[Mrtrix-discussion] streamtrack segmentation fault

[Donald Tournier]

Hi Peter,

Good to hear. It's trivial to check for this, I'll make sure to include a
fix for the next release.
Cheers,

Donald.


On 17 October 2012 21:33, Peter Neher <p.neher at dkfz-heidelberg.de> wrote:

>  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> 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
>
>
>
> --
> 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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>


-- 
*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
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