DICOM

KNIME Extensions
1

Is there a node to read image and metadata from DICOM files?

Thanks. Francecso

2

Hi Francesco,

did you try to use the `Image Reader` not with the option `Export OME Metadata` enabled?

Best,

Christian
 

3

Hi Christian,

thank you, I've tried the Image Reader and it is able to read DICOM and OME metadata (sizes ecc.). The files should contain other metadata that I'm not able to catch (even by selecting "Read non OME-XML Metadata". But where can "XML Annotations be read"?  in the XML?)

Is that what you meant with "not with the option `Export OME Metadata` enabled" ?

Thanks

Francesco

4

Hi Francesco,

yes this is what I actually meant. The data should be read from the DICOM file in the OME-XML which is output in the column next to the image. If it's not in this XML, maybe we are missing an option in BioFormats. Would it be possible that you send us a non-critical file such that we can test and check whats going wrong?

Best,

Christian

5

Unfortunately I'm not allowed to share those files. I've seen that the missing metadata are stored in the header  of the dicom, which has been generated via http://phoenix-pacs.de/

Best

Francesco

6

I solved the problem reading the DICOM header with the oro.dicom R package.

7

Ok great. Thanks for letting us know. I will file an issue in our bug-tracking system anyway to make sure we support reading dicom header files in the future.

Best,

Christian

 

8

I created a workflow using the oro.dicom R package mentioned by fcivardi. I included a small tutorial on how to setup your system to be able to do that in the workflow annotation.

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9

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