[Mrtrix-discussion] empty FA images and streamtrack questions

[Donald Tournier]

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
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>



-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078