Thanks Robert! <br><br>That does work as expected. I am wondering whether it is possible to define the seeds for tracking in the deterministic tracking in a more resolved manner. That is, how can I initiate tracking from every single voxel in an ROI and then select only those tracks that go another ROI? Essentially, I want to get exactly the same results and all the possible results in two different instantiations of the program. Is that possible? <br>
<br>Cheers, <br><br>Ariel <br><br><div class="gmail_quote">On Wed, Nov 2, 2011 at 5:36 PM, Robert Smith <span dir="ltr"><<a href="mailto:r.smith@brain.org.au" target="_blank">r.smith@brain.org.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Hi Ariel<br><br>The effect you're seeing appears to be a problem in the way the <span style="font-family:courier new,monospace">-stop</span> option is applied.<br>Currently, it detects the moment when the track enters <u>any</u> of the include regions (effectively a Boolean 'OR' operation), and terminates tracking.<br>
The <span style="font-family:courier new,monospace">-include</span> option however specifies that a track must enter <u>all</u> regions (a Boolean 'AND' operation) in order to be accepted and written to the output file.<br>
So what's happening, is that the tracks are being stopped as soon as they enter one region, none of them are succeeding in reaching the other region, and you end up with no tracks!<br><br>I will confer with Donald regarding exactly how this option should be applied, and it will likely change for the next release. In the time being, you have a couple of options:<br>
* Use one ROI as the seed region, and the other as the include region.<br>* Try the update I have attached to this message - these two files replace the existing ones in <span style="font-family:courier new,monospace">(mrtrix_directory)/src/dwi/tractography/tracker/</span> (rename and keep the existing files just in case). You will need to re-compile after replacing the files. This will change the handling of the <span style="font-family:courier new,monospace">-stop</span> option, and should hopefully make it behave a little more sensibly. Note however that it will not yield the cropped portion of tracks between the two regions as you expected - it will yield the section of track between the seed (wherever that happens to be) and the point at which it enters whichever include region it traverses last.<br>
<br>Best regards<br>Rob<br clear="all"><font color="#888888"><br>--<br><br>Robert Smith<br>Melbourne Brain Centre<br>245 Burgundy Street<br>Heidelberg VIC 3084<br>Telephone: <a href="tel:%28%2B61%203%29%209035%207128" value="+61390357128" target="_blank">(+61 3) 9035 7128</a><br>
Fax: <a href="tel:%28%2B61%203%29%209035%207301" value="+61390357301" target="_blank">(+61 3) 9035 7301</a><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></font><div><div></div><div><br><span style="font-size:9pt;font-family:"Times New Roman","serif";color:red"></span><br>
<br><br><div class="gmail_quote">On Wed, Nov 2, 2011 at 6:48 AM, Ariel Rokem <span dir="ltr"><<a href="mailto:arokem@gmail.com" target="_blank">arokem@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">
Hi Donald, <br><br>First of all, thanks for making mrtrix available! You were right: it wasn't too painful to get things compiled on fedora. The one comment that I had is that for some dependencies (gtkglext, in particular) you have to get the "-devel" version of the library, otherwise the build process throws cryptic pkg-config errors at you. That might be obvious to some, but got me puzzled for a bit there. Once I figured that out, though, it went quite smoothly and I have 0.2.9 running. <br>
<br> Now for a specific question on the "-stop" feature of streamtrack.<br><br>Running this command: <br><br>streamtrack -seed r_occipital.mif -mask wmMask.mif -include ROI1.mif -include ROI2.mif SD_STREAM CSD12.mif out.tck -number 1000 -maxnum 1000000<br>
<br>Produces 1000 tracks, as expected, which I can then view in mrview and seem to be in the right place, except that they go beyond the ROIs. That's where I thought that "-stop" can come in handy. <br><br>
Running: <br>
<br>streamtrack -seed r_occipital.mif -mask wmMask.mif -include ROI1.mif
-include ROI2.mif SD_STREAM CSD12.mif out.tck -number 1000 -maxnum
1000000 -stop <br><br>On the other hand, produced no tracks at all. Is this just bad luck in the random choice of seed points within the seed region? I tried it twice, to convince myself that wasn't it. Is this an expected behavior of streamtrack? I might be misunderstanding what it's supposed to be doing. I thought that it would give me roughly the same set of tracks, but clipped to only the bit of the fiber that is between ROI1 and ROI2. <br>
<br>Thanks again, <br><br>Ariel <br><br><br><br><div class="gmail_quote">On Sun, Oct 30, 2011 at 7:14 PM, Donald Tournier <span dir="ltr"><<a href="mailto:d.tournier@brain.org.au" target="_blank">d.tournier@brain.org.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex">Hi all,<div><br></div><div>Nice to see so much discussion going on, keep it up!</div><div><br>
</div><div>Ariel: to answer your question: the -stop option was introduced in 0.2.8. Sorry... </div><div><br></div><div>Shouldn't be that hard to compile on Fedora though, later versions should compile without modification. Let me know if it doesn't...</div>
<div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><br></div><div><br><div class="gmail_quote"><div><div></div><div>On 29 October 2011 10:03, Ariel Rokem <span dir="ltr"><<a href="mailto:arokem@gmail.com" target="_blank">arokem@gmail.com</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex"><div><div></div><div>Hi Thijs, <br><br>I am following this discussion with some interest: <br>
<br><div class="gmail_quote"><div>
On Fri, Oct 28, 2011 at 2:23 AM, Thijs Dhollander <span dir="ltr"><<a href="mailto:thijs.dhollander@uzleuven.be" target="_blank">thijs.dhollander@uzleuven.be</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204, 204, 204);padding-left:1ex"><div link="blue" vlink="purple" lang="NL-BE"><div>
<span style="font-size:10pt;color:rgb(31, 73, 125)" lang="EN-US"> </span>
<p class="MsoNormal"><span style="font-size:10pt;color:rgb(31, 73, 125)" lang="EN-US">About your question: what you're looking for is the "<b>-stop</b>" option (with no extra arguments). If you include this one in your streamtrack
command, all tracks will stop as soon as they enter any of your include regions: i.e. they will not track beyond your target ROI (but also not "within", only "up to", I suppose).<u></u><u></u></span></p>
<p class="MsoNormal"><span style="font-size:10pt;color:rgb(31, 73, 125)" lang="EN-US"><u></u> </span></p></div></div></blockquote></div><div><br>Is this a new feature? I can't seem to find it in 0.2.7, but would rather not have to build from source mrtrix (on fedora...) if that's not necessary in order to get this feature working for me. <br>
<br>Thanks, <br><font color="#888888">
<br>Ariel <br><br></font></div></div>
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<br></blockquote></div><font color="#888888"><br><br clear="all"><div><br></div>-- <br>Jacques-Donald Tournier (PhD)<br>Brain Research Institute, Melbourne, Australia<br>Tel: <a href="tel:%2B61%20%280%293%209035%207033" value="+61390357033" target="_blank">+61 (0)3 9035 7033</a><br>
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