PET image formats in TPC

DICOM

PET/CT and PET/MR scanners, including β-CUBE and X-CUBE, produce images in DICOM format. DICOM images are stored in PETPACS.

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.

Carimas can process many DICOM format images, as well as any in-house written C#/.NET software.

DICOM images can be converted to Analyze 7.5, NIfTI-1, and ECAT 7 formats using ImageConverter. In TPC, ImageConverter can be started from S:\petsoftware\bin\windows\ImageConverter.exe, elsewhere it can be downloaded from here.

Analyze 7.5 and NIfTI-1

A variant of Analyze 7.5 image file format and NIfTI-1 image file format is partially supported in TPC. NIfTI format is preferred especially in the brain studies, because it stores the image position and transformation parameters. The integrated brain image processing pipeline, MAGIA pipeline, and general analysis tool Carimas support NIfTI.

Neither Analyze or NIfTI images contain information on PET frame times; therefore PET images in these formats should always be accompanied by SIF data.

Both formats can be converted to DICOM, or each other, using ImageConverter.

ECAT 7

Currently most analysis programs can use PET image data in ECAT 7 format, which is the format that ECAT HR+ produces.

During a long transitional stage most programs will be able to read also ECAT 6.3 format, which is the format of the first PET scanner in TPC, ECAT 931. This scanner was put out of operation in the end of April 2005. PET images from GE Advance (put out of operation in the end of 2010) were also routinely stored in ECAT 6.3 format. Old image files (most of them) can be found in folder S:\Research\archive\mo\.

Tools for conversion between ECAT formats are available, and .NET program ImageConverter can be used to convert ECAT 7 files to DICOM and a few other formats.

Unit of radioactivity

By default, the radioactivity concentrations in PET images are corrected for physical decay to the injection time. Radioactivity concentrations in ECAT 6.3 format images are calibrated to units kBq/ml (ml=cc) and in ECAT 7.x format images to units Bq/cc, but there may be exceptions; when necessary, check or set the units of ECAT images using program imgunit.

Polar map

A variant of ECAT 7 polar map format will be used in Turku PET Centre for storing and modelling myocardial PET data. Polar maps will be constructed with Carimas.

Dynamic or parametric polar map can be converted to/from DFT file using programs pm2dft and dft2pm.

Inveon/Concorde MicroPET

Siemens Inveon PET images consists of two files, *.img and *.img.hdr. These can be read and processed with Carimas and Amide. ImageConverter can read microPET images, and also a very primitive command-line tool for Concorde/microPET to ECAT 7 format conversion is available.

Researcher can get the MicroPET images from PETPACS in DICOM format.

Binary flat files

PET image files can be converting to binary flat files and back using programs:

PET data may contain patient names!

Please note that images and sinograms in DICOM or ECAT 6.3/7 format may contain the name of subject. Transfer of PET images or sinograms using any media outside PET Centre and University Hospital is strictly forbidden, unless the data are anonymized.


See also:


References:

Birkfellner W: Applied Medical Image Processing - A Basic Course. CRC Press, 2011.

Dreyer KJ, Hirschhorn DS, Thrall JH, Mehta A (eds.): PACS: A Guide to the Digital Revolution, 2nd ed., Springer, 2006.

Gibaud B. The quest for standards in medical imaging. Eur J Radiol. 2011; 78: 190-198. doi: 10.1016/j.ejrad.2010.05.003.

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

Larobina M, Murino L. Medical Image file formats. J Digit Imaging 2014; 27: 200-206. doi: 10.1007/s10278-013-9657-9.

Li X, Morgan PS, Ashburner J, Smith J, Rorden C. The first step for neuroimaging data analysis: DICOM to NIfTI conversion. J Neurosci Methods 2016; 264: 47-56. doi: 10.1016/j.jneumeth.2016.03.001.

Pianykh OS: Digital Imaging and Communications in Medicine (DICOM) - A Practical Introduction and Survival Guide, 2nd ed., Springer, 2012.

Todd-Pokropek A, Cradduck TD, Deconinck F. A file format for the exchange of nuclear medicine image data: a specification of Interfile version 3.3. Nucl Med Commun. 1992; 13(9):673-699.

Whitcher B, Schmid VJ, Thornton A. Working with the DICOM and NIfTI data standards in R. J Statistical Software 2011; 44(6): 1-29.



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Updated at: 2023-09-11
Created at: 2013-10-23
Written by: Vesa Oikonen