<div dir="ltr"><div><div>Hi Robert,<br>thanks for the quick fix.<br></div>I noted your recommendations about github and mif files, I am quite a newbie to mrtrix and often have to create cross-ni-software pipelines but will try to use mif for pure-mrtrix pipelines.<br>
</div><div>Cheers.<br></div><div><br></div>basile<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Jun 25, 2014 at 3:18 PM, Robert Smith <span dir="ltr"><<a href="mailto:robert.smith@florey.edu.au" target="_blank">robert.smith@florey.edu.au</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div>Hi Basile<br><br></div>Thanks for the very informative and helpful report; it made the error much easier to locate and fix.<br>
<br></div>The <a href="https://github.com/jdtournier/mrtrix3/commit/c8e3955811fc05f3406d353028dbf1a5" target="_blank">offending commit</a> actually relates to code deep within the multi-threading framework.<br>
In every other use case this change will have had no effect whatsoever, but the dynamic seeding framework is far from a 'typical' use case (it's a <a href="https://github.com/jdtournier/mrtrix3/blob/master/src/dwi/tractography/tracking/exec.h#L78" target="_blank">thing of beauty</a>, actually). Following the change in the multi-threading code, the threads didn't know when it was time to terminate, and so the command hung at 99%.<br>
<br>
</div>I've just pushed a code commit that fixes the problem.<br><br></div>A couple of other quickies since I never get tired of hearing myself type:<br><ul><li>GitHub (which hosts the MRtrix3 code) has an <a href="https://github.com/jdtournier/mrtrix3/issues?state=open" target="_blank">issue tracking system</a>. If you ever experience behaviour in the new release that you are confident is a bug, or have a great idea for a feature, people are more than welcome to post there if they choose; it also means that you get credit for anything you report / suggest.</li>
<li>I couldn't help noticing the use of compressed NIfTI images... Given I went to the effort of coding it up, I might as well mention that the new version supports .mif.gz images. Solving all your image compression needs without the constraints of a fixed-width header and ambiguous transform :-P</li>
</ul>Good <your relevant timezone> everyone<br><br>Rob</div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>Research Officer, Imaging Division</span><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: <a href="tel:%2B61%203%209035%207128" value="+61390357128" target="_blank">+61 3 9035 7128</a><br>
Fax: <a href="tel:%2B61%203%209035%207301" value="+61390357301" target="_blank">+61 3 9035 7301</a><br><a href="http://www.florey.edu.au/" target="_blank">www.florey.edu.au</a><br>
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<br><br><div class="gmail_quote">On Wed, Jun 25, 2014 at 5:51 PM, basile pinsard <span dir="ltr"><<a href="mailto:basile.pinsard@gmail.com" target="_blank">basile.pinsard@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<div>Hi MRtrix experts,<br>
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running tckgen on a cluster and the nodes are centos 6.5, with this specific set of option:<br>
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<div>$ tckgen -force -act 5tt.nii.gz -info -maxlength 250 -nthreads 12 -number 10000 -seed_dynamic fod.nii.gz -step 0.2 fod.nii.gz track.tck<br>
....<br>
tckgen [INFO]: step size = 0.2 mm<br>
tckgen [INFO]: maximum deviation angle = 14.4 deg<br>
tckgen [INFO]: minimum radius of curvature = 1.25 mm<br>
tckgen [INFO]: iFOD2 internal step size = 0.0666667 mm<br>
tckgen [INFO]: opening image "fod.nii.gz"...<br>
tckgen [INFO]: rejection sampling will use 7 directions with a ratio of 1.0728 (predicted number of samples per step = 8.0391)<br>
61056 generated, 9984 selected [ 99%]<br>
<br>
</div>
<div>it runs until it almost reachs the total count of fibers requested then get stuck there using all the cpu resources allocated with nthreads, it only happens when using seed_dynamic.</div>
<div>A slightly earlier version of mrtrix3 ( 52617b9f3a4d58f50d0e802d2609bc7fb503da21 ) does not have this bug. Looking at the diff shows mainly changes related to strides but the fod have been generated with the latest version.<br>
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<div>thanks for you help.<br>
<br>
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<div>cheers<span><font color="#888888"><br>
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-- <br>
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<div><font size="1">Basile Pinsard<br>
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<i><font size="1">PhD candidate<br>
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<font size="1">Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS<br>
Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal</font><br>
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</blockquote></div><br></div></div></div>
</blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><div><div><font size="1">Basile Pinsard<br></font></div><i><font size="1">PhD candidate<br></font></i></div><font size="1">Laboratoire d'Imagerie Biomédicale, UMR S 1146 / UMR 7371, Sorbonne Universités, UPMC, INSERM, CNRS<br>
Unité de Neuroimagerie Fonctionnelle, CRIUGM, Université de Montréal</font><br></div>
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