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>
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<br></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>
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