Transfer syntax conversion

[George]

Hello,

I am facing an issue with the transfer syntax of this dicom file it is JPEG2000
https://drive.google.com/file/d/1rBZw-o ... drive_link

this is the result for running dcmjp2k

E: DcmDataDictionary: Cannot open file: /usr/share/libdcmtk12/dicom.dic*
W: no data dictionary loaded, check environment variable: DCMDICTPATH
F: no conversion from compressed original to uncompressed transfer syntax possible!

the most difficult part is dealing with F: no conversion from compressed original to uncompressed transfer syntax possible!

[J. Riesmeier]

First of all, you should make sure that the DICOM data dictionary file "dicom.dic" is loaded. Since the file is apparently not located in the default path (/usr/share/libdcmtk12/dicom.dic) you need to specify the location of the file with the environment variable DCMDICTPATH. See documentation for details.

Then, it would be interesting to know which DCMTK tool you've called with which parameters. You say that you were running "dcmjp2k", but there is no such command line tool.

[George]

I wanted to add that I am still trying to use it

Code: Select all

:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ locate dicom.dic
/home/george_z/dcmjp2k-3.6.7-linux-x86_64-eval/share/dcmtk/dicom.dic
/home/george_z/dcmtk/dcmdata/data/dicom.dic
/usr/local/share/dcmtk-3.6.7-DEV/dicom.dic
/usr/share/libdcmtk16/dicom.dic
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ export DCMDICTPATH=/home/george_z/dcmjp2k-3.6.7-linux-x86_64-eval/share/dcmtk/dicom.dic
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ ./dcmdjp2k_e -L dcmjp2k.lic ../../CSTORERQ_SM_1.3.46.670589.45.1.1.4993912214784.1.5436.1538561391456.5-iwatt.dcm out.dcm -v
I: --DCMJP2K: $dcmtk: dcmdjp2k_e v3.6.7 2022-04-22 $
I: --Copyright (C)2004-2011, OFFIS e.V.
I: --Licensed to: George Zaher, Israel (KNU-HBKD-35011-13868)
I:
I: reading input file ../../CSTORERQ_SM_1.3.46.670589.45.1.1.4993912214784.1.5436.1538561391456.5-iwatt.dcm
I: decompressing file
Segmentation fault (core dumped)
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ export DCMDICTPATH=/usr/local/share/dcmtk-3.6.7-DEV/dicom.dic
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ ./dcmdjp2k_e -L dcmjp2k.lic ../../CSTORERQ_SM_1.3.46.670589.45.1.1.4993912214784.1.5436.1538561391456.5-iwatt.dcm out.dcm -v
I: --DCMJP2K: $dcmtk: dcmdjp2k_e v3.6.7 2022-04-22 $
I: --Copyright (C)2004-2011, OFFIS e.V.
I: --Licensed to: George Zaher, Israel (KNU-HBKD-35011-13868)
I:
I: reading input file ../../CSTORERQ_SM_1.3.46.670589.45.1.1.4993912214784.1.5436.1538561391456.5-iwatt.dcm
I: decompressing file
Segmentation fault (core dumped)
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ export DCMDICTPATH=/home/george_z/dcmtk/dcmdata/data/dicom.dic
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ ./dcmdjp2k_e -L dcmjp2k.lic ../../CSTORERQ_SM_1.3.46.670589.45.1.1.4993912214784.1.5436.1538561391456.5-iwatt.dcm out.dcm -v
I: --DCMJP2K: $dcmtk: dcmdjp2k_e v3.6.7 2022-04-22 $
I: --Copyright (C)2004-2011, OFFIS e.V.
I: --Licensed to: George Zaher, Israel (KNU-HBKD-35011-13868)
I:
I: reading input file ../../CSTORERQ_SM_1.3.46.670589.45.1.1.4993912214784.1.5436.1538561391456.5-iwatt.dcm
I: decompressing file
Segmentation fault (core dumped)
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ export DCMDICTPATH=/home/george_z/dcmtk/dcmdata/data/dicom.dic
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$ ./dcmdjp2k_e -L dcmjp2k.lic ../../CSTORERQ_SM_1.3.46.670589.45.1.1.4993912214784.1.5436.1538561391456.5-iwatt.dcm out.dcm -v
I: --DCMJP2K: $dcmtk: dcmdjp2k_e v3.6.7 2022-04-22 $
I: --Copyright (C)2004-2011, OFFIS e.V.
I: --Licensed to: George Zaher, Israel (KNU-HBKD-35011-13868)
I:
I: reading input file ../../CSTORERQ_SM_1.3.46.670589.45.1.1.4993912214784.1.5436.1538561391456.5-iwatt.dcm
I: decompressing file
Segmentation fault (core dumped)
:~/dcmjp2k-3.6.7-linux-x86_64-eval/bin_static$

[Marco Eichelberg]

The problem with this image file is that it is compressed with JPEG 2000, and cannot be decompressed. In compressed form, the pixel data already allocates about 3 GBytes of data (17444 frames of 512x512 color pixels). In decompressed form, the image would be 12.8 GBytes large, but uncompressed DICOM images (in the original Explicit/Implicit VR encoding) are limited to about 4 GBytes (more precisely: the pixel data cannot allocate more than 2^32-2 bytes, because that is the largest possible value for the 32-bit length field).

The segmentation fault should not happen (I will register that in our issue tracker), the tool should just terminate with an error message.

Unfortunately, processing such a file is not possible using the DCMJP2K command line tools. For this, you would need access to the source code and compile a tool that extracts and decompresses the image frame by frame.