[slicer-users] firts steps in tractography

Carolina Valencia cvalencia at linkdx.com.co
Wed Aug 3 10:30:57 EDT 2011


Dear Slicers users,

I attached the error log file output after run the tensor estimation module,
I really appreciate your help,

Thanks,

Carolina

2011/7/28 cvalencia <cvalencia at linkdx.com.co>

> Hi Xiaodong,
>
> Thanks for your reply.
> I use the diffusion tensor estimation module I can run it but show a
> message finish with errors, and I can not see the outputs in the 2d views,
> i.e the blue mask.
>
> Thanks,
>
> Carolina
>
> 2011/7/28 Xiaodong Tao-3 [via slicer-users] <[hidden email]<http://user/SendEmail.jtp?type=node&node=3207022&i=0>
> >
>
>> Hello Carolina,
>>
>> That is because the images were acquired in oblique planes. The default
>> view mode in Slicer is axial/coronal/sagittal. Please see if you are able to
>> do tractography using the converted nrrd file.
>>
>> Hope this helps,
>> Xiaodong
>>
>> On Jul 28, 2011, at 11:17 AM, Carolina Valencia wrote:
>>
>> Hi Steve,
>>
>> Thanks for your reply.
>> I used the tool you mention but when I see it in the volumes module and
>> play with the window level, I noticed in the beginning an in the end of the
>> slices in the tree views a few slices cut in diagonal.
>> Then, when I use the diffusion tensor estimation module I can run it but
>> show a message finish with errors, and I can not see the outputs in the 2d
>> views, i.e the blue mask.
>>
>> Thanks,
>>
>> Carolina
>>
>> 2011/7/28 Steve Pieper <[hidden email]<http://user/SendEmail.jtp?type=node&node=3206982&i=0>
>> >
>>
>>> Hi Carolina -
>>>
>>> Did you run the DicomToNrrd tool?  This is what we usually use to convert
>>> the scanner data into a format compatible with slicer:
>>>
>>> http://www.slicer.org/slicerWiki/index.php/Modules:DicomToNRRD-3.6
>>>
>>> Then you should be able to follow the steps in the Diffution MRI
>>> tutorial.
>>>
>>> HTH,
>>> Steve
>>>
>>> On Thu, Jul 28, 2011 at 10:43 AM, Carolina Valencia <[hidden email]<http://user/SendEmail.jtp?type=node&node=3206982&i=1>
>>> > wrote:
>>>
>>>> Hello Slicer users,
>>>>
>>>> I would like to perform tractography on my own data, but I'm uck in the
>>>> very first step. I add the DICOM serie from the scanner (GE Signa 1.5T) the
>>>> protocol's names are TENSOR ASSET and DIFFUSION DWI, I assume is the last
>>>> one, when I load it, the axial view is correct, but the other two views
>>>> shown 2 images, one below to the other, it seems the b0 is extracted from
>>>> the other ones. Then I converted them in dcm2nii, and I load the .nii.gz
>>>> file, and the views are correct, but when I start with the diffusion tensor
>>>> estimation, I can not choose any option in Input DWI volume, my voume loaded
>>>> doesn't appear in the list.
>>>>
>>>> Thanks for your help,
>>>>
>>>> Best regards,
>>>>
>>>> Carolina
>>>>
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>>>
>>>
>>
>>
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Type: Error
Time: Fri Jul 29 10:36:04 2011
Description: ERROR: In /home/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1524
vtkCommandLineModuleLogic (0xcaf66b8): Diffusion Tensor Estimation completed with errors




Type: Error
Time: Fri Jul 29 10:36:04 2011
Description: ERROR: In /home/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1499
vtkCommandLineModuleLogic (0xcaf66b8): Diffusion Tensor Estimation standard error:

/home/cvalencia/Descargas/Slicer3-3.6.2-2010-11-03-linux-x86/lib/Slicer3/Plugins/DiffusionTensorEstimation: Error parsing Diffusion information




Type: Information
Time: Fri Jul 29 10:36:00 2011
Description: Diffusion Tensor Estimation command line: 

/home/cvalencia/Descargas/Slicer3-3.6.2-2010-11-03-linux-x86/lib/Slicer3/Plugins/DiffusionTensorEstimation --enumeration LS --otsuomegathreshold 0.5 --removeislands --applymask /home/cvalencia/Slicer3cvalencia/BDICB_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd /home/cvalencia/Slicer3cvalencia/BDICB_vtkMRMLDiffusionTensorVolumeNodeC.nrrd /home/cvalencia/Slicer3cvalencia/BDICB_vtkMRMLScalarVolumeNodeC.nrrd /home/cvalencia/Slicer3cvalencia/BDICB_vtkMRMLScalarVolumeNodeD.nrrd 


Type: Information
Time: Fri Jul 29 10:35:59 2011
Description: CommandLineModule

Type: Information
Time: Fri Jul 29 10:35:59 2011
Description: /home/cvalencia/Descargas/Slicer3-3.6.2-2010-11-03-linux-x86/lib/Slicer3/Plugins/DiffusionTensorEstimation

Type: Information
Time: Fri Jul 29 10:35:59 2011
Description: Found CommandLine Module, target is 

Type: Error
Time: Thu Jul 28 10:10:22 2011
Description: ERROR: In /home/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1524
vtkCommandLineModuleLogic (0xcaf66b8): Diffusion Tensor Estimation completed with errors




Type: Error
Time: Thu Jul 28 10:10:22 2011
Description: ERROR: In /home/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1499
vtkCommandLineModuleLogic (0xcaf66b8): Diffusion Tensor Estimation standard error:

/home/cvalencia/Descargas/Slicer3-3.6.2-2010-11-03-linux-x86/lib/Slicer3/Plugins/DiffusionTensorEstimation: Error parsing Diffusion information




Type: Information
Time: Thu Jul 28 10:10:22 2011
Description: Diffusion Tensor Estimation command line: 

/home/cvalencia/Descargas/Slicer3-3.6.2-2010-11-03-linux-x86/lib/Slicer3/Plugins/DiffusionTensorEstimation --enumeration LS --otsuomegathreshold 0.5 --removeislands --applymask /home/cvalencia/Slicer3cvalencia/BDICB_vtkMRMLDiffusionWeightedVolumeNodeB.nrrd /home/cvalencia/Slicer3cvalencia/BDICB_vtkMRMLDiffusionTensorVolumeNodeC.nrrd /home/cvalencia/Slicer3cvalencia/BDICB_vtkMRMLScalarVolumeNodeC.nrrd /home/cvalencia/Slicer3cvalencia/BDICB_vtkMRMLScalarVolumeNodeD.nrrd 


Type: Information
Time: Thu Jul 28 10:10:21 2011
Description: CommandLineModule

Type: Information
Time: Thu Jul 28 10:10:21 2011
Description: /home/cvalencia/Descargas/Slicer3-3.6.2-2010-11-03-linux-x86/lib/Slicer3/Plugins/DiffusionTensorEstimation

Type: Information
Time: Thu Jul 28 10:10:21 2011
Description: Found CommandLine Module, target is 

Type: Error
Time: Thu Jul 28 10:09:03 2011
Description: ERROR: In /home/pieper/slicer3/release/Slicer3/Modules/CommandLineModule/vtkCommandLineModuleLogic.cxx, line 1624
vtkCommandLineModuleLogic (0xcaf3070): Dicom to Nrrd Converter standard error:

Warning: Output file does not have extension .nhdr or .nrrd.
         Extension .nrrd added.




Type: Information
Time: Thu Jul 28 10:09:03 2011
Description: Dicom to Nrrd Converter standard output:

/home/cvalencia/Documentos/CORBIC/OrtegaGIlJuliethTatiana/nrrdDWI/DWIdata
ORIGINAL\PRIMARY\OTHER
Image acquired using a GE scanner
=================== numberOfSlicesPerVolume:20
Dicom images are ordered in a volume interleaving way.
ImageOrientationPatient (0020:0037): LPS Orientation Matrix
0.994063 0.0729693 0.0807246
-0.063632 0.991601 -0.11259
-0.0882608 0.106784 0.990357

SpacingMatrix
0.9375 0 0
0 0.9375 0
0 0 6.5

NRRDSpaceDirection
0.931934 0.0684087 0.52471
-0.059655 0.929626 -0.731837
-0.0827445 0.10011 6.43732

Slice 0: -126.95\-142.477\-38.781
Slice 1: -126.426\-143.208\-32.3437
Slice order is IS
Row: 0.931934, -0.059655, -0.0827445
Col: 0.0684087, 0.929626, 0.10011
Sli: 0.52471, -0.731837, 6.43732
Number of Slices: 40
Number of Volume: 2
Number of Slices in each volume: 20
B-value: 0; diffusion direction: 0, 0, 0
B-value: 1000; diffusion direction: -0, -0, 0
Number of usable volumes: 2
For Multiple BValues: 0 -- 0 / 1000 = 0
For Multiple BValues: 1 -- 1000 / 1000 = 1


Type: Information
Time: Thu Jul 28 10:09:02 2011
Description: Dicom to Nrrd Converter command line: 

slicer:0xa9ee76f0 --processinformationaddress 0xe146ecc --inputDicomDirectory /home/cvalencia/Documentos/CORBIC/OrtegaGIlJuliethTatiana/dicomDWI --outputDirectory /home/cvalencia/Documentos/CORBIC/OrtegaGIlJuliethTatiana/nrrdDWI --outputVolume DWIdata 


Type: Information
Time: Thu Jul 28 10:09:02 2011
Description: SharedObjectModule

Type: Information
Time: Thu Jul 28 10:09:02 2011
Description: Found SharedObject Module



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