[Gate-users] 3-D image reconstruction using STIR from GATE Results

[Claude Comtat]

Hi Kris,

indeed, the sinogram looks crazy ! By looking on Guifen's GATE macro, it
looks like he set the azimuthal mashing to 1, when the default for the
HR+ (system 962) is 2. As a result, the number of angular bins is 288
and not 144 (the default for the HR+). I would recommand Guifen to try
its macro again with

/gate/output/ecat7/mashing 2

To answer your question about sinogram visualization, we do not provide
inside gate such a tool. I usually use iv_volumetool from Mérence Sibomana.

All the best,

Claude

Kris wrote:

> Dear Claude
> 
> STIR does know about this offset. 
> 
> However, I think there's is something wrong with the simulation (or on how
> Guifen reads the data). If you look at the screenshot if the sinogram (made
> with STIR), it's completely impossible that this is a sinogram of an
> existing object. So, obviously any image recon will go wrong. In particular,
> if you simulate a point source in the centre of the scanner, the ECAT
> conventions are such that your sinogram should show a straight-line.
> 
> I haven't looked at Guifen's GATE macros to see what he is doing though.
> 
> Do you have any sino display tools in GATE that GUifen could use to check
> how GATE thinks that the sino looks like?
> 
> Kris
> 
> 
>>-----Original Message-----
>>From: gate-users-bounces at lists.healthgrid.org 
>>[mailto:gate-users-bounces at lists.healthgrid.org] On Behalf Of 
>>Claude Comtat
>>Sent: 06 April 2007 08:57
>>To: gate-users at lists.healthgrid.org
>>Subject: Re: [Gate-users] 3-D image reconstruction using STIR 
>>from GATE Results
>>
>>Hi Guifen,
>>
>>I do not know if this helps, but in a ecat7 sinogram, the 
>>center of the sinogram along the radial direction is offset 
>>by the half of the bin size. This is due to the fact that the 
>>number of radial bins is even.
>>For example, if you have 4 radial bins, numbered from 0 to 3, 
>>bin 2 will be at the center. I would imagine that the 
>>reconstruction algorithm should know that (at least, the 
>>ecat7 based reconstruction algorithms).
>>
>>Claude
>>
>>Guifen Lin wrote:
>>
>>
>>>Hi
>>>simulate a point source (x=0,y=0) in the file PET_Ecat.mac.I 
>>>reconstructe the image in two mwthod:
>>>1.Method one
>>><1>.
>>>cd /usr/local/gate/gate_v3.0.0/examples/my_example/PET
>>>source /usr/local/gate/gate_v3.0.0/env_gate.csh
>>>/usr/local/gate/g4work/bin/Linux-g++/Gate PET_Ecat.mac ......
>>>
>>><2>.
>>>[root at localhost ~]# cd /usr/local/gate/STIR/my_test [root at localhost 
>>>my_test]# /usr/local/gate/STIR/bin/ifheaders_for_ecat7
>>>MySinogramFile.S
>>>Attempt all data-sets (Y) or single data-set (N) [Y/N D:Y]:
>>>Data number ? [0,8 D:0]:
>>>WARNING: ECAT7 IO: Bin size from header.x_resolution 
>>
>>(2.2471) does not 
>>
>>>agree with expected value 2.25 for scanner ECAT 962. Using bin size 
>>>from header...
>>>
>>><3>.
>>>[root at localhost my_test]# /usr/local/gate/STIR/bin/display_projdata
>>>MySinogramFile_S_f1g1d0b0.hs
>>> 
>>>The sinogram shows a clear discontinuity in the line and the 
>>>reconstructing image shows  horseshoe shape . A friend said 
>>
>>that this 
>>
>>>horseshoe shape is usually a result of an offset of 1 pixel 
>>
>>along the 
>>
>>>x-axis in the sinogram.this means I need to shift my sinogram by n 
>>>pixels in the +x or -x direction.How I can shift my sinogram by n 
>>>pixels in the +x or -x direction.Do I modify STIR's program?
>>>I'm looking forward to your help.
>>>Thank you in advance!
>>>guifen
>>> 
>>>
>>>
>>
>>--------------------------------------------------------------
>>----------
>>
>>>Mp3疯狂搜-新歌热歌高速下 
>>><http://music.yahoo.com.cn/?source=mail_mailbox_footer>
>>>
>>>
>>>
>>--------------------------------------------------------------
>>----------
>>
>>>_______________________________________________
>>>Gate-users mailing list
>>>Gate-users at lists.healthgrid.org
>>>http://lists.healthgrid.org/mailman/listinfo/gate-users
>>
>>-- 
>>Claude Comtat						
>>Laboratoire d'Imagerie Moléculaire Expérimentale	
>>CEA/DSV/I2BM/SHFJ
>>
>>
>>
>>
>>
>>_______________________________________________
>>Gate-users mailing list
>>Gate-users at lists.healthgrid.org
>>http://lists.healthgrid.org/mailman/listinfo/gate-users
>>
> 
> 
> 
> 

-- 
Claude Comtat						
Laboratoire d'Imagerie Moléculaire Expérimentale	
CEA/DSV/I2BM/SHFJ