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

[Subrahmanyam Gorthi]

Dear Mathieu,

Thank you for your mail.

As you suggested, I will send you the diff files of GDCM layer once I am
done with that.

Thank you.

Warm Regards,
Subrahmanyam Gorthi.



On Tue, Sep 16, 2008 at 9:24 AM, Mathieu Malaterre <
mathieu.malaterre at gmail.com> wrote:

> Subrahmanyam,
>
> 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,
> --
> Mathieu
>
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