Problems Recognizing RT Structure DICOM File

[Matthew Strugari]

Hi Greg,

I am having trouble loading an RT Structure from Oncentra Prostate 4.1.6. The file is of type .dcm but when I try to convert the RT Structure file to a .nrrd file, I receive an error stating: Sorry, could not load input as any known type. 3D Slicer also cannot load this file. There doesn't seem to be anything wrong with the file specifically since I am able to load it back into Oncentra without any problems.

Could it be that Plastimatch and Slicer cannot load DICOM files from Oncentra? I don't image that this would be the problem. My work term is wrapping up in a couple of weeks here and it would be really great to get this working since all of my research now relies on using Oncentra RT Structures.

Matthew

[Sharp, Gregory C.]

Hi Matthew,

 

What is the DICOM Modality of the file?  For example:

 

dcmdump structure.dcm | grep Modality

 

I just want to make sure it really is RTSTRUCT. 

 

Can you send an anonymized sample?

Note also, that DICOM import, plastimatch and SlicerRT have separate implementation.

So also worth trying plastimatch.

 

Greg

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[Matthew Strugari]

W: DcmItem: Length of element (0002,0016) is odd

W: DcmItem: Length of element (0008,0020) is odd

(0008,0060) CS [RTSTRUCT]                               #   8, 1 Modality

This is what I received after entering your outlined command.

What is your email? I will send it via that since I am not too sure if the file is anonymized. It is from an RTOG study.

Matthew

[Sharp, Gregory C.]

If it’s not anonymized, better not send.  We can work out by e-mail.

 

Or, you can check if it’s anonymized.  Try this:

 

dcmdump | less

 

Then look especially at PatientID, PatientName, and other important fields.

 

The problem you describe is importing using SlicerRT?

Can you confirm the extension is installed?  Do you know which version?

Does plastimatch also fail to load it?

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[Matthew Strugari]

I have also installed a DicomImageViewer program from the Ubuntu Software Centre which is able to read the header information. When I attempt to read the header info with Plastimatch, I receive:

ITK exception.

itk::ImageFileReaderException (0x1be1360)

Location: "unknown" 

File: /home/matthew/Programs/InsightToolkit/InsightToolkit-4.6.1/Modules/IO/ImageBase/include/itkImageFileReader.hxx

Line: 143

Description:  Could not create IO object for reading file MATT_test.dcm

  Tried to create one of the following:

    NiftiImageIO

    NrrdImageIO

    GiplImageIO

    HDF5ImageIO

    JPEGImageIO

    GDCMImageIO

    BMPImageIO

    LSMImageIO

    PNGImageIO

    TIFFImageIO

    VTKImageIO

    StimulateImageIO

    BioRadImageIO

    MetaImageIO

    MRCImageIO

    GE4ImageIO

    GE5ImageIO

  You probably failed to set a file suffix, or

    set the suffix to an unsupported type.

Error, unsupported input type in load_native(): 0

Type = undefined

Planes = 0

Unhandled image type (PLM_IMG_TYPE_UNDEFINED) in set_from_plm_image

Just for you info.

Matthew

[Sharp, Gregory C.]

Yeah, sorry, I should fix that.  Plastimatch is foolishly trying to use the ITK reader.

 

Could you put the file in a directory, and then tell plastimatch to load the directory?

 

 

 

From: plast...@googlegroups.com [mailto:plast...@googlegroups.com] On Behalf Of Matthew Strugari

Sent: Wednesday, December 17, 2014 10:29 AM
To: plast...@googlegroups.com
Cc: Sharp, Gregory C.

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[Matthew Strugari]

Alright, it appears to be anonymized for the trail so I will send it over.

Importing using SlicerRT returns: 

Sorry, could not load input as any known type.

DICOM / DICOM-RT Import terminated with an unknown exception.

I attempted to use Plastimatch Convert with returned:

ITK exception.

itk::ImageFileReaderException (0x1b327e0)

Location: "unknown" 

File: /home/matthew/Programs/InsightToolkit/InsightToolkit-4.6.1/Modules/IO/ImageBase/include/itkImageFileReader.hxx

Line: 143

Description:  Could not create IO object for reading file MATT_test.dcm

  Tried to create one of the following:

    NiftiImageIO

    NrrdImageIO

    GiplImageIO

    HDF5ImageIO

    JPEGImageIO

    GDCMImageIO

    BMPImageIO

    LSMImageIO

    PNGImageIO

    TIFFImageIO

    VTKImageIO

    StimulateImageIO

    BioRadImageIO

    MetaImageIO

    MRCImageIO

    GE4ImageIO

    GE5ImageIO

  You probably failed to set a file suffix, or

    set the suffix to an unsupported type.

Sorry, could not load input as any known type.

Matthew

[Matthew Strugari]

SlicerRT is running in the 2014-12-12 nightly build.

[Matthew Strugari]

Okay thank-you.

What command would you like me to use to "load" the directory? If I use plastimatch header <directory> or plastimatch stats <directory>, Segmentation fault (core dumped) is returned in both cases.

The DICOM file is attached.

Matthew

[Sharp, Gregory C.]

Thanks.  I could reproduce the problem.  Both SlicerRT & plastimatch have trouble with this,

for seemingly different reasons.  I will investigate.  -Greg

 

From: Matthew Strugari [mailto:matt.s...@gmail.com]

Sent: Wednesday, December 17, 2014 10:46 AM
To: plast...@googlegroups.com
Cc: Sharp, Gregory C.

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[Sharp, Gregory C.]

OK, I found the problem.  The file is missing a Series Instance UID.

This is illegal, it is a required attribute.  I patched plastimatch to force loading

even when no Series Instance UID.  Will look into SlicerRT.

 

However, I realize there is another problem, which is that if you try to load

an RTSTRUCT, and then rasterize to an image, there is ambiguity in how it gets rasterized.

Still working on this.

 

-Greg

--

[Sharp, Gregory C.]

Small update.  The plastimatch importer does work on these structures.

Could you please update your plastimatch and give another try?

For example:

 

plastimatch convert --input matt_test.dcm --output-prefix labelmaps/

[Matthew Strugari]

Hi Greg,

I updated Plastimatch and everything works as expected. 

One thing I noticed is that there are many slices missing throughout the labelmaps. I had not anticipated this but it makes sense since the contours are created by only contouring the desired anatomy on a few slices. Oncentra Prostate automatically interpolates the structure in between the contoured slices in order to complete a continuous structure volume. When the structure sets were exported, they originally appeared as continuous structures in the Oncentra suite. 

Is the problem that I am seeing related to this random contouring on various slices or is there a further problem with the data set or Plastimatch? Or is this what you were referring to when you mentioned that there is an ambiguity in how the RTSTRUCT file gets rasterized?

Matthew

[Gregory Sharp]

Hi Matthew,

Indeed, your DICOM file only contains contours on some of the slices.

The ambiguity I talked about still exists, but only for structure
sets drawn on "tilted planes". Your planes are not tilted,
so it is not a problem for you.

If it is helpful, there is a method to fill the gaps in 3D Slicer.
You can do a dilate operation followed by an erode operation.

Greg