[ITK-users] SimpleITK | read a 3D image from a non DICOM file and write it as a series of DICOM slices

[Matt McCormick]

Hi,

Generating a valid DICOM series can be a pretty complex task.

New UID's need to be generated, for example. Some more information can
be found here [1].

HTH,
Matt

[1]  http://gdcm.sourceforge.net/wiki/index.php/Writing_DICOM

On Thu, Jan 15, 2015 at 10:07 AM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Hello,
>
> I have just added an ImageSeriesWriter to SimpleITK:
>
> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1ImageSeriesWriter.html
>
> The hooks for getting the meta-data dictionary in the dicom series aren't
> quite there yet. But its a step closer. It's actually rather confusing how
> the tags are handled in the example you linked too, and I'm not sure what
> exactly needs to be done to create a "valid" dicom series.
>
> Brad
>
> On Dec 31, 2014, at 10:46 AM, Bradley Lowekamp <blowekamp at mail.nih.gov>
> wrote:
>
> Hello,
>
> Sorry for the slow reply. Earlier you linked to this nice example for
> reference:
> http://www.itk.org/Doxygen/html/Examples_2IO_2ImageReadDicomSeriesWrite_8cxx-example.html
>
> With SimpleITK I have done the following when I needed to write a series in
> Python:
>
> for i in range(img.GetSize()[2]):
>     sitk.WriteImage(img[:,:,i],"test_{0:04}.tif".format(i))
>
>
> However it is not quite this simple for a DICOM series. The metadata tags
> need to be correct too. SimpleITK is not designed to be a full fledge
> interface to DICOM files. Other tools may be better for that. But this seems
> like a reasonable thing to do but it's not currently readily available in
> the SimpleITK interface. Perhaps after some discussion on the best way to do
> it it and be added.
>
>
> There are 3 main components to this example:
>
> 1) MetaDataDictionary
>
> In SimpleITK the MetaDataDictionary interface is only part of the Image
> class. Currently it provides a read only interface, with the
> GetMetaDataKeys(), and GetMetaData(key) methods[1]. This get method only
> returns the type of data in the dictionary converted to a string.
>
> The required method would be Image::SetMetaData(key,value). The issue would
> be what types of value need to be supported. For this example only
> std::string is needed, perhaps others should be overloaded?
>
> 2) NumericSeriesFileNameGenerator
>
> This class only produces a "list" of file names. I think that many of the
> languages may have a more convenient way to do this. For example in Python:
>
> [ "test_{0:04}.png".format(i) for i in range(img.GetSize()[2]) ]
>
> So I don't think this is so important.
>
> 3) SeriesWriter
>
> What we just used above is different then the SeriesWriter, as special
> metadata is passed from the ImageSeriesWriter to the ImageIO [2]. Here is
> the JIRA issue for this task [3].
>
>
> So after these get done something like the following would do what you ask:
>
> import SimpleITK as sitk
>
> img = stik.ReadImage(argv[1])
> img.SetMetaData("008|0060", "MR") // Modality
> img.SetMetaData("008|0008", "DERIVED\\SECONDARY") // Image Type
> img.SetMetaData("008|0064", "DV") // Conversion Type
> sitk.WriteImage(img, [ "test_{0:04}.dcm".format(i) for i in
> range(img.GetSize()[2]) ])
>
> Does that look like what you are looking for?
>
> Brad
>
> [1]
> http://www.itk.org/SimpleITKDoxygen/html/classitk_1_1simple_1_1Image.html#a3d6cb12a211352ee38da5405b9c75928
> [2]
> https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/IO/ImageBase/include/itkImageSeriesWriter.hxx#L327-L368
> [3] https://issues.itk.org/jira/browse/SIMPLEITK-122
>
> On Dec 29, 2014, at 2:48 PM, Matias Montroull <matimontg at gmail.com> wrote:
>
> Hi,
>
> Is there an example for SimpleITK to read a 3D image from a non Dicom file
> such as mhd and then write it as a series of DICOM Slices?
>
> I can do this with C++ but I haven't been able to figure out how to do it
> using simpleITK.
>
> Thanks,
>
> Matias.
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