[Mrtrix-discussion] streamtrack - segmentation fault

[Donald Tournier]

Hi Danilo,

Sounds to me like your diffusion encoding file is causing trouble. Given
your strace output, it looks like the values in the first line of that file
are separated by tabs ('\t'), with rows delimited by carriage returns
('\r'). The tabs shouldn't be a problem, but using carriage returns for
newlines is unusual. Try replacing these by standard Unix line feeds
('\n'), or DOS-style newline sequences (carriage return + line feed,
'\r\n').

Hope that sorts out the problem...
Cheers,

Donald.


On 15 December 2011 02:19, Danilo Scelfo <dscelfo at inpe.unipi.it> wrote:

> Hi Donald, hi everyone,
>
> I'm running a standard DTI-based tractography on a few subjects but I'm
> getting a segmentation fault error with streamtrack. The same command,
> however, is correctly running on other subjects.
> Below is the output of the command run a) with gdb and the -debug option
> and b) with the strace command, but I'm not able to see the cause of the
> error.
>
> Could you give me some hints on how to solve this issue?
> If needed, I'm running mrtrix-0.2.1 on a Ubuntu 10.04 64bit VM on a Mac
> 10.6.5 host machine.
>
> Thanks in advance.
>
> Danilo
>
>
> subject/procdata/DWI/MRtrix$ gdb --args streamtrack DT_STREAM DWIecc.nii
> -grad /path/to/encoding30dir.b1000.v9.0.txt -number 10000 -seed
> nodif_brain_mask.nii -debug tract_DT.tck
>
> GNU gdb (GDB) 7.1-ubuntu
> Copyright (C) 2010 Free Software Foundation, Inc.
> License GPLv3+: GNU GPL version 3 or later <
> http://gnu.org/licenses/gpl.html>
> This is free software: you are free to change and redistribute it.
> There is NO WARRANTY, to the extent permitted by law.  Type "show copying"
> and "show warranty" for details.
> This GDB was configured as "x86_64-linux-gnu".
> For bug reporting instructions, please see:
> <http://www.gnu.org/software/gdb/bugs/>...
> Reading symbols from /usr/local/mysofts/mrtrix/bin/streamtrack...(no
> debugging symbols found)...done.
> (gdb) run
> Starting program: /usr/local/mysofts/mrtrix/bin/streamtrack DT_STREAM
> DWIecc.nii -grad /path/to/encoding30dir.b1000.v16.0.txt -number 10000
> -seed nodif_brain_mask.nii -debug tract_DT.tck
> [Thread debugging using libthread_db enabled]
> streamtrack [DEBUG]: reading key/value file "/home/dscelfo/.mrtrix.conf"...
> streamtrack [INFO]: opening image "DWIecc.nii"...
> streamtrack [DEBUG]: preparing file "./DWIecc.nii"
> streamtrack [DEBUG]: file "./DWIecc.nii" mapped at 0x7ffff3da5000, size
> 14681952 (read-only)
> streamtrack [DEBUG]: sanitising transformation matrix...
> streamtrack [DEBUG]: unmapping file "./DWIecc.nii"
> streamtrack [DEBUG]: setting up image "DWIecc.nii"...
> streamtrack [DEBUG]: sanitising transformation matrix...
> streamtrack [DEBUG]: setting up data increments for "DWIecc.nii"...
> streamtrack [DEBUG]: data increments initialised with start = 79, stride =
> [ -1 80 6400 236800 ]
> streamtrack [INFO]: error parsing spherical ROI specification
> "nodif_brain_mask.nii" - assuming mask image
>
> Program received signal SIGSEGV, Segmentation fault.
> 0x00007ffff7ba88cc in MR::Math::Matrix::load(std::string const&) () from
> /usr/local/mysofts/mrtrix/lib/libmrtrix-0_2_9.so
> (gdb) ^CQuit
> (gdb)
>
>
> subject/procdata/DWI/MRtrix$ strace streamtrack DT_STREAM DWIecc.nii -grad
> /path/to/encoding30dir.b1000.v9.0.txt -number 10000 -seed
> nodif_brain_mask.nii -debug tract_DT.tck
>
> futex(0x7fd88e750190, FUTEX_WAKE_PRIVATE, 2147483647) = 0
> write(2, "streamtrack", 11streamtrack)             = 11
> write(2, " [INFO]: ", 9 [INFO]: )                = 9
> write(2, "error parsing spherical ROI spec"..., 86error parsing spherical
> ROI specification "nodif_brain_mask.nii" - assuming mask image) = 86
> write(2, "\n", 1
> )                       = 1
>
> open("/mnt/nas-rm/data/diffusione/GRADIENTS/MRtrix/encoding30dir.b1000.v16.0.txt",
> O_RDONLY) = 3
> read(3, "0\t0\t0\t0\r1.000000 0.000000 0.0000"..., 8191) = 1008
> read(3, "", 8191)                       = 0
> --- SIGSEGV (Segmentation fault) @ 0 (0) ---
> +++ killed by SIGSEGV +++
> Segmentation fault
>
>
> --
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> mittente e di provvedere alla sua distruzione, Grazie.
>
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-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9035 7033
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