Hi there Yu<br><br>By default, MRtrix performs <i>bidirectional</i> tracking i.e. it tracks both forwards and backwards from the seed point. To construct a single continuous streamline from this data, it 'stitches' the two half-streamlines together - as such, the point along the streamline which was the seed point cannot be determined. This is partly by design; ideally the path of a streamline should not be dependent upon exactly which point along its length was used as the seed, so this information is deemed irrelevant. It's conceptually possible to modify <span style="font-family: courier new,monospace;">streamtrack</span> to provide you with the exact seed point of each streamline in a separate file, but it's not a trivial change and would require a decent grasp of C++ programming.<br>
<br>By contrast, if you are using <i>unidirectional</i> tracking (by specifying the <span style="font-family: courier new,monospace;">-unidirectional</span> option), the first point of each track will always be the seed point. But be careful, the track data provides points in 'real space', not voxels; these data need to be transformed first if you wish to determine which voxel each point lies within. The program <span style="font-family: courier new,monospace;">tracks2prob</span> is an example of where this sort of transformation is used if you are looking to implement a similar functionality.<br clear="all">
<br>In terms of the random seeding, I won't bore you with the statistics but as long as your number of streamlines is much greater than your number of seed voxels, you can expect at least one streamline to be seeded from each voxel. But bear in mind that the random seeding is not only a selection of which voxel to seed from; it also randomly selects a position within the volume occupied by that voxel. This is important as a streamline seeded from one corner of a voxel could traverse a very different path to one seeded from the opposing corner. You could consider the ratio between your number of streamlines, and the number of voxels in your seed, as a sort of 'over-sampling ratio', defining the approximate number of streamlines which are seeded from different starting points within each voxel. The greater this ratio (i.e. the more tracks you generate), the less likely you are to 'miss' potential pathways due to the random nature of the sampling.<br>
<br>Hope this is of some help to you<br>Rob<br><br>--<br><br>Robert Smith<br>Melbourne Brain Centre<br>245 Burgundy Street<br>Heidelberg VIC 3084<br>Telephone: (+61 3) 9035 7128<br>Fax: (+61 3) 9035 7301<br>Email: <a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a><br>
<a href="http://www.fni.edu.au" target="_blank">www.florey.edu.au</a> <a href="http://www.brain.org.au" target="_blank">www.brain.org.au</a><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span><br>
<br><br><div class="gmail_quote">On Fri, Dec 9, 2011 at 9:25 PM, yu zhang <span dir="ltr"><<a href="mailto:zhangyu2ustc@gmail.com">zhangyu2ustc@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Dear all:<br><br> I wanted to use the streamtrack to generate the connectivity pattern of the seed mask.<br> I have extracted the streamlines from the .tck files. It included 5000 streamlines without any information about seed voxels. <br>
At first, I assumed that the first voxel in track.data was the seed voxel. However, the generated seed mask was far different from the original seed mask which I had used.<br><br>I was wondering how could I define the seed voxel for each streamline?<br>
<br>Besides, how could I ensure that the random seeds starting from each voxel in the seed mask?<br><br>Thank you very much!<br><br>Sincerely,<span class="HOEnZb"><font color="#888888"><br> Yu Zhang.<br> <br>
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