PET raw data (sinogram)
Scanners and file formats
ECAT HR+, produces ECAT 7.x format sinogram files (format is defined e.g. in ECAT Software Operating Instructions Version 7.2). Because of this and Imanet co-operation, ECAT 7.x format is supported by most computer programs; if a program does not yet support ECAT 7.x format, please contant the software team.
Currently most analysis programs can also read PET data in CTI ECAT 6.3 format, which is the format of the old PET scanner, ECAT 931. This scanner was put out of operation in the end of April 2005. During a long transitional stage the programs will be able to read both ECAT 6.3 and 7.x formats. Tools for conversion between ECAT formats are already available. ECAT 6.3 format for sinograms, normalization and attenuation files is defined in Siemens manual (Operating Instructions ECAT Scanner Software). To reconstruct the ECAT sinograms (*.scn) to images, also the attenuation (*.atn) and normalization (*.nrm) files are required!
2D raw data from GE Advance is automatically converted to CTI ECAT 6.3 format. 3D raw data from GE Advance can be read from the GE database (please ask Mika Teräs), but this data cannot yet be used by analysis programs. The GE Advance sinograms in ECAT format are already attenuation and normalization corrected, thus separate files for these purposes are not needed.
HRRT produces Interfile format sinograms, which can be converted to ECAT 7 format using if2ecat program (PC/Windows XP) provided by the scanner manufacturer.
PET data may contain patient names!
Note that images and sinograms in ECAT 6.3 or 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 names are first removed; see Patient privacy protection.
Working with raw data:
- Extracting line-of-response: lor2dft
- Making a grey-scale or rainbow color-scale TIFF image file for insertion into PowerPoint etc: ecat2tif
- Simple arithmetic calculation for ECAT sinogram and image files: ecatcalc
- Combining two or more ECAT sinogram or image files: ecatcat
- Turning images or sinograms horizontally and/or vertically: ecatflip
- Produce a "head curve", i.e. an average of all pixels as a function of time: ecathead
- Using a look-up table to replace the pixel values in sinogram or image: ecatlkup
- Sorting matrices in ascending order: ctisort
- Extracting specified planes and frames to a new file: esplit
- Sum together the speficied frames from a dynamic sinogram to emulate static scan: ecatssum
- Correction of the frame times relative to the injection time, when scanning was started later: ecattime
- Setting ECAT sinogram and image frame times: eframe
- Setting ECAT 6.3 sinogram and image frame times and scan start time from SIF: sif2ecat
- Set sinogram values outside specified transaxial FOV to zero: scnfovrm.
- Tools for calculation of scatter fraction: scnmshft and scatterf.
- Editing ECAT 7 main header: e7emhdr and 3D scan subheader: e7eshdr.html
- Removing patient name from ECAT 6.3 and 7 files: ecatanon
- Listing segments and sinograms in 3D scan file: e7lsegm
- Extracting the segment 0 sinograms from a 3D scan file: e7segm0
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
- List the ECAT 6.3 or 7.x matrices: lmlist
- List the ECAT frame times: eframe
- Report the zero (injection) date and time and scan start time in ECAT file: ecattime
- Computation of SIF from dynamic images or sinograms in ECAT format: cti2sif, and specifically from HR+ scan files: hrp2sif
- Extract TAC of bin(s) specified by column, row and plane: epxl2dft
Converting ECAT files to binary flat files and back:
- Dumping bin values to a binary file: ecat2flo
- Constructing an ECAT file from binary (4-byte) float data file: flo2ecat
- 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
