[Mrtrix-discussion] empty FA images and streamtrack questions
Donald Tournier
d.tournier at brain.org.au
Mon Oct 27 23:27:08 PDT 2008
Hello again,
Just having a look at your encoding file: the b=0 "directions" (i.e.
the first 6 volumes) have a b-value set to 1200 (the last column), and
the direction vector set to zero. MRtrix assumes the b-values in the
last column are correct, which in this case they are not - these first
6 should be set to zero.
Try modifying the encoding file by hand, by setting the first 6
b-values to zero. Save the file, and analyse with the command:
> dwi2tensor dwi.mif -grad encoding.b dt.mif
In fact, any command that makes use of the encoding information will
need to have the new encoding file supplied in this way to override
the incorrect one in the header. This includes estimate_response and
csdeconv. That should sort out the problem.
To avoid having this problem happen again, it might be wise to fix up
the code that was used to generate that incorrect DW scheme. Did you
convert those images straight from DICOM? What scanner were the images
acquired on? I'll see if there's an easy way to avoid this kind of
issue for the next release.
Cheers,
Donald.
On Tue, Oct 28, 2008 at 4:56 PM, Kerstin Pannek <k.pannek1 at uq.edu.au> wrote:
> Hi
> I have attached the output of mrinfo (xxx-ed patient name and DOB), and
> encoding.b for this person, along with bvecs, which was generated using
> dcm2nii. bvecs and encoding.b are the same (just the sign of the x-values
> changed). I am guessing that this is not causing the problem...
> Another difference between other datasets and this one is that the data is
> not in mosaic format. Could that have anything to do with it?
> I could probably put the dwi data onto our website, but I will need to
> figure out how to do that...
> Cheers
> Kerstin
>
>
>
> Donald Tournier wrote:
>>
>> Hi again,
>>
>> About the empty FA/DT image: the only thing I can think of is an
>> incorrect DW encoding file. Can you send me the output of the
>> following command, along with the "encoding.b" file it will produce:
>>
>>
>>>
>>> mrinfo dwi.mif -grad encoding.b
>>>
>>
>> Otherwise, I guess there's nothing I can do really without having a
>> look at the data themselves. If that last step doesn't give us a good
>> clue, is there any way you can send me the DW data?
>>
>> Cheers,
>>
>> Donald.
>>
>>
>> On Tue, Oct 28, 2008 at 10:09 AM, Kerstin Pannek <k.pannek1 at uq.edu.au>
>> wrote:
>>
>>>
>>> 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
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>>
>
>
> ************************************************
> Image: "dwi.mif"
> ************************************************
> Format: MRtrix
> Dimensions: 128 x 128 x 42 x 56
> Voxel size: 1.79688 x 1.79688 x 2.75 x 2.75
> Dimension labels: 0. left->right (mm)
> 1. posterior->anterior (mm)
> 2. inferior->superior (mm)
> 3. sequence (?)
> Data type: unsigned 16 bit integer (little endian)
> Data layout: [ -0 -1 +2 +3 ]
> Data scaling: offset = 0, multiplier = 1
> Comments: xxx [MR] ep2d_DTI_27H50_56_68
> study: Research Head
> DOB: xxx
> DOS: 19/07/2007 11:30:47
> Transform: 1 0 -0 -113.2
> 0 1 -0 -92.19
> -0 -0 1 -26.54
> 0 0 0 1
> DW scheme: 56 x 4
>
>
>
--
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078
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