[Mrtrix-discussion] filter_tracks issues

[Robert Smith]

Hi Anna,

The filter_tracks program is relatively simple, so it's almost certain that
the number of tracks it reads is the actual number of tracks in the input
file.
A couple of things to look for:

   - In streamtrack, the -number option sets the desired number of output
   streamlines, while -maxnum sets the maximum number of streamline *
   attempts*; the latter will be greater than the former due to the minimum
   length criterion, as well as any include/exclude regions. Just double-check
   that you used the correct option.
   - If you do not set the -maxnum option explicitly, streamtrack will
   automatically set it to 100 times the -number option; so depending on
   the ROIs in your initial tracking, it's possible that the tracking was
   terminated at 586,456 streamlines rather than your desired 1,910,000 due to
   the number of streamline attempts reaching 58,645,600. To stop this kind of
   behaviour, you can set -maxnum to 0, and tracking will always continue
   until the desired number is reached.
   - If the tracking was terminated prematurely (this can occur due to a
   wide range of reasons), then there may not be as many streamlines in the
   file as you wanted. Furthermore, the 'count' field in the header of the
   .tck file can be malformed if this is the case, so even MRtrix is unsure
   of how many streamlines there are. (This won't affect
filter_tracksthough; it just reads streamline data until it reaches
the end of the file)
   - We have had reports of streamtrack crashing on Windows systems;
   Windows fails to free the memory used by MRtrix, and subsequently the
   system runs out of memory. Running the Linux version of MRtrix inside a
   virtual machine is preferable.

MRtrix shouldn't have any problems with the number of streamlines in an
individual .tck file until you reach about 4 billion.
If you still can't find the source of the error, please run the
track_infoprogram on your streamlines file and send us the output.

Best regards
Rob

--

Robert Smith
PhD Candidate

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 Fri, Mar 8, 2013 at 4:32 AM, Anna Varentsova <avarents at gmail.com> wrote:

> Hi all,
>
> It looks like when I am running flter_tracks not all the tracks from the
> input file are read.
> For example, there is a test file test.tck with 1910000 tracks in it,
> after running <filter_tracks -include roi1.nii -include roi2.nii test.tck
> test_out.tck> I get the following message <586456 read, 80 selected [100%]>
> Has anyone else had this problem? Is there any limit on number of tracks
> that can be saved in a single file?
>
> Sincerely yours,
> Anna
>
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>
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