[Insight-users] Dicom and Image Spacing

[Alexander Schmidt-Richberg]

Hi Bill,

I just use the simple ImageWriter since I want 3D images written and the file type is unknown at compile time:

 typedef ImageFileWriter< ImageType > ImageWriterType;
 ImageWriterType::Pointer writer;
 writer = ImageWriterType::New();
 writer->SetInput( image );
 writer->SetFileName( imageName );
 writer->Update();

Is this a problem in ITK4? That means, do DICOM images now require a special handling?

Regards,
Alex

On 07.12.2012, at 17:27, Bill Lorensen <bill.lorensen at gmail.com> wrote:

> Our handing of Image Position Patient in ITK is tricky to use. How are
> you writing your DICOM volume? SeriesWriter or ImageWriter?
> 
> Bill
> 
> On Fri, Dec 7, 2012 at 9:02 AM, Alexander Schmidt-Richberg
> <schmidt-richberg at imi.uni-luebeck.de> wrote:
>> Thanks, Bill and Rômulo, for pointing that out. I just checked the
>> current git version and the problem still remains: If I read, for
>> example, a .mhd volume image with a spacing not equal to one (not a
>> DICOM series), write it as DICOM volume file and then read the file, it
>> will get a z-spacing of 1 (the in-plane spacing, however, is
>> maintained). If this is really intended, it is kind of an awkward
>> behavior, imo.
>> 
>> Best regards
>> Alex
>> 
>> On Thu, 2012-12-06 at 15:52 +0000, Bill Lorensen wrote:
>>> In ITK 3 and 4 we compute the distance between slice centers (spacing)
>>> form the image position patient and orientation.
>>> In ITKv4 there was a bug that was recently fixed. It will appear in
>>> the 4.3 release. For now, you can try the latest 4.3 release candidate
>>> which was announced recently on the mailing list.
>>> 
>>> On Thu, Dec 6, 2012 at 4:35 AM, Rômulo Pinho
>>> <romulo.pinho at lyon.unicancer.fr> wrote:
>>>> Hello, Alex
>>>> It is indeed a change in GDCM 2.x. You can read about it at
>>>> 
>>>> 
>>> 
>> http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Using_GDCM_API#Automatic_ordering_of_slices_for_vtkGDCMImageReader.SetFileNames
>>>> 
>>>> 
>>> 
>> http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Imager_Pixel_Spacing#Spacing_along_Z_.28third_dimension.29
>>>> 
>>>> 
>>> 
>> http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Using_GDCM_API#Where_is_the_value_of_gdcm.Image.Spacing_coming_from_.3F
>>>> 
>>>> Kind regards,
>>>> Rômulo
>>>> 
>>>> 
>>>> 
>>>> On 12/06/2012 10:16 AM, Alexander Schmidt-Richberg wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> sorry if this has been discussed before. I'm sure I'm not the first
>> to
>>>> realize, but I couldn't find anything in the mailing lists.
>>>> 
>>>> I have a problem with reading/writing volume images as Dicom files
>>> with
>>>> ITKv4, presumably due to the change from GDCM 1.x to 2.x.
>>>> 
>>>> In ITK 3, the image spacing was stored in the tags
>>>> "SpacingBetweenSlices" and "ImagerPixelSpacing". In v4,
>>>> "NominalScannedPixelSpacing" is used for the in-plane spacing,
>>> however,
>>>> the z-spacing is not stored at all (if I'm right). That means, all
>> of
>>>> the "old" images I'm reading with ITK4 have a uniform spacing of 1,
>>>> since the old tags are not interpreted. Moreover, programs like
>>> MeVisLab
>>>> ignore the new tag.
>>>> 
>>>> Has this behavior been discussed? Is it working as intended and is
>>> there
>>>> any workaround?
>>>> 
>>>> Best regards Alex
>>>> 
>>>> 
>>>> 
>>>> _____________________________________
>>>> Powered by www.kitware.com
>>>> 
>>>> Visit other Kitware open-source projects at
>>>> http://www.kitware.com/opensource/opensource.html
>>>> 
>>>> Kitware offers ITK Training Courses, for more information visit:
>>>> http://www.kitware.com/products/protraining.php
>>>> 
>>>> Please keep messages on-topic and check the ITK FAQ at:
>>>> http://www.itk.org/Wiki/ITK_FAQ
>>>> 
>>>> Follow this link to subscribe/unsubscribe:
>>>> http://www.itk.org/mailman/listinfo/insight-users
>>>> 
>>> 
>> 
>> 
>> _____________________________________
>> Powered by www.kitware.com
>> 
>> Visit other Kitware open-source projects at
>> http://www.kitware.com/opensource/opensource.html
>> 
>> Kitware offers ITK Training Courses, for more information visit:
>> http://www.kitware.com/products/protraining.php
>> 
>> Please keep messages on-topic and check the ITK FAQ at:
>> http://www.itk.org/Wiki/ITK_FAQ
>> 
>> Follow this link to subscribe/unsubscribe:
>> http://www.itk.org/mailman/listinfo/insight-users
> 
> 
> 
> -- 
> Unpaid intern in BillsBasement at noware dot com