[ITK] Writing a 3D image into DICOM series with correct geometry

[Fijoy Vadakkumpadan]

Hi Francois,

Even after explicitly setting the geometry metadata before saving the DICOM
series, the metadata is not loaded back when I read the saved image in ITK.
I believe ITK saves the metadata (I can see it when I load the saved series
in ImageJ), but it's just not loaded back.

It seems to me that ITK/GDCM saves the DICOM series under Secondary Capture
SOP class by default, and since the geometry metadata are not mandatory for
this class, ITK just doesn't load it back. When I change the SOP class (see
Stackoverflow post below), the geometry metadata are indeed loaded back.

Do you or anyone else here know if there is another appropriate SOP class
that we can save images coming from non-DICOM sources such that the
geometry metadata are saved & loaded by ITK/GDCM?

https://stackoverflow.com/questions/40462879/image-position-orientation-not-written-when-saving-itkimage-as-dicom

Thanks,
--Fijoy

On Fri, Jul 7, 2017 at 12:43 PM, Francois Budin <francois.budin at kitware.com>
wrote:

> Hello Fijoy,
>
> As far as I know this example is the best way to do what you are trying to
> do. ITK does not currently have an easy way to save an itk::Image as a
> DICOM series.
> Thanks,
>
> Francois
>
> On Fri, Jul 7, 2017 at 11:04 AM, Fijoy Vadakkumpadan <tofijoy at gmail.com>
> wrote:
>
>> Hello,
>>
>> What is the best way to write a 3D itk::Image to DICOM series in a way
>> that preserves geometry metadata (slice positions, orientation, and
>> spacing)?
>>
>> The itk::Image I'm referring to is coming from a non-DICOM source. I
>> tried to use itk::ImageSeriesWriter with itk::GDCMImageIO as the IO type to
>> do the above writing. But that does not seem to automatically pick up the
>> metadata from the image object - when I read the written series back (using
>> itk::ImageSeriesReader), only the in-plane spacing is correctly set. After
>> some research, I found this example
>>
>> https://itk.org/Wiki/ITK/Examples/DICOM/ResampleDICOM
>>
>> which explicitly sets the metadata dictionary for each slice before
>> writing. Is this the best way?
>>
>> Thanks,
>> --Fijoy
>>
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>>
>
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