Hi Anna,<br><br>The <span style="font-family:courier new,monospace">filter_tracks</span> 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.<br>
A couple of things to look for:<br><ul><li>In <span style="font-family:courier new,monospace">streamtrack</span>, the <span style="font-family:courier new,monospace">-number</span> option sets the desired number of output streamlines, while <span style="font-family:courier new,monospace">-maxnum</span> sets the maximum number of streamline <i>attempts</i>; 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.<br>
</li><li>If you do not set the <span style="font-family:courier new,monospace">-maxnum</span> option explicitly, <span style="font-family:courier new,monospace">streamtrack</span> will automatically set it to 100 times the <span style="font-family:courier new,monospace">-number</span> 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 <span style="font-family:courier new,monospace">-maxnum</span> to 0, and tracking will always continue until the desired number is reached.</li>
<li>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 <span style="font-family:courier new,monospace">.tck</span> file can be malformed if this is the case, so even MRtrix is unsure of how many streamlines there are. (This won't affect <span style="font-family:courier new,monospace">filter_tracks</span> though; it just reads streamline data until it reaches the end of the file)<br>
</li><li>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.<br>
</li></ul>MRtrix shouldn't have any problems with the number of streamlines in an individual <span style="font-family:courier new,monospace">.tck</span> file until you reach about 4 billion.<br>If you still can't find the source of the error, please run the <span style="font-family:courier new,monospace">track_info</span> program on your streamlines file and send us the output.<br>
<br>Best regards<br>Rob<br><br><div>--<br><br>Robert Smith<br>PhD Candidate <br><br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>Heidelberg Vic 3084<br>
Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span></div>
<br><br><div class="gmail_quote">On Fri, Mar 8, 2013 at 4:32 AM, Anna Varentsova <span dir="ltr"><<a href="mailto:avarents@gmail.com" target="_blank">avarents@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi all,<br><br>It looks like when I am running flter_tracks not all the tracks from the input file are read.<br>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%]><br>
Has anyone else had this problem? Is there any limit on number of tracks that can be saved in a single file?<br><br>Sincerely yours,<br>Anna<br>
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