[Mrtrix-discussion] empty FA images and streamtrack questions

Mon Oct 27 16:09:59 PDT 2008

Hi Donald

I follow the instructions in the documentation to get the fa. The tensor 
image I get is also empty.

For streamtrack, I use a binary brain mask (generated using FSL bet, 
then eroded by 2 voxels) to terminate tracking. I found that 
segmentation faults occur more often (but not only) when I use the 
-include option. I guess this is simply because a larger number of 
streamlines has to be generated then, increasing chances to see a 
segfault, and does not actually have anything to do with -include itself.
This is the command I ran:
$ streamtrack SD_PROB CSD/csd.mif -seed AC-seed.mif -include 
AC-target.mif -number 100 -mask data/mask-ero2.mif AC-targets.tck

This is the output of the debugger:

$ gdb --args streamtrack SD_PROB CSD/csd.mif -seed AC-seed.mif -include 
AC-target.mif -mask data/mask-ero2.mif AC-targets.tckGNU 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/streamtrack SD_PROB 
CSD/csd.mif -seed AC-seed.mif -include AC-target.mif -mask 
data/mask-ero2.mif AC-targets.tck
[Thread debugging using libthread_db enabled]
[New Thread 0x7f5b155f2780 (LWP 30061)]
    9096 generated,      537 selected    [ 53%]
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7f5b155f2780 (LWP 30061)]
0x0000000000410404 in MR::DWI::SH::value_precomputed ()
Current language:  auto; currently asm
(gdb) bt full
#0  0x0000000000410404 in MR::DWI::SH::value_precomputed ()
No locals.
#1  0x000000000043066b in 
MR::DWI::Tractography::Tracker::SDProb::next_point ()
No locals.
#2  0x0000000000423b48 in MR::DWI::Tractography::Tracker::Base::next ()
No locals.
#3  0x00000000004094c9 in MyApp::execute ()
No locals.
#4  0x00000000004057c0 in main ()
No locals.

Thanks for your help!
Cheers
Kerstin

Donald Tournier wrote:
> Hi Kerstin,
>
> I'm a bit surprised that you're having problem with the tensor
> analysis. Are you generating the tensor image (i.e. the dt.mif file)
> first with dwi2tensor, and then feeding that through tensor2FA? Does
> the tensor image look OK?
>
>
> About your other questions:
>
> 1) the -initdirection option format is -initdirection 0,0.5,1 (i.e. a
> comma-separated list of floating point values, no spaces). The
> direction is relative to the usual coordinate system (in the
> documentation: General Information => Overview).
>
> 2) Any segmentation fault is A Bad Thing. Could you post the entire
> command that you actually type? I would also be interested to know
> whether you use a mask image that allows the tracks to reach the edge
> of the data set: maybe the program crashes if the track wonders
> outside the image data set. In any case, there's a bug and it needs to
> be fixed...
>
> If you're feeling particularly adventurous, maybe you can run the
> tracking within the debugger? That way, if it crashes you would be
> able to attach the full debugging information when/if it crashes. It's
> quite simple to do that. If the command you normally run is:
>
>   
>> streamtrack SD_PROB some_image.mif track.tck -some_option etc
>>     
>
> then just insert "gdb --args" at the beginning, and then type "run" at
> the GDB prompt:
>
>   
>> gdb --args streamtrack SD_PROB some_image.mif track.tck -some_option etc
>>     
> 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 "i486-linux-gnu"...
> (gdb) run
>
> If the program crashes it will display something like "SIGSEGV
> exception occurred" or something. If that happens, then type "bt full"
> at the prompt, and copy/paste all of the session into an email so I
> can have a good look at what went wrong.
>
> By the way, this is only for debugging. There is a performance penalty
> for running within the debugger, and it can be significant. I wouldn't
> recommend doing this routinely...
>
> Cheers!
>
> Donald.
>
>
>
> On Fri, Oct 24, 2008 at 4:38 PM, Kerstin Pannek <k.pannek1 at uq.edu.au> wrote:
>   
>> Hello again everyone,
>>
>> Donald, thank you for fixing find_SH_peaks. Unfortunately I did not quite
>> get around to really playing with it yet.
>>
>> I was just trying to analyze some DTI data that had not been optimized for
>> CSD and tractography (b value 1200; slice gap...). When running tensor2FA, I
>> get only an empty image. Image conversion from DICOM works, i.e. I get a
>> non-empty dwi.mif and encoding - just a warning about the slice gap, no
>> error message. What might be causing this problem?
>>
>> Some more question about streamtrack:
>> 1) When I want to use the option -initdirection <dir>, what format should
>> <dir> be?
>> 2) I do get segmentation faults fairly frequently using streamtrack SD_PROB.
>> I did get segmentation faults using fslview in the past, making me think
>> that this was a hardware problem at my end. With the new version of FSL and
>> a different video card, the fslview segmentation fault issue has been
>> resolved, but the streamtrack segmentation fault remains. Any thoughts on
>> what this problem might be related to? I case it is important, I get some
>> "failed to converge" messages from csdeconv.
>>
>> Thanks for your help.
>> Kerstin
>> _______________________________________________
>> Mrtrix-discussion mailing list
>> Mrtrix-discussion at www.nitrc.org
>> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>>
>>     
>
>
>
>   