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             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.





may@pet.mni.mcgill.ca