[Insight-users] Loading DICOM RTStructs

Fri Oct 16 19:30:31 EDT 2009

Hi Mark,

No I don't use an itk mesh.  I needed a binary volume for each structure  (you can then mesh your binary volume if you want).  In the DICOM RT file each each structure is represented as a set of points for a single slice (nb there might be > 1 sets of points for a single contour in a single slice, eg for bone).   I work on  a  temporary 2D slice which is inserted back into the 3D volume after it's updated.   I use some of Mathieu's code from the excellent GDCM 2.0 library  to extract the RT points.   For each structure region , I  convert the physical RT points into image space and generate pointlist,  which are used to generate  polygon spatial objects for each contour .  Then I use the SpatialObjectToImageFilterType to copy that structure component onto the 2D slice.  And iterate through the RT file:  at the end of I have one binary volume for each structure.  

If anyone's interested, last year I also wrote an itk RTOG file parser which does a similar thing. 

I've sent the code and test data to you - please let me know if you have any feedback?

Cheers,
Jason

________________________________________
From: Mark Roden [mmroden at gmail.com]
Sent: Saturday, 17 October 2009 1:54 AM
To: Dowling, Jason (ICT Centre, Herston - RBWH)
Cc: mathieu.malaterre at gmail.com; insight-users at itk.org; gdcm-developers at lists.sourceforge.net
Subject: Re: [Insight-users] Loading DICOM RTStructs

Hi Jason,

That would be very useful, thanks.

My code, as I said, is written using the C# wrappers to gdcm.  It then
converts the masks into a char image, where a 1 indicates the presence
of a mask and a 0 does not, and I was going to implement a marching
squares algorithm to go back to an rtstruct.  I'm guessing that your
code goes to an itk mesh; is there a way to convert a mesh into an
image and back again?  I'm messing around with segmentations, and the
papers I'm finding are all pixel-based rather than mesh-based, so
getting the mesh is just part of the problem.

Thanks!
Mark

On Fri, Oct 16, 2009 at 12:27 AM,  <Jason.Dowling at csiro.au> wrote:
> Hi Mathieu and Mark,
>
> Yes, I've written a C++ DICOM-RT Struct importer which uses ITK and GDCM 2. I've been testing it on MR and CT volumes of the pelvis (I have also testing it on some head and neck and chest volumes) over the past few weeks.
> I have been planning to write an Insight Journal paper over the past week and will try to do this over the weekend.  I'm happy to send you the code today (as is) if you would like to test/compare it?
>
> Cheers,
> Jason
>
>
> -----Original Message-----
> From: Mathieu Malaterre [mailto:mathieu.malaterre at gmail.com]
> Sent: Friday, October 16, 2009 6:13 PM
> To: Mark Roden
> Cc: insight-users at itk.org; Dowling, Jason (ICT Centre, Herston - RBWH); gdcm-developers
> Subject: Re: [Insight-users] Loading DICOM RTStructs
>
> Hi Mark,
>
>  I made a mistake and had a private conversation with Jason Dowling (CC), without CCing gdcm-dev sorry :(
>  He also has been working on a C++ RT Importer using gdcm 2.x. This has been tested on multilpe platform and gives proper results.
>  If you would like we could compare both C++ code and merge them. I know Jason was really close to making a release to the IJ. Jason, any comments ?
>
> cheers
>
> On Fri, Oct 16, 2009 at 1:43 AM, Mark Roden <mmroden at gmail.com> wrote:
>> Hi all,
>>
>> I note that there is now the capability of exporting DICOM RT structs:
>>
>> http://www.insight-journal.org/browse/publication/316
>>
>> However, I can't find any information on how to import these structs.
>> It may just be that my google-fu is weak, so if there is such an
>> example or the like, please let me know.
>>
>> I've written C# code to wrap around gdcm to go into my own image
>> format, so I can use that if I have to, but the conversion would
>> probably be irritating since I'm extremely inexperienced with the itk.
>>  I'd rather follow some sample code.
>>
>> Barring that, should I just post my importer to the development list
>> to get some help on converting it into an itk C++ class?
>>
>> Thanks!
>> Mark
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>
>
> --
> Mathieu
>