Tools for processing image data
Retrieving information on PET image
- List the image dimensions or pixel sizes: imgdim
- Get the maximum pixel value of one or more PET images: imgmax, or the position of maximum pixel value: imgmaxp
- Checking, setting and conversion of radioactivity concentration units in PET images: imgunit
- Saving profile line from image or sinogram, either from specified location or from peak value: imgprofi
- Make a grey-scale or rainbow color-scale TIFF image file for insertion to PowerPoint etc.: img2tif.
Retrieving and editing information on ECAT files
- List the contents of ECAT 6.3 or 7.x main header: lmhdr; edit ECAT 7.x main header: e7emhdr; edit ECAT 7.x image volume headers: e7evhdr; edit ECAT 6.3 main header: e63emhdr.
- 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: imgdecay.
- 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: eframe, cti2sif, and specifically from HR+ scan files: hrp2sif.
- Copying subheader information between CTI ECAT 6.3 files: cpshdrs and e6cphdrs.
- Set ECAT sinogram and image frame times: eframe.
- Correction of the frame times relative to the injection time, when scanning was started later: ecattime.
- Correction of missing matrices in ECAT 6.3 image: e63mreg tries to remove odd image planes and frames, and add matrices with zero pixel values in place of missing matrices.
- Changing ECAT plane and frame numbers to continuous sequence beginning from 1: efixplnr.
Retrieving and editing information on Analyze 7.5 files:
Retrieving and editing information on NIfTI files:
Extracting or removing part of image
- Delete certain time frames or planes from dynamic or static image: imgdelfr and imgdelpl.
- Extracting smaller volume in PET image to a new file: imgbox or ImageConverter (consult Timo Laitinen).
- Extracting certain planes and frames from ECAT format to a new file: esplit.
- Cut off empty sides to reduce image file size: imgslim versions below 1.0.0 for ECAT images and from version 1.0.0 and above (.NET versions) for microPET image files.
- Cutting the size of PET images by reducing the dimensions: imgshrink.
- Extract TAC of single pixel(s) specified by column, row and plane: pxl2tac.
- Extract all pixel values, or pixels inside specified ROI(s), in ECAT images: imgpext (replaces extrimg); also a new experimental version which supports Carimas VOIs is available from Timo Laitinen.
Converting between image file formats
- ImageConverter (consult Timo Laitinen) can convert between DICOM and other image formats.
- ECAT format to Analyze 7.5: ecat2ana
- ECAT format to NIfTI: ecat2nii
- Conversion between ECAT 6.3 and 7.x formats: e63to7 and e7to63.
- Conversion to and from flat format.
Misc tools:
- Subtract background radioactivity: imgbkg.
- Subtract reference region TAC from dynamic image: imgbound.
- Simple arithmetic calculation for image files: imgcalc.
- 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): imgflip.
- Produce a "head curve", i.e. an average of all pixels as a function of time: imghead.
- Replace the pixel values in sinogram or image using a look-up table: imglkup.
- Sort ECAT 6.3 image matrices in ascending order: ctisort.
- Combine the adjacent ECAT 7.x volume image planes to reduce data size and noise: e7vplavg.
- 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, preferably, image integral over certain time range: imginteg. DICOM images can be summed using program ImageSum.exe (contact Timo Laitinen).
- Calculating an average over time or sum over time from Analyze 7.5 images in Matlab: sum_frame.
- Correction of physical decay and removing of the decay correction: imgdecay.
- Removing patient name from PET images.
- Image filtering.
See also:
- PET image
- PETPACS
- Parametric image
- ROI drawing
- Mask images
- Image file formats in TPC
- Scan Information File (SIF)
- Image anonymization
Tags: Image, Analyze 7.5, ECAT, NIfTI, File format
Updated at: 2020-02-22
Created at: 2005-05-24
Written by: Vesa Oikonen