<HTML> <HEAD> <TITLE>Re: voxellized phantom attenuation (no) problem</TITLE> </HEAD> <BODY> Ahmet, in your GateMaterials.db file there are several material definitions that contain elements with a fraction of zero, for example:                                                                                                                                                               RibBone: d=1.92 g/cm3 ; n=11         +el: name=Hydrogen  ; f=0.034         +el: name=Carbon    ; f=0.155         +el: name=Nitrogen  ; f=0.042         +el: name=Oxygen    ; f=0.435         +el: name=Sodium    ; f=0.001         +el: name=Magnesium ; f=0.002         +el: name=Phosphor  ; f=0.103         +el: name=Sulfur    ; f=0.003         +el: name=Calcium   ; f=0.225        +el: name=Scandium  ; f=0.0         +el: name=Titanium  ; f=0.0 Try to remove those lines (don’t forget to update the number of elements), e.g.:                                                                                                                                                                 RibBone: d=1.92 g/cm3 ; n=9        +el: name=Hydrogen  ; f=0.034         +el: name=Carbon    ; f=0.155         +el: name=Nitrogen  ; f=0.042         +el: name=Oxygen    ; f=0.435         +el: name=Sodium    ; f=0.001         +el: name=Magnesium ; f=0.002         +el: name=Phosphor  ; f=0.103         +el: name=Sulfur    ; f=0.003         +el: name=Calcium   ; f=0.225 and run your simulation again.  While there is nothing wrong in doing that, I believe that causes a problem to Gate.  If you confirm this, we’ll work to fix that bug. By the way, if you want to collect info from the voxellized phantom and use the “comptonPhantom” field the use the attachVoxelPhantomSD command instead of attachPhantomSD. Richard On 3/4/08 12:17 PM, "Ahmet Ayan" <ahmetsedat.ayan@gmail.com> wrote: <BLOCKQUOTE><TT>Dear Richard, Thank you very much for your reponse. I tried to replicate your numbers. Attached "spherical.mac"  is what I did according to your description. For each run (10^4 emissions), I looked at the number of photons with E>0.139 as Singles->Draw("energy","energy>0.139") For these runs, I did a fresh gate 3.1.1 installation, I did NOT modify any part of GATE code. I used the attached GateMaterials.db. The attenuation range table (att.dat) is like the below example except I changed the material from RibBone to Lung to Water etc. I used the attached mcat.dat for the full MCAT phatom (uncompressed). The voxellized phantom was the one that I sent you earlier (154x102x256).  I also moved the source to (1,1,1) micrometers position. I get the numbers below which I still do not understand much. The numbers that I got for Water and Lung s similar to yours. However MCAT and Ribbone is way off.. No Phantom : 9907/1e4 ~ 99% Water Only   : 795/1e4    ~ 8% Lung Only     : 4895/1e4  ~ 49% Ribbone Only : 7180/1e4  ~ 72% MCAT           : 7936/1e4  ~ 79% Would you please be kind to look at the macro that I am sending to see if I am doing something that is wrong ? This macro should run just fine in your gate installation. Thank you very much for your time and help, Best Regards, Ahmet. att.dat ---------------   2   0  0   Air     false  0  0.0  0.0  0.7   1  20  RibBone true 0.7  0.  0.  1. --------------------- On Mon, Mar 3, 2008 at 8:37 PM, Richard Taschereau <RTaschereau@mednet.ucla.edu> wrote: > >  Hi Ahmet, > >  Here is what I did.  I used standard Gate code (not your stepping action). > I defined a spherical shell detector, large enough to contain the phantom > and I "attached" a phantomSD to the voxel phantom (uncompressed).  I > collected "singles" in a root file and I looked at the distribution of > scattered/unscattered photons using the field "comptonPhantom".  Here's my > results with 5000 photons: > >                                          %unscattered >  All Bone phantom:                   3.1 >  All water phantom:                  7.1 >  MCAT phantom:                       9.0 >  All Lung phantom:                  48.3 > >  These results make sense to me.  I did have one problem though: since the > phantom has an even number of voxels in each direction, the source at > (0,0,0) is at the corner of 8 voxels, and the GEANT4 navigator couldn't > determine in which voxels the particle was.  I moved the source by 1 micron > in each direction.  You may want to try this approach (spherical shell > detector) instead of using GateSteppingAction. > >  Richard >  -- >  Richard Taschereau, Ph.D. >  Crump Institute for Molecular Imaging >  University of California Los Angeles >  700 Westwood Plaza, A222 >  Los Angeles, CA 90095-1770 >  Phone: (310) 825-0697 >  Fax:     (310) 206-8975 >  email: RTaschereau@mednet.ucla.edu > > > ---------------------------------------------------------- > IMPORTANT WARNING: This email (and any attachments) is only intended for the > use of the person or entity to which it is addressed, and may contain > information that is privileged and confidential. You, the recipient, are > obligated to maintain it in a safe, secure and confidential manner. > Unauthorized redisclosure or failure to maintain confidentiality may subject > you to federal and state penalties. If you are not the recipient, please > immediately notify us by return email, and delete this message from your > computer. > ---------------------------------------------------------- > </TT></BLOCKQUOTE><TT> </TT> -- Richard Taschereau, Ph.D. Crump Institute for Molecular Imaging University of California Los Angeles 700 Westwood Plaza, A222 Los Angeles, CA 90095-1770 Phone: (310) 825-0697 Fax:     (310) 206-8975 email: RTaschereau@mednet.ucla.edu ---------------------------------------------------------- IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the recipient, please immediately notify us by return email, and delete this message from your computer. ---------------------------------------------------------- </BODY> </HTML>