connectome    -include roi1    -include roi2    -invert output.tck
or
filter_tracks    -include roi1    -include roi2    -invert    my-intput-connectome    output.tck

Is that working for you?
Am I doing something wrong/different?

Thanks,
Ilaria

From: Robert Smith [mailto:robert.smith at florey.edu.au]
Sent: Monday, June 12, 2017 9:05 PM
To: Ilaria Sani <isani01 at rockefeller.edu<mailto:isani01 at rockefeller.edu>>
Cc: mrtrix-discussion at www.nitrc.org<mailto:mrtrix-discussion at www.nitrc.org>
Subject: Re: [Mrtrix-discussion] filter_tracks

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