unable to read a file

[George]

Hello,

I have a list of files that are YBCR and JPEG2000 but gdcmconv and dcmtk tool are unable to read it.
This is the link to the file:
https://drive.google.com/file/d/1Wjqsng ... drive_link
This is the code I tried to run:

Code: Select all

$ gdcmconv -V -w -i Anonymous.MR._.15.1.2017.06.28.09.41.02.294.59320538.dcm -o fixed.dcm
Could not read (pixmap): Anonymous.MR._.15.1.2017.06.28.09.41.02.294.59320538.dcm

Also, I tried using the normal dicomImage constructor and it failed compilaining about photometric interpretations.

let me know what you can do to fix that problem.

Best Regards
George

[J. Riesmeier]

Short answer: The public and freely available DCMTK does not support decompression of JPEG 2000-compressed DICOM images unless you use an extension such as DCMJP2K.

[George]

I apologize, please take a look at this file
https://drive.google.com/file/d/1I_smfo ... sp=sharing

[J. Riesmeier]

The second file is not an image:

Code: Select all

> dcmdump +P SOPClassUID Anonymous.MR._.15.1.2017.06.28.09.41.02.294.59320538.dcm 
(0008,0016) UI =MRSpectroscopyStorage                   #  28, 1 SOPClassUID

[George]

Hello,

I also wish to examine how to convert the SOP class:

Code: Select all

$ dcmdump +P SOPClassUID ./fix/fixed.dcm
(0008,0016) UI =VLWholeSlideMicroscopyImageStorage      #  30, 1 SOPClassUID
$ gdcmtar -i ./fix/ -o op1.dcm
Sorry MediaStorage not supported: [1.2.840.10008.5.1.4.1.1.77.1.6]

I noticed that gdcmtar do have the support that I need but it fails due to SOP class, so how can I use dcmtk to convert it.

Code: Select all

gdcminfo fix/fixed.dcm
MediaStorage is 1.2.840.10008.5.1.4.1.1.77.1.6 [VL Whole Slide Microscopy Image Storage]
TransferSyntax is 1.2.840.10008.1.2.1 [Explicit VR Little Endian]
NumberOfDimensions: 3
Dimensions: (512,512,2)
SamplesPerPixel    :3
BitsAllocated      :8
BitsStored         :8
HighBit            :7
PixelRepresentation:0
ScalarType found   :UINT8
PhotometricInterpretation: RGB
PlanarConfiguration: 0
TransferSyntax: 1.2.840.10008.1.2.1
Origin: (0,0,0)
Spacing: (1,1,1)
DirectionCosines: (1,0,0,0,1,0)
Rescale Intercept/Slope: (0,1)
Orientation Label: AXIAL

Best Regards
George

[J. Riesmeier]

I am sorry, but I still don't know what you want to do and what you mean by "how to convert the SOP class". In order to help you, you should describe your problem in more detail, i.e. what do you want to achieve, what have you tried, what does not work, etc.

[George]

Hello,

I humbly request to learn how to convert this tag in dicom (0008,0016) to another using dcmtk.

The SOP Class UID and SOP Instance UID Attributes are defined for all DICOM IODs. However, they are only encoded in Composite IODs with the Type equal to 1. See Section C.1.2.3. When encoded they shall be equal to their respective Attributes in the DIMSE Services and the File Meta Information header (see PS3.10 Media Storage).

Best Regards
George

[J. Riesmeier]

I am sorry, but this very short explanation does not help (and it also makes no sense to me to "convert this tag in dicom"). Please describe in detail what you want to achieve. Otherwise no one will be able to help you in this regard.

[George]

Hello,

I am trying to run gdcmtar but it keeps failing with this error Sorry MediaStorage not supported: [1.2.840.10008.5.1.4.1.1.77.1.6]
This means that the media is not supported in here becuase the tag of SOP Class in dicom (0008,0016) is not supported so how do I convert
this tag to another that can be supported so I might be able to extract multiframe dicom images to single frame dicoms

Best Regards
George