Hi Peter,<div><br></div><div>Good to hear. It's trivial to check for this, I'll make sure to include a fix for the next release.</div><div>Cheers,</div><div><br>Donald.</div><div><br></div><div><br><div class="gmail_quote">
On 17 October 2012 21:33, Peter Neher <span dir="ltr"><<a href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Donald,<br>
<br>
thanks for your reply. The resampling of the seed image was indeed
the problem. It actually didn't contain any nonzero voxels anymore,
which I didn't check after resampling. Now everything runs fine. But
anyways, this should probably be handled somehow.<br>
<br>
Best,<br>
Peter<div><div class="h5"><br>
<br>
<div>On 10/17/2012 08:44 AM, Donald Tournier
wrote:<br>
</div>
<blockquote type="cite">Hi Peter,
<div><br>
</div>
<div>Not sure I completely get what is going on. When you say
"this is a resampled image", do you mean that the CSD4 file has
been regridded in some way? Or the original DWI image from which
the CSD4 file was generated? And was the regridding done for
upsampling the data or to reorient the images? In any case,
regardless of what processing was actually done, there is the
possibility that your seed.mif image no longer maps onto the
CSD4.mif image correctly, so that some of the seed points end up
outside the volume of the CSD4.mif image - I have a feeling
streamtrack doesn't check for this, which would indeed cause a
segfault. Bear in mind that streamtrack does its processing in
scanner coordinates, so having a seed image that is 'correct'
voxel-wise with respect to the CSD image is not sufficient if
the image transform matrices don't also match.</div>
<div><br>
</div>
<div>Can you post the output of "mrinfo CSD4.mif" and "mrinfo
seed.mif"? I just want to check whether the transform matrices
are the same. Also, try to load CSD4.mif in mrview, and overlay
seed.mif using either the ROI or overlay sidebar tools, to check
for alignment. </div>
<div><br>
</div>
<div>Hopefully that'll be the problem. If so, I'll add an explicit
bounds check in the code to make sure this doesn't happen for
the next release.</div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div>Donald.</div>
<div><br>
</div>
<div><br>
<div class="gmail_quote">On 17 October 2012 16:02, Peter Neher <span dir="ltr"><<a href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi everyone,<br>
<br>
I am trying to use streamtrack (probabilisatic with CSD)
on one of my datasets and get the following error:<br>
<br>
<small>streamtrack [DEBUG]: reading key/value file
"/etc/mrtrix.conf"...<br>
streamtrack [INFO]: opening image "CSD4.mif"...<br>
streamtrack [DEBUG]: reading key/value file
"./CSD4.mif"...<br>
streamtrack [DEBUG]: sanitising transformation matrix...<br>
streamtrack [DEBUG]: preparing file "./CSD4.mif"<br>
streamtrack [DEBUG]: setting up image "CSD4.mif"...<br>
streamtrack [DEBUG]: sanitising transformation matrix...<br>
streamtrack [DEBUG]: setting up data increments for
"CSD4.mif"...<br>
streamtrack [DEBUG]: data increments initialised with
start = 0, stride = [ 15 1395 161820 1 ]<br>
streamtrack [INFO]: error parsing spherical ROI
specification "seed.mif" - assuming mask image<br>
streamtrack [DEBUG]: mapping image "CSD4.mif"...<br>
streamtrack [DEBUG]: file "./CSD4.mif" mapped at
0x7fa59c174000, size 29775147 (read-only)<br>
streamtrack [DEBUG]: data mapper for image "CSD4.mif"
mapped with segment size = 7443720 (optimised)<br>
streamtrack [INFO]: launching 12 threads<br>
streamtrack [INFO]: opening image "seed.mif"...<br>
streamtrack [DEBUG]: reading key/value file
"./seed.mif"...<br>
streamtrack [DEBUG]: sanitising transformation matrix...<br>
streamtrack [DEBUG]: preparing file "./seed.mif"<br>
streamtrack [DEBUG]: setting up image "seed.mif"...<br>
streamtrack [DEBUG]: sanitising transformation matrix...<br>
streamtrack [DEBUG]: setting up data increments for
"seed.mif"...<br>
streamtrack [DEBUG]: data increments initialised with
start = 92, stride = [ -1 93 10788 ]<br>
streamtrack [DEBUG]: mapping image "seed.mif"...<br>
streamtrack [DEBUG]: file "./seed.mif" mapped at
0x7fa5a12b1000, size 496501 (read-only)<br>
streamtrack [DEBUG]: data mapper for image "seed.mif"
mapped with segment size = 496248</small><br>
<small>./invivo_start.sh: line 14: 12913 Segmentation
fault (core dumped) streamtrack SD_PROB CSD4.mif
fibers.tck -seed seed.mif -debug &>log.txt</small><br>
<br>
streamtrack is running fine on the original dataset. This
is a resampled image. But the CSD seems to run just finy,
only the tracking fails. <br>
I am using Ubuntu 12.4 and mrtrix-0.2.10_2012-02-10.<br>
Any suggestions?<br>
<br>
Best,<br>
Peter </div>
<br>
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</blockquote>
</div>
<br>
<br clear="all">
<div><br>
</div>
-- <br>
<font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br>
</b></font>
<div><font color="#ff6600" size="1">Research Fellow</font></div>
<div><font size="1"><br>
</font></div>
<div><font size="1">The Florey Institute of Neuroscience and
Mental Health</font></div>
<div><font size="1">Melbourne Brain Centre - Austin Campus</font></div>
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<br>
<br>
</div>
</blockquote>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><pre cols="72">--
Dipl.-Inform. Peter Neher
German Cancer Research Center
(DKFZ, Deutsches Krebsforschungszentrum in der Helmholtz-Gemeinschaft, Stiftung des öffentlichen Rechts)
Division of Medical and Biological Informatics
Im Neuenheimer Feld 280, D-69120 Heidelberg
Phone: 49-(0)6221-42-3552, Fax: 49-(0)6221-42-2345
E-Mail: <a href="mailto:p.neher@dkfz-heidelberg.de" target="_blank">p.neher@dkfz-heidelberg.de</a>, Web: <a href="http://www.dkfz.de" target="_blank">www.dkfz.de</a>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><font color="#ff6600" size="1"><b>Dr Jacques-Donald Tournier<br></b></font><div><font color="#ff6600" size="1">Research Fellow</font></div><div><font size="1"><br>
</font></div><div><font size="1">The Florey Institute of Neuroscience and Mental Health</font></div><div><font size="1">Melbourne Brain Centre - Austin Campus</font></div><div><font size="1">245 Burgundy Street</font></div>
<div><font size="1">Heidelberg Vic 3084</font></div><div><font size="1">Ph: +61 3 9035 7033</font></div><div><font size="1">Fax: +61 3 9035 7307</font></div><div><font size="1"><a href="http://www.florey.edu.au" target="_blank">www.florey.edu.au</a></font></div>
<br><br>
</div>