[Insight-users] Exporting Segmentation Results to RTSTRUCT using ITK

Mathieu Malaterre mathieu.malaterre at gmail.com
Tue Sep 16 03:24:20 EDT 2008


On Mon, Sep 15, 2008 at 5:41 PM, Subrahmanyam Gorthi
<subrahmanyam.gorthi at gmail.com> wrote:
> Dear Mathieu,
> I am very happy to inform that I am now able to export the segmentation
> results to RTSTRUCT using ITK.

Kudos !

> Thanks a lot for your valuable guidance on the pipeline, handling DICOM
> sequences and converting 3-D mask to contour.
> The inputs to the current Exporter are:
>   1. A DICOM slice of the CT image:
>       For extracting patient related and other common information.
>   2. 3-D Masks of the segmentation regions:
>      These are converted to contours using the
> itkContourExtractor2DImageFilter & itkExtractImageFilter and is given as
> input input to the RTSTRUCT writer.
>   3. Few other parameters:
>      Parameters like names to be assigned to the ROIs, Number of ROIs to be
> exported, type of contours etc...
> The output of the Exporter:   RTSTRUCT DICOM file.
> I verified the results by viewing the output file in a DICOM dumper, and
> also by superposing the RTSTRUCT contours over the DICOM CT image, using
> some third party tools. The code seems to work fine :-)
> Now RTSTRUCT Writer part is done. but RTSTRUCT Reader is yet to be written
> :-(
> Since the above application does not need RTSTRUCT Reader, I first started
> with the RTSTRUCT Writer.
> Still many modifications and cleanup are to be done for RTSTRUCT writer
> itself for using it for other general applications.
> My doubt is: for contributing this part to ITK (Insight Journal?), how
> should I manage the modified/added files?
> In my code, I added the following files to the ITK\Code\IO direcory:
> 1. itkRTSTRUCTIO.h
> 2. itkRTSTRUCTIO.cxx
> 3. itkRTSTRUCTIOFactory.h
> 4. itkRTSTRUCTIOFactory.cxx

This is exactly the minimum required.

> I modified the following files in ITK\Utilities\gdcm\src directory by adding
> few additional functions:
> 1. gdcmFile.cxx
> 2. gdcmFileHelper.h
> 3. gdcmFileHelper.cxx

Those will be slightly more difficult to handle, since the IJ
mechanism does not handle patch (AFAIK), but only external project to
ITK. If you can send me the diff of those files, so that I can
integrate them in ITK/gdcm before IJ submission. Therefore the day you
do your IJ submission the API in gdcm will already be augmented with
your patch.

> There are two other files: mask2contour.cxx & Export2RTSTRUCT.cxx.

Great !

> Can I simply put all the above files in a single folder and submit to the
> Insight journal along with the paper?
> (I still need to do significant cleanup and write the IJ-Paper :D)

If we except the gdcm patch, then everything else nicely fit in the process.

> The DICOM files that I am using for testing are bit large (around 60 MB).
> Is there any size limit for IJ submission?

Not that I know of. The only restriction is that you are responsible
for anonymizing the RTSTRUCT object before submission.

> Once again many thanks for your help.

np :)

good luck,

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