This page is obsolete: please read the new pages about image file formats and tools for image data.

PET image data

Scanners

HRRT

HRRT produces Interfile format images, which can be converted to ECAT 7 format using if2ecat program (PC/Windows XP) provided by the scanner manufacturer, or an in-house program if2e7 by Roman Krais. ECAT 7 format images are copied to PETO system. More information on HRRT and also other scanners.

ECAT HR+

ECAT HR+ produces ECAT 7.x format files. HR+ image data is copied to the PETO system by the imaging laboratory personnel.

GE Advance

GE Advance image data is extracted from the GE database, converted to ECAT 6.3 format, and copied to the PETO system by the imaging laboratory personnel. Images can also be extracted in PET DICOM format and converted to ECAT 7 format if necessary (contact Chunlei Han).

GE Discovery STE VCT

GE Discovery STE VCT (Teräs et al., 2007) stores the PET and CT images in DICOM format, which can be converted to ECAT 7 format if necessary within-house program dicom2ecat (please contact Harri Merisaari).

Inveon small-animal PET/CT

Siemens Inveon small-animal PET/CT is located in Turku Center for Disease Modeling. Image data is stored in Concorde/microPET format. Images can be sent to PETO system. A very primitive tool for Inveon to ECAT 7 image format conversion is available.

Image file formats

ECAT 7

Currently most analysis programs can use PET image data in ECAT 7 format, which is the format that ECAT HR+ produces. ECAT 7 format definition is in ECAT Software Operating Instructions Version 7.2, Appendix B; PDF in intranet.

During a long transitional stage most programs will be able to read also ECAT 6.3 format, which is the format of our first PET scanner, ECAT 931. This scanner was put out of operation in the end of April 2005. ECAT 6.3 format for images is defined in Siemens manual (Operating Instructions ECAT Scanner Software).

Tools for conversion between ECAT formats are available, and tools for conversion between ECAT 7 and PET DICOM are under development/testing.

Polar map

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

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

Analyze 7.5

A variant of Analyze 7.5 image format is partially supported. A few image processing and analysis programs are able to read and write this format. Tools for conversion between ECAT and Analyze formats are available.

DICOM

Carimas can process DICOM format images, as well as new C#/.NET software. DICOM images can also be converted to ECAT 7 format, if necessary, within-house program dicom2ecat (please contact Harri Merisaari).

Inveon/Concorde MicroPET

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

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 using program ecatunit. Correction for partial volume effect, is available in Turku PET Centre (contact Harri Merisaari).

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 name is first removed; see Patient privacy protection.

Working with image data:

Subtract background radioactivity: imgbkg
Subtract reference region TAC from dynamic image: imgbound
Make a grey-scale or rainbow color-scale TIFF image file for insertion to PowerPoint etc
Simple arithmetic calculation for ECAT sinogram and image files: ecatcalc
Combining two or more ECAT sinogram or image files: ecatcat
Turning images or sinograms in X, Y, and/or Z direction (flip the order of slices): ecatflip
Produce a "head curve", i.e. an average of all pixels as a function of time: ecathead
Replace the pixel values in sinogram or image using a look-up table : ecatlkup
Sort ECAT 6.3 image matrices in ascending order: ctisort
Combine the adjacent ECAT 7.2 volume image planes to reduce data size and noise: e7vplavg
Cutting the size of PET images by reducing the dimensions: imgshrink
Combining two or more static Analyze 7.5 images into one dynamic image in Matlab: combine
Calculating a "sum image", i.e. an average over certain time frames from dynamic ECAT or Analyze image: ecatsum , or image integral over certain time range: imginteg
Calculating an average over time or sum over time from Analyze 7.5 images in Matlab: sum_frame
Copying subheader information between CTI ECAT 6.3 files: cpshdrs and e6cphdrs
Set ECAT sinogram and image frame times: eframe
Setting ECAT 6.3 sinogram and image frame times and scan start time from SIF: sif2ecat
Correction of the frame times relative to the injection time, when scanning was started later: ecattime
Correction of physical decay and removing of the decay correction: edecay
Changing ECAT plane numbers to continuous sequence beginning from 1: efixplnr
Editing ECAT 7 main header or image volume headers
Removing patient name from ECAT 6.3 and 7 files: ecatanon
Checking, setting and conversion of radioactivity concentration units in ECAT 6.3 and 7 images: ecatunit
Renaming HR+ files by study number stored in main header user_process_code: eren2upc

Extract part of image:

Extracting certain planes and frames to a new file: esplit
Extracting smaller volume in PET image to a new file: imgbox
Extracting planes from ECAT7 image volumes: e7vplavg
Cut off empty sides to reduce ECAT image file size: imgslim
Saving profile line from image or sinogram, either from specified location or from peak value: eprofile

Retrieving information on ECAT files:

List the contents of ECAT 6.3 or 7.x main header: lmhdr; Edit ECAT 7.x main header: e7emhdr
List the content(s) of ECAT 6.3 or 7.x subheader(s): lshdr; edit the contents of ECAT 7.x image volume headers: e7evhdr
List the ECAT 6.3 or 7.x matrices: lmlist
List (or change) the ECAT frame times: eframe
Report the status of decay correction in an ECAT image: edecay
Report the zero (injection) date and time and scan start time in ECAT file: ecattime and egetstrt
Computation of SIF from dynamic images or sinograms in ECAT format: cti2sif, and specifically from HR+ scan files: hrp2sif
Extract TAC of single pixel(s) specified by column, row and plane: epxl2dft
Extract all pixel values, or pixels inside specified ROI(s), in ECAT images: imgpext (replaces extrimg)
Get the maximum pixel value of one or more ECAT files: ecatmax

Retrieving and editing information on Analyze 7.5 files:

Image filtering:

Gaussian smoothing: imgfiltg
Spatial filtering using pixels with similar TACs: imgdysmo
Thresholding sinograms and images: ecatthrs
Image segmentation using Bentourkia's clustering technique: eflexseg
Calculate average and SD of several normalized images: ecatavg

Converting ECAT files to binary flat files and back:

Dumping pixel values to a binary float file: ecat2flo
Constructing an ECAT file from binary (4-byte) float data file: flo2ecat and
converting numerical data in ASCII file into binary float data file: asc2flo
Copying subheader information from one CTI ECAT 6.3 file to another: cpshdrs and e6cphdrs
Converting the data type from and to traditional VAX format: ctivax

Converting between ECAT and DICOM formats

dicom2ecat 2.0.0 beta
ecat2dicom 2.0.0 (not ready, consult Harri Merisaari)