<HTML> <HEAD> <TITLE>Re: [Gate-users] voxellized phantom attenuation problem</TITLE> </HEAD> <BODY> Ahmet, I would need the rest of your script (geometry, physics, etc) to try to find out what is going on. Richard On 2/28/08 11:28 AM, "Ahmet Ayan" <ahmetsedat.ayan@gmail.com> wrote: <BLOCKQUOTE><TT>Dear Richard,  I think the attachments  of the e-mail I had sent to you earlier did  not make  it through out server.  Here it is below/attached again,  Ahmet.  ------------------------------  Dear Richard,  Attached are the phantom (154x102x256) tc_bkgd_atn_1.bin.short.trunc,  gray scale attenuation to material table tc_bkgd_atn_1.AtnRange.dat.ori,  phantom load macro tc_bkgd_atn_1.PHANTOM.mac,  and interfile header info file tc_bkgd_atn_1.h33.  The way I record the photons making out of the torso is the following:  At this stage I do not use any collimator/crystal etc to detect photons.  I put a cylindrical envelope around the mcat torso. The envelope is ultra thin  (~10^-11mm) and vacuum. I modified the GateSteppingAction.cc such that when a  track steps through this envelope, it records all of this track's information  into a root ntuple.  As mentioned in my earlier mail, when the mcat is made of only one material, I  get a number of un-scattered photons (140keV) that makes sense.  (for Lung material only mcat torso, ~46% un-scattered photons)  The source is a point source at the center (0,0,0).  When I make mcat with Lung and Adipose as shown below , I get ~80% un-scattered  photons. (Lung is the least dense of all, besides air which outside of torso  anyway).  ---------   3   0  0  Air       false  0  0.0  0.0  0.7   1  4  Lung      true 0.7  0.7  0.7  0.8   5  20 Adipose   true 0.7  0.7  0.7  0.8  ---------  I also tried parameterizedBoxMatrix instead of compressedMatrix. The numbers did  not change (same problem).  I hope this information helps to figure out what might be  going on (or What I might be doing wrong) ...  Thanks much for your time,  ahmet.  Quoting Richard Taschereau <RTaschereau@mednet.ucla.edu>:  > Hi Ahmet,  >  > Could you send your script file and your phantom please ? I’ll try to  > reproduce the problem.  >  > (Sebastien what is that patch in 3.1.2 ?)  >  > Richard  >  >  > On 2/27/08 3:38 PM, "ayanas@mail.med.upenn.edu" <ayanas@mail.med.upenn.edu>  > wrote:  >  > >  > > Dear Gate'rs  > >  > > I am observing a problem with a voxelized phantom (using compressed voxel)  > > with gate-3.1.1.  > > Here is what happens:  > > I load a voxellized MCAT phantom as the attenuating medium.  > > The source is a simple point source at the center of the phantom.  > >  > > I am recording the un-scattered photons (140 keV) making out  > > of the MCAT torso.  > >  > > Obervations:  > > 1) When I make the material definitions of the all voxels as "Bone",  > > (a uniform material made of bone) I get a sensible number of photons  > > un-scattered. This is fine..  > >  > > 2) When I make the material definitions of the all voxels as, "Lung"  > > I, again,  get a sensible number of photons un-scattered. This is also  > fine..  > >  > > 3) However, When I make the original MCAT definition, that is with  > > Body (muscle),  Lung, Bone etc, I get a number of  > > un-scattered photons much higher than the "All Bone" case  > > making out of the MCAT torso;  > > while I would expect to get a number between "All Bone" and "All Lung"  > case,  > > (the densest material is the Bone, and the least dense is Lung).  > >  > > Has anybody observed such a behaviour?  > > Any ideas/suggestions as to what my problem might be?  > >  > > I also saw a patch for gate 3.1.2 (patch_v3.1.2.tar.bin) with a mention  > > to "compressed voxel capabilities". Does (Should) this patch apply  > > also to gate 3.1.1 ?  > >  > > Thank you very much,  > > ahmet.  >  >  > --  > 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.  > ----------------------------------------------------------  >  >  --  Ahmet Sedat Ayan, Ph.D  Department of Radiology  University of Pennsylvania  Philadelphia, PA 19104  Voice      : (++ 1 215) 349-5751 (W) (GMT-5) </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>