DICOM image format

DICOM standard defines image and other data sets, and also data transport protocols and services. DICOM standard is established by American College of Radiology (ACR) and National Electrical Manufacturers Association (NEMA). Part 10 of the standard describes the file format for the distribution of images. At present, DICOM 3.0 is widely used by the PET scanner manufacturers.

In Turku PET Centre, PET/CT and PET/MR scanners, and β-CUBE, produce images in DICOM format. DICOM images are stored in PETPACS.

Carimas^™ can process many DICOM format images. Notice that DICOM files from different scanner manufacturers, even from different scanner generations, can be very different. Therefore it is common that a certain DICOM image cannot be (correctly) processed by the software, before support for the specific format is added.

Converting DICOM to other formats

DICOM images can also be converted to ECAT 7, NIfTI, or Analyze 7.5 format, if necessary, with .NET program ImageConverter, which can be found in P:\bin\windows\, or downloaded from here. To start the program, double-click the *.exe file, or select "Run" in Windows "Start" menu and write imageconverter_1_1_5 (or later version) in the "Open" field and click "Ok". In ImageConverter GUI do the following steps for each PET study:

click "Open DICOM folder" icon in the upper panel
find and select the PET DICOM folder that you uncompressed in previous step
in "Output options" tab: select Ecat7 as the Output image format
in "Output options" tab: uncheck "Convert files in place" check box
in "Output options" tab: change Output folder to your working folder, for example C:\work\ (make sure there is no '*' in the end of folder name)
in "Output options" tab: change "Output filename pattern" to contain study number (for example ck29) or other name which identifies this PET image from other image files
if you plan to copy data outside hospital or PET Centre, you should go to tab "General options" and check "Anonymize data"; otherwise you do not need to change anything in this tab or in "Dicom options"
Click the big "Convert" button, and wait; there should now be single ECAT 7 file created in the specified folder (for example C:\work\ck29.v).

ImageConverter can also be used in Windows command prompt, which is faster when many image sets need to be converted. Enter command ImageConverter --help to get usage information. File and path names should not contain special characters, including spaces.

For example, to convert a DICOM image in subfolder kuvat\moin\ into ECAT7 file moin.v, enter command:

ImageConverter kuvat\moin -c=Ecat7 -o=.\moin

If current working folder contains DICOM PET and CT images, each in its own sub-folder, you can list the directories in Windows command prompt window with tree command:

D:\work\Inveon>tree
Folder PATH listing for volume Datadisk
D:.
├───P115625_3D.pet_P115625_3D.pet
│   └───20190322_P115625_3D
│       └───PT_P115625_3D.pet
├───P115625_XAT_Attenuation-CT_MORRAT_v6.ct_P115625_XAT_Attenuation-CT_MORRAT_v6.ct
│   └───20190322_P115625
│       └───CT_P115625_XAT_Attenuation-CT_MORRAT_v6.ct
├───P115628_3D.pet_P115628_3D.pet
│   └───20190329_P115628_3D
│       └───PT_P115628_3D.pet
...

In this case, if you like to convert all DICOM PET images, but not CT images, into NIfTI format, each with SIF, and store the converted files under current working directory, you can enter command:

for /r /d %A in (PT_*.pet) do ImageConverter %A -c=Nifti -s -o=.\%~nA

This will create NIfTI images

D:\work\Inveon>dir PT*
 Volume in drive D is Datadisk
 Directory of D:\work\Inveon

22/02/2020  18:53       104,202,592 PT_P115625_3D.nii
22/02/2020  18:53               535 PT_P115625_3D.sif
22/02/2020  18:53       104,202,592 PT_P115628_3D.nii
22/02/2020  18:53               535 PT_P115628_3D.sif
...

The precise command format will need to be modified depending on the data tree. For example:

D:\work\Molecubes>tree
Folder PATH listing for volume Datadisk
D:.
├───P115623 CT DICOM
├───P115623 PET DICOM
├───P115624 CT DICOM
├───P115624 PET DICOM
├───P115627 CT DICOM
├───P115627 PET DICOM
...
for /r /d %A in (*PET*) do ImageConverter "%A" -c=Nifti -s -o=".\%~nA"
...
D:\work\Molecubes>dir P*
 Volume in drive D is Datadisk
 Directory of D:\work\Molecubes

22/02/2020  19:52       566,231,392 P115623 PET DICOM.nii
22/02/2020  19:52               505 P115623 PET DICOM.sif
22/02/2020  19:54       566,231,392 P115624 PET DICOM.nii
22/02/2020  19:54               505 P115624 PET DICOM.sif
22/02/2020  19:56       566,231,392 P115627 PET DICOM.nii
22/02/2020  19:56               504 P115627 PET DICOM.sif
...

Note that in this example the double quotes are required because of spaces in directory names.

References:

Archie KA, Marcus DS. DicomBrowser: software for viewing and modifying DICOM metadata. J Digit Imaging 2012; 25(5): 635-645. doi: 10.1007/s10278-012-9462-x.

Aryanto KY, Oudkerk M, van Ooijen PM. Free DICOM de-identification tools in clinical research: functioning and safety of patient privacy. Eur Radiol. 2015; 25(12): 3685-3695. doi: 10.1007/s00330-015-3794-0.

Bidgood Jr WD, Horii SC, Prior FW, Van Syckle DE. Understanding and using DICOM, the data interchange standard for biomedical imaging. J Am Med Inform Assoc. 1997; 4(3): 199-212.

Branstetter IV BF, Rubin DL, Griffin S, Weiss DL (eds.): Practical Imaging Informatics - Foundations and Applications for PACS Professionals. Springer, 2009. doi: 10.1007/978-1-4419-0485-0.

Clunie DA: DICOM Structured Reporting. PixelMed Publishing, 2000. pdf.

Dreyer KJ, Hirschhorn DS, Thrall JH, Mehta A (eds.): PACS: A Guide to the Digital Revolution, 2nd ed., Springer, 2006. doi: 10.1007/0-387-31070-3.

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Huang HK: PACS and Imaging Informatics - Basic Principles and Applications, 2nd ed., Wiley-Blackwell, 2010. doi: 10.1002/9780470560525.

Kamauu AW, Duvall SL, Avrin DE. Using Java to generate globally unique identifiers for DICOM objects. J Digit Imaging 2009; 22(1): 11-14. doi: 10.1007/s10278-007-9079-7.

Liu Y, Wang J: PACS and Digital Medicine - Essential Principles and Modern Practice. CRC Press, 2011. ISBN 9781420083651.

Moore SM, Maffitt DR, Smith KE, Kirby JS, Clark KW, Freymann JB, Vendt BA, Tarbox LR, Prior FW. De-identification of medical images with retention of scientific research value. Radiographics 2015; 35(3): 727-735. doi: 10.1148/rg.2015140244.

Noumeir R. DICOM structured report document type definition. IEEE Trans Technol Biomed. 2003; 7(4): 318–328. doi: 10.1109/TITB.2003.821334.

Noumeir R. Benefits of the DICOM structured report. J Digit Imaging 2006; 19(4): 295–306. doi: 10.1007/s10278-006-0631-7.

Noumeir R, Pambrun J-F. Teaching DICOM by problem solving. J Digit Imaging 2012; 25(5): 653-661. doi: 10.1007/s10278-012-9471-9.

Pianykh OS: Digital Imaging and Communications in Medicine (DICOM) - A Practical Introduction and Survival Guide, 2nd ed., Springer, 2012. doi: 10.1007/978-3-642-10850-1.

Revet B: DICOM Cook Book for Implementations in Modalities. Philips Medical Systems, 1997. http://www.archive.org/details/DicomCookbook.

Riddle WR, Pickens DR. Extracting data from a DICOM file. Med Phys. 2005; 32(6): 1537-1541. doi: 10.1118/1.1916183.

Rosset A, Spadola L, Ratib O. OsiriX: an open-source software for navigating in multidimensional DICOM images. J Digit Imaging 2004; 17(3): 205-216. doi: 10.1007/s10278-004-1014-6.

Shin H-B, Sheen H, Lee H-Y, Kang J, Yoon D-K, Suh TS. Digital imaging and communications in medicine (DICOM) information conversion procedure for SUV calculation of PET scanners with different DICOM header information. Physica Medica: Eur J Med Phys. 2017; 44: 243-248. doi: 10.1016/j.ejmp.2017.05.063.

Tags: Image, DICOM, PACS, File format

Updated at: 2020-02-22
Created at: 2017-04-11
Written by: Vesa Oikonen

DICOM image format

Converting DICOM to other formats

See also:

References:

Turku PET Centre

Modelling

Analysis