ROI drawing

Manual delineation of regions-of-interest (ROIs) or volumes-of-interest (VOIs) is a time-consuming and error-prone task with considerable inter- and intra-operator variability. Therefore, we suggest using pre-defined ROI templates with SPM software (consult Jarkko Johansson or brain researchers in TPC). An automated anatomy-based analysis can be performed using standardized ROIs defined on magnetic resonance template image representing brain anatomy in accordance with the Montreal Neurologic Institute (MNI) space database (Nagano et al., 2000; Brück et al., 2005).

However, ROI templates are not suitable for all tracers or study protocols even in the brain studies, and seldom applicable to other organs. Currently ROIs can be drawn on MR and parametric or sum PET images in TPC using:

• Carimas 2.0 beta
• Imadeus on PC/Windows. Images must be in Analyze format. Time-activity curve (TAC) file format is fully supported by other programs in TPC. Imadeus ROI format is not yet supported by all other programs, but Carimas 2.0 can read it, and iit can be converted to other formats (consult Harri Merisaari).
• Vinci on PC/Windows. Images can be in several formats, including ECAT 7.x and Interfile. If TACs are saved in CPT format, they can be converted to our standard DFT format using program cpt2dft. Currently, Vinci can not be used for commercial studies in TPC.
• Xeleris workstation; TAC files calculated in Xeleris can be converted to DFT files using xel2dft.
• Amide: TAC data in *.tsv files can be converted to DFT format: tsv2dft
• YaIT was available on all Solaris workstations, but there are only few left. YaIT ROIs are in the same format as the ancient CTI Imagetool, and this format is supported by all TPC software, and TACs can be calculated using program img2dft.

In addition, ROIs can be drawn using GE Display on GE Advance images, but TACs produced there can not be extracted from the database or used in further calculations, except the ones provided in the Display program.

Working with YaIT/Imagetool ROI files

• Listing ROI file contents: roilist
• Splitting ROI file into parts: roisplit
• Calculating ROI TACs: img2dft in Sun/Solaris and PC/Windows, or img2kbq on Sun/Solaris
• Seeing ROI placement by setting blank the outside areas in images: eroi2img
• Masking high-activity image regions by setting pixel values inside ROIs to zero: eroi2img
• Extracting TACs of separate pixels from dynamic image: roipxl
• Extracting pixel values inside ROI(s): imgpext (replaces extrimg)
• Extracting one image line: lor2dft
• Find out the size of ROIs