PET image formats in TPC
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
P:\bin\windows\ImageConverter.exe, elsewhere it can be downloaded from
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.
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
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.
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.
Siemens Inveon PET images consists of two files,
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.
PET image files can be converting to binary flat files and back using programs:
- Dumping pixel values to a binary float file: img2flat
- Constructing an ECAT file from binary (4-byte) float data file:
and converting numerical data in ASCII file into binary float data file: asc2flat
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.
- Tools for processing PET image data
- Image anonymization
- PET image
- Units of PET data
- PET data
- File formats
- Batch mode analysis
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Updated at: 2020-02-22
Created at: 2013-10-23
Written by: Vesa Oikonen