[Mrtrix-discussion] mrview segmentation fault

Sun Nov 30 18:15:13 PST 2008

Hi Kerstin
I can open all csd.mif files as regular images.
I recompiled the debugging version of MRtrix. I have attached the output 
of running mrview -debug and in gdb as text files to this email.
Interestingly, I just discovered that orientation plots that worked this 
morning work only occasionally now...
Thanks for your help
Kerstin

Donald Tournier wrote:
> Hi Kerstin,
>
> This is really strange. Can you open the csd.mif file as a regular
> image (i.e. using the File->Open dialog)? If you can, then there is
> probably something else going on. Someone else had a very similar
> issue when running MRtrix within a virtual PC (i.e. an emulator),
> which I guess was related to the poor graphics card support and/or the
> limited memory available. In any case, it sounded more like a
> limitation of the system rather than the software itself. Things might
> be different in your case though, since you are able to display some,
> but not all your csd.mif files...
>
> Here's a couple of things you can do to try to narrow down the problem:
>
> 1. run mrview from the command line with the -debug option, and repeat
> the steps taken to get it to crash. Then copy/paste and send me the
> command-line output.
>
> 2. run mrview within the debugger:
> $ gdb mrview
> followed by "run" at the gdb prompt"
> (gdb) run
>
> then load your csd.mif file to get mrview to crash, at which point the
> debugger will print out a message about the error. You can send me a
> full diagnostic by typing "bt full" at the prompt and copy/pasting the
> output:
> (gdb) bt full
>
> If you have the time, BEFORE doing the steps above, you could
> recompile a debugging version of MRtrix. This will make the diagnostic
> information produced by "bt full" much more comprehensive. To do this,
> use these commands (from the MRtrix installation folder):
> $ ./build clean
> $ ./build -debug
> And proceed as per the installation instructions.
>
> Thanks!
>
> Donald.
>
>
> On Mon, Dec 1, 2008 at 11:23 AM, Kerstin Pannek <k.pannek1 at uq.edu.au> wrote:
>   
>> Hi!
>> I have a problem looking at the orientation plots of several datasets.
>> mrview crashes on opening csd.mif (view->sidebar->orientation
>> plot->browse->open --- segmentation fault). This happens only for a few
>> datasets. All datasets are processed the same way. Deleting the file and
>> rerunning csdeconv doesn't solve the problem. Any ideas?
>> Thanks
>> Kerstin
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>>     
>
>
>
>   

-------------- next part --------------
sneed:mrtrix$ mrview tensor/fa.mif -debug
mrview [INFO]: opening image "tensor/fa.mif"...
mrview [DEBUG]: reading key/value file "tensor/fa.mif"...
mrview [DEBUG]: sanitising transformation matrix...
mrview [DEBUG]: preparing file "tensor/fa.mif"
mrview [DEBUG]: setting up image "tensor/fa.mif"...
mrview [DEBUG]: sanitising transformation matrix...
mrview [DEBUG]: setting up data increments for "tensor/fa.mif"...
mrview [DEBUG]: data increments initialised with start = 99, stride = [ -1 100 10000 ]
NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
NVIDIA: Direct rendering failed; attempting indirect rendering.
mrview [DEBUG]: mapping image "tensor/fa.mif"...
mrview [DEBUG]: file "tensor/fa.mif" mapped at 0x7fbab4150000, size 2400272 (read-only)
mrview [DEBUG]: data mapper for image "tensor/fa.mif" mapped with segment size = 600000 (optimised)
NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
NVIDIA: Direct rendering failed; attempting indirect rendering.
mrview [INFO]: DWI renderer successfully initialised
mrview [INFO]: GL_RENDERER   = GeForce 7100 GS/PCI/SSE2
mrview [INFO]: GL_VERSION    = 2.1.0 NVIDIA 96.43.05
mrview [INFO]: GL_VENDOR     = NVIDIA Corporation
mrview [DEBUG]: preparing file "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/response.txt"
mrview [INFO]: opening image "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
mrview [DEBUG]: reading key/value file "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
mrview [DEBUG]: sanitising transformation matrix...
mrview [DEBUG]: preparing file "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"
mrview [DEBUG]: setting up image "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
mrview [DEBUG]: sanitising transformation matrix...
mrview [DEBUG]: setting up data increments for "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
mrview [DEBUG]: data increments initialised with start = 0, stride = [ 45 4500 450000 1 ]
mrview [DEBUG]: mapping image "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif"...
mrview [DEBUG]: file "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif" mapped at 0x7fbaabaf8000, size 108000282 (read-only)
mrview [DEBUG]: data mapper for image "/giglo/sneed-01/kerstin/data/EKBERG/DTI_b3000/mrtrix/csd/csd.mif" mapped with segment size = 27000000 (optimised)
Segmentation fault
-------------- next part --------------
sneed:mrtrix$ gdb mrview 
GNU gdb 6.8-debian
Copyright (C) 2008 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"...
(gdb) run
Starting program: /data/home/kerstin/bin/mrtrix/bin/mrview 
[Thread debugging using libthread_db enabled]
[New Thread 0x7f4bb4fe1730 (LWP 25807)]
NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
NVIDIA: Direct rendering failed; attempting indirect rendering.
NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
NVIDIA: Direct rendering failed; attempting indirect rendering.

Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7f4bb4fe1730 (LWP 25807)]
0x000000000048322e in MR::Image::Mapper::re (this=0xaf6c60, offset=18445767945754771456) at lib/image/mapper.h:251
251           if (optimised) return (((float32*) segment[0])[offset]);
(gdb) bt full
#0  0x000000000048322e in MR::Image::Mapper::re (this=Cannot access memory at address 0x7fffbd1cfdb8
) at lib/image/mapper.h:251
        nseg = Cannot access memory at address 0x7fffbd1cfdc8
(gdb) 