Hi Peter,
I didn¹t use a threshold. As I said in the previous email, this issue was
caused by skull-stripped brain. To avoid this issue, I have to use whole
head and brain mask.
For the particle weight estimation, would you recommend to specify one
certain value for whole study, or let the program calculate it for each
scan?
Thanks,
Wayne
On 14-05-03 4:21 AM, "Peter Neher" <[email protected]> wrote:
> Hi Wayne,
>
> as I can see from the output you are not using a mask image. Did you use a
> threshold when reconstructing your tensors/Qballs? This results in voxels
> containing only 0, which again results in this issue with the particle weight
> estimation. You can either use a mask image to restrict the weight estimation
> and tracking to valid voxels or you should reconstruct the image without the
> threshold to avoid zero-value voxels. I recommend using a mask image because
> the particle weight estimation will be much better if only performed inside of
> the brain/WM.
>
> Cheers
> Peter
>
>
>
> On 05/02/2014 09:05 PM, Wayne Su wrote:
>
>
>> MITK-DT hanging on Gibbs Tracking Hi There,
>>
>> I found MITK-DT was hanging on Gibbs Tracking whenever I set
>> ³particle_length² ³particle_width² or ³particle_weight² to ³auto² (³0² for
>> gtp file). Here are messages I got:
>>
>> [Fri May 2 11:49:28 2014
>> 0.320] In AutoLoadModulesFromPath at
>> /home/wsu/devel/MITK/Core/CppMicroServices/core/src/util/usUtils.cpp:160 :
>> Auto-loading module /usr/local/MITK/bin/MitkCore/libMitkVtkShaders.so
>> [0.330] In AutoLoadModulesFromPath at
>> /home/wsu/devel/MITK/Core/CppMicroServices/core/src/util/usUtils.cpp:160 :
>> Auto-loading module /usr/local/MITK/bin/MitkCore/libMitkIpPicSupportIO.so
>> [0.340] In AutoLoadModulesFromPath at
>> /home/wsu/devel/MITK/Core/CppMicroServices/core/src/util/usUtils.cpp:160 :
>> Auto-loading module /usr/local/MITK/bin/MitkCore/libMitkIOExt.so
>> [0.340] In AutoLoadModulesFromPath at
>> /home/wsu/devel/MITK/Core/CppMicroServices/core/src/util/usUtils.cpp:160 :
>> Auto-loading module /usr/local/MITK/bin/MitkCore/libMitkDiffusionIO.so
>> [0.380] Start GibbsTracking ..
>> [4.770] Loading qball image ...
>> [5.290] GibbsTrackingFilter: generating default mask image
>> [5.290] GibbsTrackingFilter: loading parameter file param.gtp
>> [5.290] GibbsTrackingFilter: parameter file loaded successfully
>> [5.290] GibbsTrackingFilter: estimating particle weight
>> [5.290] SphereInterpolator: loading lookuptables
>> ParticleGrid: allocated 4mb for 100k particles.
>> EnergyComputer: 1130496 active voxels found
>>
>> I guess something wrong with the automatic searching these parameters.
>>
>> I also got following messages from MitkDIffusion GUI:
>> [56.780] enabling shader
>> [56.790] enabling shader
>> [56.820] enabling shader
>> #57.870# [VtkError] ERROR: ERROR: In
>> /home/wsu/devel/MITK-superbuild/VTK-src/Rendering/OpenGL/vtkShader2.cxx, line
>> 82
>> vtkShader2 (0x5ffa570): failed at glDeleteShader 1 OpenGL errors detected
>> 0 : (1281) Invalid value
>> #57.870# [VtkError] ERROR: ERROR: In
>> /home/wsu/devel/MITK-superbuild/VTK-src/Rendering/OpenGL/vtkShader2.cxx, line
>> 82
>> vtkShader2 (0x5fe0fe0): failed at glDeleteShader 1 OpenGL errors detected
>> 0 : (1281) Invalid value
>> #57.870# [VtkError] ERROR: ERROR: In
>> /home/wsu/devel/MITK-superbuild/VTK-src/Rendering/OpenGL/vtkShaderProgram2.cx
>> x, line 103
>> vtkShaderProgram2 (0x5a80fd0): failed at glDeleteProgram 1 OpenGL errors
>> detected
>> 0 : (1281) Invalid value
>> #57.870# [VtkError] ERROR: ERROR: In
>> /home/wsu/devel/MITK-superbuild/VTK-src/Rendering/OpenGL/vtkShader2.cxx, line
>> 82
>> vtkShader2 (0x57609d0): failed at glDeleteShader 1 OpenGL errors detected
>> 0 : (1281) Invalid value
>> #57.870# [VtkError] ERROR: ERROR: In
>> /home/wsu/devel/MITK-superbuild/VTK-src/Rendering/OpenGL/vtkShader2.cxx, line
>> 82
>> vtkShader2 (0x567ab10): failed at glDeleteShader 1 OpenGL errors detected
>> 0 : (1281) Invalid value
>> #57.870# [VtkError] ERROR: ERROR: In
>> /home/wsu/devel/MITK-superbuild/VTK-src/Rendering/OpenGL/vtkShaderProgram2.cx
>> x, line 103
>> vtkShaderProgram2 (0x657c8d0): failed at glDeleteProgram 1 OpenGL errors
>> detected
>> 0 : (1281) Invalid value
>>
>> I tried the official release and found the same issues.
>>
>> Wayne
>
>
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