[Mrtrix-discussion] streamline counting

[Parker, Christopher]

Hi Markus,

Thanks for your quick reply. The command line option looks good, just what I need. I will try it when my ROIs are ready for the tracking and let you know if I have any difficulty with it. Thanks a lot!

Best,
Chris


________________________________
From: Markus Gschwind [markus.gschwind at gmail.com]
Sent: 05 April 2012 19:23
To: Parker, Christopher
Cc: mrtrix-discussion at www.nitrc.org
Subject: Re: [Mrtrix-discussion] streamline counting

Hi,

You can use the command "track_info" that gives displays among others the value "count"

You can also read the command into a variable "count" using the following:

count=`track_info mytrack.tck | grep '\<count:' | awk '{ print $2 }'`

Hope this helps!
Markus


2012/4/5 Parker, Christopher <christopher.parker.10 at ucl.ac.uk<mailto:christopher.parker.10 at ucl.ac.uk>>
Hi everyone,

Someone may know the answer to this question. I'm hoping to apply probabilistic streamline tractography between two ROI using MrTrix. But, instead of analysing the tract density images I would like to count the total number of streamlines that connect the two ROI. Is there some way to do this using MrTrix? I have not seen any mention of it in the Documentation or the forum, though it would be perfect for my analysis.

Chris

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