[Insight-users] Problem in copying DICOM image: Study instance UID value is changed

[Subrahmanyam Gorthi]

Dear Dan,

Thank you very much for your timely reply.
The information is very helpful and is what I am looking for regarding the
conversion to contours.

It's nice to know that DICOM is going to support a new segmentation module
:-)

Thank you.

Warm Regards,
Subrahmanyam Gorthi.

EPFL-STI-LTS5
Station 11
CH - 1015 Lausanne
Switzerland.



On Thu, Jul 3, 2008 at 6:59 AM, Dan Mueller <dan.muel at gmail.com> wrote:

> Hi Subrahmanyam,
>
> 2008/7/2 Subrahmanyam Gorthi <subrahmanyam.gorthi at gmail.com>:
> > Currently, at the end of my segmentation in ITK, I have ROIs in mask
> format.
> > I still have to work on converting this mask to a polygon so that in can
> be
> > written to a ROI module.
> > Because of my little exposure to ITK, I am not aware whether this
> conversion
> > involves Mesh or Meta Objects.
>
> From my understanding, RTSTRUCTs are an array of contours; therefore,
> you will need a mechanism to convert your ITK mesh to a set of
> contours. Unfortunately, I don't think such an algorithm exists in ITK
> (yet), so you will have to write one yourself. It's not too difficult
> given a starting mesh:
>    // Find intersecting points
>    foreach plane intersecting mesh
>        foreach edge in mesh
>            determine if plane intersects edge, record intersection
>        end
>    end
>    // Order intersection points into closed contour
>   get random starting face with intersection
>    while more intersections
>        for current face, add intersection to contour
>        current face = adjacent face sharing same intersection as
> current face
>    end
>
> On a side note, DICOM is about to be extended to support meshes proper
> via the "Surface Segmentation" module:
>    ftp://medical.nema.org/medical/dicom/supps/sup132_lb.pdf
> If you really need to use RTSTRUCTs right now, too bad. Otherwise the
> surface segmentation module seems much more flexible...
>
> HTH
>
> Regards, Dan
>
> > On Wed, Jul 2, 2008 at 12:03 PM, Mathieu Malaterre
> > <mathieu.malaterre at gmail.com> wrote:
> >>
> >> Subrahmanyam,
> >>
> >> On Wed, Jul 2, 2008 at 11:30 AM, Subrahmanyam Gorthi
> >> <subrahmanyam.gorthi at gmail.com> wrote:
> >> > Dear Mathieu,
> >> >
> >> > Many THANKS for your detailed & prompt reply.
> >> >
> >> > Here is what I am actually trying to implement in ITK:
> >> >
> >> > Using a segmentation algorithm in ITK, I obtained the coordinates for
> >> > 3-D
> >> > ROI of a patient's image .
> >> > I am now trying to export these results into a "DICOM-RT
> Structure-Set"
> >> > file, for RT-Planning in IMRT.
> >>
> >> *Very* cool ! Is this integrated with any of the Mesh and/or the Meta
> >> Object in ITK too ?
> >>
> >> > In addition to ROI module, as the DICOM-RT structure-set file has to
> >> > contain
> >> > other
> >> > mandatory modules like patient-module, study module etc.,
> >> > I am trying to selectively copy those modules from the associated
> >> > patient's
> >> > 3-D CT image.
> >>
> >> Ah, I see why the UID can remains the same here. You did not modify the
> >> image :)
> >>
> >> > I compared the tags of structure-set file that I am creating in ITK
> with
> >> > the  file generated by another software that
> >> > a Physician here is using in his hospital;
> >> > he was manually drawing the contours on the CT image and the
> >> > corresponding
> >> > DICOM-RT structure-set file is generated by the software.
> >>
> >> ok
> >>
> >> > I observed that for the "structure-set" file generated by that
> software,
> >> > "study-instance UID" tag is same as that of the
> >> > other 3-D CT DICOM images and hence, I am trying to do the same for
> the
> >> > file
> >> > created through ITK.
> >>
> >> Yup, in this very special case, then you are even encouraged to keep
> >> the same UID :)
> >>
> >> > From your reply, I understand the importance safety issues in
>  changing
> >> > the
> >> > default behavior.
> >> > I would like to know:
> >> > 1. Is it possible to change the default behavior for ONLY selected
> UIDs
> >> > that
> >> > are specified by the user?, and how?
> >>
> >> I am not sure I understand that. but I guess you can do the in your
> >> code (application level):
> >>
> >>  if( currentuid match [set of known uids] )
> >>    GDCMImageIO->KeepOriginalUIDOn ()
> >>
> >> > 2. I want to finally contribute this code to ITK.
> >>
> >> Even better !
> >>
> >> > It would be very happy to know and most probably, implement any better
> >> > ways
> >> > or modifications to the current approach.
> >> > Your suggestions in this regard will be of great help to me.
> >>
> >> IMHO ITK is clearly lacking support for RTSTRUCT object, so any kind
> >> of contribution would be AFAIK very welcome. For instance in a newer
> >> release of GDCM, we have now integrated RTSTRUCT object nicely in VTK:
> >>
> >> See:
> >>  http://gdcm.sourceforge.net/html/classvtkGDCMPolyDataReader.html
> >>
> >> Thus RTSTRUCT now appears as a set of vtkPolyData which is the base
> >> object for 2D unstructred data in VTK.
> >> I would think that a similar approach can (should?) be taken for ITK.
> >> You would need to implement a itk::somethingIO that will read RTSTRUCT
> >> and then convert it to either a itk::Mesh/itkQEMesh or SpatialObject
> >> and convert back to file. This would be IMHO the most flexible for
> >> people.
> >>
> >> And thus you pipeline would become:
> >>
> >> 1. GDCMImageIO read (filename)
> >> 2. Segmentation
> >> 3. RTSTRUCT_IO write ouput_filename
> >>
> >> does this make sense ?
> >>
> >> Regards,
> >> --
> >> Mathieu
> >
> >
> > _______________________________________________
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> > Insight-users at itk.org
> > http://www.itk.org/mailman/listinfo/insight-users
> >
> >
>
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