Hi Chris & Ivan,<div><br></div><div>OK, I think there are a few issues to consider here. The first thing is to figure out why the response function estimated for these data is not right. Are you using just a single shell of the HARDI data, or are you simply feeding all 3 shells to MRtrix? MRtrix is only designed to handle single shell data, so if you're doing the latter, it's no surprise that it will have issues. It may be possible to analyse these kinds of data in a future version, but for now you should stick to single-shell HARDI, unfortunately.</div>
<div><br></div><div>As to why the tracking hangs: the most likely reason is that the program is failing to find a suitable seed point. The procedure in MRtrix is to select a random point and a random orientation, compute the FOD amplitude, and start tracking if that amplitude is greater than the -init_cutoff threshold (by default, 0.2). If your response function is incorrect, there is a good chance that the scaling of the resulting FODs will also be off, giving you smaller FODs than expected - in which case streamtrack will try in vain to find a single suitable seed point/orientation, and appear to hang. To verify this, you could try using a -cutoff value of zero to see if that at least produces tracks. You could also use the find_SH_peaks command on the CSD output file, and check the FOD peak amplitudes (although it's a little more work to figure out how to extract the amplitude from that).</div>
<div><br></div><div>If none of this helps, I'm happy to have a look at the data - usually quicker to troubleshoot that way...</div><div><br></div><div>Cheers,</div><div><br></div><div>Donald.</div><div><div><br></div>
<div><br><div class="gmail_quote">On 12 January 2013 02:49, Parker, Christopher <span dir="ltr"><<a href="mailto:christopher.parker.10@ucl.ac.uk" target="_blank">christopher.parker.10@ucl.ac.uk</a>></span> wrote:<br>
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<div style="direction:ltr;font-size:10pt;font-family:Tahoma">Hi Ivan and Mrtrix users,
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<div>I have just experienced the same problem with streamtrack SD_PROB. It does not produce any streamlines and hangs although still uses a lot of CPU. I think it might have something to do with the SH harmonic coefficient file (source argument in streamtrack),
since when I use a harmonic coefficient file from a different scan it works fine (all other arguments were the same files). I need to find a solution to this also.</div>
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<div>Best,</div>
<div>Chris<br>
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<div style="direction:ltr"><font face="Tahoma" color="#000000"><b>From:</b> <a href="mailto:mrtrix-discussion-bounces@www.nitrc.org" target="_blank">mrtrix-discussion-bounces@www.nitrc.org</a> [<a href="mailto:mrtrix-discussion-bounces@www.nitrc.org" target="_blank">mrtrix-discussion-bounces@www.nitrc.org</a>] on behalf of Ivan Alvarez [<a href="mailto:ivan.alvarez.11@ucl.ac.uk" target="_blank">ivan.alvarez.11@ucl.ac.uk</a>]<br>
<b>Sent:</b> 09 January 2013 15:03<br>
<b>To:</b> <a href="mailto:mrtrix-discussion@www.nitrc.org" target="_blank">mrtrix-discussion@www.nitrc.org</a><br>
<b>Subject:</b> [Mrtrix-discussion] Human Connectome Project dataset issue<br>
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<div>Hello Mrtrix users,<br>
<br>
I tried analysing a sample subject from the recently available Human Connectome Project dataset (<a href="https://db.humanconnectome.org" target="_blank">https://db.humanconnectome.org</a>), and encountered an issue with CSD tractography
in Mrtrix. In brief, the dataset has 1.25 mm isotropic voxels, 270 directions, 3 b-shells (1000,2000,300) and 2 repeats.<br>
<br>
The tensor estimation worked fine, and am able to compute sensible-looking FA maps. The mask erosion is also fine, but when I view the response function coefficient, it displays an unusual shape (<a href="http://postimage.org/image/cl7tpwc3p/" target="_blank">RCF</a>).
The csdeconv command returns no errors and the orientation plot looks reasonable. My problem is, when I attempt to perform tractography with the streamtrack command, the program hangs.<br>
<br>
Any idea as to why this might be?<span class="HOEnZb"><font color="#888888"><br>
<pre cols="72">--
Kind regards,
Ivan Alvarez
PhD Candidate
Imaging and Biophysics Unit
UCL Institute of Child Health
30 Guilford Street, London, WC1N 1EH</pre>
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