error for converting dicom to nrrd& diffusion estimation modules

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

error for converting dicom to nrrd& diffusion estimation modules

Akiko U
Hi all,

I'm having trouble with converting dicom (SIMENS diffusion weighted data) to nrrd with the DicomtoNrrd Converter module. 

Whenever I tried to apply it, 3D slicer always crash down and I couldn't convert to nrrd/nhrd from dicom data. other workstations (all are windows, though) also got into the same situation.

Instead of this module, I used the Resample Scatar/vector/DWI volume, but the created output volume brought errors in the Diffusion Tensor Estimation saying;

-------------------------------------------------------------------------------------------------------------------------------------------
" ERROR: In ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line 1497
vtkCommandLineModuleLogic (11629768): Diffusion Tensor Estimation standard error:

C:/PROGRA~2/SLICER~1.201/lib/Slicer3/Plugins/DiffusionTensorEstimation.exe: Error parsing Diffusion information

ERROR: In ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line 1522
vtkCommandLineModuleLogic (11629768): Diffusion Tensor Estimation completed with errors"
------------------------------------------------------------------------------------------------------------------------------------------
are there anyway to fix these errors??

thank you,

akiko

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: error for converting dicom to nrrd& diffusion estimation modules

Mathieu Malaterre
akiko,

  If you have gdcm 2.x on your machine could you please run the
following command on one of your DICOM file:

$ gdcmdump --csa input.dcm | grep B_matrix

 ($ is the prompt).

Thanks

On Thu, Mar 10, 2011 at 4:06 AM, Akiko U <[hidden email]> wrote:

> Hi all,
> I'm having trouble with converting dicom (SIMENS diffusion weighted data) to
> nrrd with the DicomtoNrrd Converter module.
> Whenever I tried to apply it, 3D slicer always crash down and I couldn't
> convert to nrrd/nhrd from dicom data. other workstations (all are windows,
> though) also got into the same situation.
> Instead of this module, I used the Resample Scatar/vector/DWI volume, but
> the created output volume brought errors in the Diffusion Tensor Estimation
> saying;
> -------------------------------------------------------------------------------------------------------------------------------------------
> " ERROR: In
> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
> line 1497
> vtkCommandLineModuleLogic (11629768): Diffusion Tensor Estimation standard
> error:
> C:/PROGRA~2/SLICER~1.201/lib/Slicer3/Plugins/DiffusionTensorEstimation.exe:
> Error parsing Diffusion information
> ERROR: In
> ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx,
> line 1522
> vtkCommandLineModuleLogic (11629768): Diffusion Tensor Estimation completed
> with errors"
> ------------------------------------------------------------------------------------------------------------------------------------------
> are there anyway to fix these errors??
> thank you,
> akiko
> _______________________________________________
> slicer-users mailing list
> [hidden email]
> http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
> To unsubscribe: send email to [hidden email]
> with unsubscribe as the subject
>



--
Mathieu
_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: error for converting dicom to nrrd& diffusion estimation modules

inorton
In reply to this post by Akiko U
Akiko,
What version of Slicer you are using? How many files are in your sequence?

Also, make sure you are selecting the exact directory with DICOMs.

There were several bugs in DicomToNrrd Converter, one of which led to crash for single-file sequences, or if a directory without any DICOM files was selected  (it does not parse trees). These were fixed in January, so should be in the latest release.

-Isaiah

On Wed, Mar 9, 2011 at 10:06 PM, Akiko U <[hidden email]> wrote:
Hi all,

I'm having trouble with converting dicom (SIMENS diffusion weighted data) to nrrd with the DicomtoNrrd Converter module. 

Whenever I tried to apply it, 3D slicer always crash down and I couldn't convert to nrrd/nhrd from dicom data. other workstations (all are windows, though) also got into the same situation.

Instead of this module, I used the Resample Scatar/vector/DWI volume, but the created output volume brought errors in the Diffusion Tensor Estimation saying;

-------------------------------------------------------------------------------------------------------------------------------------------
" ERROR: In ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line 1497
vtkCommandLineModuleLogic (11629768): Diffusion Tensor Estimation standard error:

C:/PROGRA~2/SLICER~1.201/lib/Slicer3/Plugins/DiffusionTensorEstimation.exe: Error parsing Diffusion information

ERROR: In ..\..\..\Slicer3\Modules\CommandLineModule\vtkCommandLineModuleLogic.cxx, line 1522
vtkCommandLineModuleLogic (11629768): Diffusion Tensor Estimation completed with errors"
------------------------------------------------------------------------------------------------------------------------------------------
are there anyway to fix these errors??

thank you,

akiko

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: error for converting dicom to nrrd& diffusion estimation modules

Akiko U
Hi Mathieu and Isaiah,

thank you for quick replying. 

> Mathieu,
    I typed what u said, but didnt show any..are u asking base raw matrix size? I instead typed

gdcmdump --csa my file.dcm| grep B 

, which says

 (0019, 14d14) ?? (IS) [128]    #6,1 base matrix size 

is this what u need to know?

> Isaiah, 
I use version 3.6.1  and have  8-file sequences but all slices(140 slices) are contained in one folder... is that the reason?I'm sure that I chose .dcm files.

thanks,
akiko



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: error for converting dicom to nrrd& diffusion estimation modules

inorton
Hi Akiko,

I tried a quick test with two sets of DWIs in one directory and it didn't crash but I'm not quite sure what is in the output nrrd. I think it's just the 1st series in lexical order.

From my less-than-expert reading of the code I don't remember DicomToNrrd sorting by study/series UID, so it is probably best to separate each series into a separate folder. For non-DWI images File->Add Volume is otherwise best because it parses by several UIDs.

HTH,
-Isaiah

On Fri, Mar 11, 2011 at 2:04 AM, Akiko U <[hidden email]> wrote:
Hi Mathieu and Isaiah,

thank you for quick replying. 

> Mathieu,
    I typed what u said, but didnt show any..are u asking base raw matrix size? I instead typed

gdcmdump --csa my file.dcm| grep B 

, which says

 (0019, 14d14) ?? (IS) [128]    #6,1 base matrix size 

is this what u need to know?

> Isaiah, 
I use version 3.6.1  and have  8-file sequences but all slices(140 slices) are contained in one folder... is that the reason?I'm sure that I chose .dcm files.

thanks,
akiko



_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject


_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject
Reply | Threaded
Open this post in threaded view
|

Re: error for converting dicom to nrrd& diffusion estimation modules

Akiko U
In reply to this post by Akiko U
Hi Mathieu and Isaiah, 

thank you for replying.

>Mathieu,
  you meant you need all the shown information? I attached it in word doc. I put --csa file.dcm |grep B_matrix and --csa file.dcm | grep B_ but didnt show any. 

>Isaiah, 
okay, I'll separate my data and see what will happen.


akiko

_______________________________________________
slicer-users mailing list
[hidden email]
http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users
To unsubscribe: send email to [hidden email] with unsubscribe as the subject

gdcmdump.docx (19K) Download Attachment