[Mrtrix-discussion] streamtrack - segmentation fault

[Danilo Scelfo]

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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