[gate-users] Gate LMF-Sinogram (ECAT7) patch

[null99 at mails.tsinghua.edu.cn]

Dear Schmidtlein,

I have the code. Thank you! :-) It looks so beautiful and well writen.

The LMF to sinogram conversion isn't diffcult itself (as Kris said), however,
confusing. It is quiet easy to see that if CPS like ring, detector number used, a
cylinder output can be binned into sinogram during the simulation. But this will
not consitent with the original intention of LMF. The LMF file researves all the
information necessaried for the best possible resolution, both spatial and
temporal, by keep all event, and so gives great flexiable on how to build the
sinogram (eg. a user defined time window and energy window can be defined.)

Thus, a key problem rises when we define logical rings and detector numbers: when
to build the sinogram, before or after the formation of LMF file. Before means
when every coicidence event got, we use its (rsect, module, sub module, crystal)
number and hence produce sinogram together with LMF output, That's the exact
reason why I mentioned to use GateSinogram in the request for help. While "after",
just like what I mentioned before, purly a conversion process. The "before" method
seems not very good, but it is feasible since we are simulating, in my option. The
"after" method is the standard way in ClearPET project, as described in the lmf
document (Please refer to Fig 1 in LMF.pdf, pg. 2, in lmfv1.0/document/).

In a word, there are three choice in my option:
1. "Before" method, that is why I said "found no reason not to" in the help
request. It is feasible, useful, but inconsistent with LMF intention.
2. "After" method in GATE, consistent with LMF and capable of generating
multi-sinogram output.
3. Stand alone conversion module, out of GATE, one kind of "after" method.

If the root output also contains all events, it is the same as lmf, then this
conversion is of "after" method. If not, it is one kind of the "before" method.

In the GATE patch, the 2, "after" method is implemented with a ability to extract
sinogram from LMF with several user defined parameters, though not finished yet.

About the "before" method, now, I have something unsure: although we can build
different sinogram with different parameters, the random data set is not the same
(By run Gate on the same .mac, with corresponding parameters modification, several
time). And if we make the all random data the same (we shouldn't), there is little
necessarinity to generating them multi-time.

Your option is highly appreciated! :-)

Regards,

Long



In your mail:
>From: "Schmidtlein, Ross/Medical Physics" <schmidtr at mskcc.org>
>Reply-To: GATE feedback and helpline for Users <gate-users at lphe1pet1.epfl.ch>
>To: null99 at mails.tsinghua.edu.cn,
  "GATE feedback and helpline for Users" <gate-users at lphe1pet1.epfl.ch>
>Subject: RE: [gate-users] Gate LMF-Sinogram (ECAT7) patch
>
>Hi Long,
>
>I've attached a root program that reads the coincidence branch
>information and uses the detector ID numbers to give a pair of crystal
>numbers and a ring numbers for each coincidence event.  The program then
>bins these positions into a block matrix of sinograms.  I think that
>this approach has some advantages over using the xyz's as it handles
>non-uniform angle conversions.  From Chris' email it sounds like it is
>probably quite similar to what the STIR conversions do.  If I understand
>the discussions so far, it sounds like Chris's conversions are clean and
>well tested but require crystal and ring numbers that Gate doesn't
>readily supply.  The root program I've attached I'm sure is not as clean
>and well tested as the STIR code but it does have a translation from
>rsector, module, submodule, and crystal ID's to crystal and ring #'s.
>Maybe a combination of these two pieces of code will do the trick.
>
>Cheers,
>
>ross
>
>-----Original Message-----
>From: gate-users-bounces at lphe1pet1.epfl.ch
>[mailto:gate-users-bounces at lphe1pet1.epfl.ch] On Behalf Of
>null99 at mails.tsinghua.edu.cn
>Sent: Friday, August 13, 2004 11:48 PM
>To: gate-users at lphe1pet1.epfl.ch
>Subject: RE: [gate-users] Gate LMF-Sinogram (ECAT7) patch
>
>
>Dear Schmidtlein,
>
>Sorry for a null email, for a misoperation. :-(
>
>Thank you for your interesting in this patch, and esp. your question and
>your code. :-) I am really eager to see your code. Thank you! :-) The
>patch uses uniform spaceing when building sinogram, but with no
>weighting. It simply binning the events into unifromly spaced logical
>detector ID by their position (x,y,z). (In my understanding, the (x,y,z)
>position is of the detector ID uniquely specified by the Cylindrical
>system's rsector, module, submodule, crystal ID, so weighting is a
>must). I have had a glance at STIR's List data mode classes, it do the
>similar work, but the list data is based on ECAT system and they have
>(ring,detector) in nature. However, because of the similarity between
>ECAT and Cylindrical systems, each logical (ring, detector ID) can have
>a one-to-one relationship with a crystal in physical world by applying a
>uniform angle conversion.
>
>That's what implymented in the patch. Thank you! :-)
>
>Regards,
>
>Long
>
>
>
>In your mail:
>>From: "Schmidtlein, Ross/Medical Physics" <schmidtr at mskcc.org>
>>Reply-To: GATE feedback and helpline for Users 
>><gate-users at lphe1pet1.epfl.ch>
>>To: null99 at mails.tsinghua.edu.cn,
>  "GATE feedback and helpline for Users" <gate-users at lphe1pet1.epfl.ch>
>>Subject: RE: [gate-users] Gate LMF-Sinogram (ECAT7) patch
>>
>>Hi Long,
>> 
>> I've been listening to the discussions surrounding your implementation
>
>> of sinogram output for cylindrical PET, and I am very interested in 
>> seeing you produce these additions.  It is my impression that you're 
>> using Claude's coincidence position binning strategy.  This strategy 
>> works very well for uniformly spaced detectors, but if the detectors 
>> are not uniformly spaced, the sinograms may be incorrect.  Non-uniform
>
>> detector spacing is one of the advantages that the "Cylindrical PET" 
>> system has over the "ECAT System".  The logical volume ID's can be 
>> used to avoid this problem.  I have some code that is fairly general 
>> that does this.  I'd be more than happy to send it if you think it 
>> will help.
>> 
>> 
>> I've glanced through your code and it looks like you have done a 
>> really nice job. ;)
>> 
>> Cheers,
>> 
>> ross
>> 
>> null99 at mails.tsinghua.edu.cn
>>Sent: Friday, August 13, 2004 12:09 PM
>>To: gate-users at lphe1pet1.epfl.ch
>>Subject: [gate-users] Gate LMF-Sinogram (ECAT7) patch
>>
>>
>>Dear all,
>>
>>This is the LMF to ECAT7 patch for Gate. Please refer to my previouse 
>>E-mail for details.
>>
>>Something important:
>>This version is an test version. It's aim is to provide a base for 
>>other possible conversion. E.g. by using the root output. Also, I 
>>looking forwards any questions, bug reports, or new idea of implement 
>>the conversion. Questiones on conversion theory is esp. highly 
>>appreciated! Thank you!
>>
>>USAGE:
>>1. patch it and recompile it.
>>2. Run Gate on a existing Cylindrical PET system macro file (without 
>>any
>>modification)
>>
>>It will generate all kinds of output by default: ecat7 file, interfile 
>>head, lmf file, lmf file header, and coincidence file.
>>
>>Because I am not sure that if my design philosophy valide (By 
>>introducing logical rings and detector number for Cylindrical System, 
>>which is, actually, very similiar to that of a ecat system). So the UI 
>>command is not well supported at present. They might work, I haven't 
>>test it yet.
>>
>>Thank you!
>>
>>Regards,
>>
>>Long
>>
>>
>>
>> 
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