USER'S GUIDE TO 3-D PET SIMULATION SYSTEM Introduction PET images are reconstructed from measured projection data of positron source distributions. This simulation system can generate realistic projection data from computer-simulated objects, normally the segmented MRI data. Projection data are reconstructed by the filtered backprojection algorithm to obtain simulated PET images. Image protocols scan_type = 1 MR, FDG or CBF imaging, fuzzy phantom scan_type = 2 FDG or CBF imaging, clear phantom scan_type = 3 Transmission imaging, clear phantom scan_type = 4 F-DOPA Imaging, clear phantom scan_type = 5 Transmission imaging, fuzzy phantom scan_type = 6 F-DOPA with caudate shrinkage scan_type = 7 blank scan with a rod source scan_type = 8 transmission scan with a rod source Program name petsimu Synopsis petsimu <studyname> <scantype> [<options>] > ! logfile & Description petsimu is a script to control the PET simulation system. It sends info about the parameters/progress of the simulation to stdout. This is usually redirected to a logfile with a patient specific name for record. Its I/O file structures are as follows: Input infile ! 3-D organ model images tacfile ! object creation parameter parfile ! projection simulation parameter recfile ! image reconstruction paramter Output studyname.att ! attenuation lengths (cm) studyname.att_hd ! header file studyname.bla ! blank projection data (counts) studyname.bla_hd ! header file studyname.tra ! transmission data (counts) studyname.tra_hd ! header file studyname.dat ! emission data (counts) studyname.dat_hd ! header file studyname_FBP_itm.mnc ! transmission image (1/cm) studyname_FBP_ima.mnc ! emission image (nCi/cc) studyname_t_e1.mnc ! axial weighted image studyname_tr_e1.mnc ! true tra image studyname_e_e1.mnc ! axial weighted image studyname_pet_e1.mnc ! true emi image studyname_voi_e1.mnc ! resampled tissue maps Infile is usually the segmented MRI data registered with real PET images. It is in the form of studyname_string.mnc with a patient or subject name and any user-specified string. A typical filename is miche_seg_e1.mnc. MRI model contains gray matter, white matter, CSF,ventricle,tumor, skull bone and a set of functional anatomical structures. They are obtained using mincclassify/msp and roi programs at the BIC with the following coding convention: GM WM CSF VEN MS BRN BKG BON LCN RCN LPU RPU ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 0 1 2 3 4 5 6 8 21 22 23 24 Each code identifies a tissue type or structure. MS and BRN are for internal tissue types other than GM, WM, CSF and VEN. BON refers to skull bone and BKG everything else. LCN, RCN, LPU and RPU are for left and right caudate nucleus and putamen in the basel ganglia. Of course they can be used to represent any structures as long as user knows what they are. Table 1: Tissue attenuation coefficients for 511 Kev photons Tissues Electron Density (1/cm3) Att (1/cm) Ratio -------------------------------------------------------------- Air 3.622E+20 0.00010 0.001 Blood 3.513E+23 0.10066 1.051 Bone 5.267E+23 0.15092 1.575 Brain 3.438E+23 0.09851 1.028 BrainStem 3.500E+23 0.10029 1.047 Cerebellum 3.428E+23 0.09823 1.025 Cerebrum 3.433E+23 0.09837 1.027 CSF 3.420E+23 0.09800 1.023 Fat 3.061E+23 0.08771 0.916 Hair 4.202E+23 0.12040 1.257 Heart 3.415E+23 0.09785 1.021 Lucite 3.833E+23 0.10983 1.146 Lung 8.607E+22 0.02466 0.257 Muscle 3.445E+23 0.09871 1.030 Polystyrene 3.380E+23 0.09685 1.011 Skin 3.639E+23 0.10427 1.088 Water 3.343E+23 0.09579 1.000 -------------------------------------------------------------- Usage User begins a simulation session by editing I/O information in the script petsimu. Copy parameter files tacfile, parfile, recfile from /usr/people/may/demo and edit them according to the header info therein and specific applications. User should first run att scan to get attenuation data for emission simulation. This step is done once for each study. Later emission protocols for the same subject can use the same att data to model photon attenuation effect.