[Mrtrix-discussion] streamtrack segmentation fault

Wed Oct 17 03:33:54 PDT 2012

Hi Donald,

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.

Best,
Peter

On 10/17/2012 08:44 AM, Donald Tournier wrote:
> Hi Peter,
>
> 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.
>
> 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.
>
> 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.
>
> Cheers,
>
> Donald.
>
>
> On 17 October 2012 16:02, Peter Neher <p.neher at dkfz-heidelberg.de 
> <mailto:p.neher at dkfz-heidelberg.de>> wrote:
>
>     Hi everyone,
>
>     I am trying to use streamtrack (probabilisatic with CSD) on one of
>     my datasets and get the following error:
>
>     streamtrack [DEBUG]: reading key/value file "/etc/mrtrix.conf"...
>     streamtrack [INFO]: opening image "CSD4.mif"...
>     streamtrack [DEBUG]: reading key/value file "./CSD4.mif"...
>     streamtrack [DEBUG]: sanitising transformation matrix...
>     streamtrack [DEBUG]: preparing file "./CSD4.mif"
>     streamtrack [DEBUG]: setting up image "CSD4.mif"...
>     streamtrack [DEBUG]: sanitising transformation matrix...
>     streamtrack [DEBUG]: setting up data increments for "CSD4.mif"...
>     streamtrack [DEBUG]: data increments initialised with start = 0,
>     stride = [ 15 1395 161820 1 ]
>     streamtrack [INFO]: error parsing spherical ROI specification
>     "seed.mif" - assuming mask image
>     streamtrack [DEBUG]: mapping image "CSD4.mif"...
>     streamtrack [DEBUG]: file "./CSD4.mif" mapped at 0x7fa59c174000,
>     size 29775147 (read-only)
>     streamtrack [DEBUG]: data mapper for image "CSD4.mif" mapped with
>     segment size = 7443720 (optimised)
>     streamtrack [INFO]: launching 12 threads
>     streamtrack [INFO]: opening image "seed.mif"...
>     streamtrack [DEBUG]: reading key/value file "./seed.mif"...
>     streamtrack [DEBUG]: sanitising transformation matrix...
>     streamtrack [DEBUG]: preparing file "./seed.mif"
>     streamtrack [DEBUG]: setting up image "seed.mif"...
>     streamtrack [DEBUG]: sanitising transformation matrix...
>     streamtrack [DEBUG]: setting up data increments for "seed.mif"...
>     streamtrack [DEBUG]: data increments initialised with start = 92,
>     stride = [ -1 93 10788 ]
>     streamtrack [DEBUG]: mapping image "seed.mif"...
>     streamtrack [DEBUG]: file "./seed.mif" mapped at 0x7fa5a12b1000,
>     size 496501 (read-only)
>     streamtrack [DEBUG]: data mapper for image "seed.mif" mapped with
>     segment size = 496248
>     ./invivo_start.sh: line 14: 12913 Segmentation fault      (core
>     dumped) streamtrack SD_PROB CSD4.mif fibers.tck -seed seed.mif
>     -debug &>log.txt
>
>     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.
>     I am using Ubuntu 12.4 and mrtrix-0.2.10_2012-02-10.
>     Any suggestions?
>
>     Best,
>     Peter
>
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>
>
>
> -- 
> *Dr Jacques-Donald Tournier
> *
> Research Fellow
>
> The Florey Institute of Neuroscience and Mental Health
> Melbourne Brain Centre - Austin Campus
> 245 Burgundy Street
> Heidelberg  Vic  3084
> Ph:  +61 3 9035 7033
> Fax:  +61 3 9035 7307
> www.florey.edu.au <http://www.florey.edu.au>
>
>

-- 
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: p.neher at dkfz-heidelberg.de, Web: www.dkfz.de

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