[Gate-users] Report of GATEv8.2 bugs

Sat Mar 7 04:33:36 CET 2020

Hi Matthew,

First, thank you very much for your suggestion. I am using Users Guide
V8.0. I learned the system type *PETScanner* from previous gate user group
correspondence which is forwarded below. Actually, PETScanner is a valid
PET system in GATE. Because of the problem of coincidence with other types
of PET system under certain conditions (I will raise this bug later
separately), PETScanner is my only valid option. I have been using
*PETScanner* for quite a while in GATE v8.2. The only problem I have with
PETScanner is that it does not allow me to add any 5th level to the system.
It looks like that level5 is not defined in PETScanner.

As to changing PETScanner to *scanner*, it indeed allows me to add the 5th
layer. However, it does not allow using any coincidence flags.[image:
Screenshot from 2020-03-06 19-16-16.png]
Unfortunately, I am desperate to need coincidence sorter and data.

Dear Dr. Kang,

Sincere I learned this initially from you, I was wondering whether you had
been able to add a 5th level to PETScanner? Could you share your thoughts
on this?
Thank you very much.

Zhengzhi

Forwarded message:

On Mon, Jan 27, 2020 at 8:27 PM 강한규 <lovehangulp at naver.com> wrote:

> Dear Zhengzhi, and Christian,
>
>
>
> As you already know, Christian (pommranz at astro.uni-tuebingen.de) shared
> the git patch file to solve the coincidence output issue.
>
>
> http://lists.opengatecollaboration.org/pipermail/gate-users/2019-February/010729.html
>
>
>
> I have also *succeeded *in acquiring coincidence output using *generic
> repeater* in* PETscanner *system with the patch file shared by Christian.
>
> Below is an example of the detector arrangement with genericRepeater.
>
> Thanks Christian for your great contribution~!
>
>
>
>
>
> Here is a brief manual how to apply the git patch in GATEv8.2.
>
>
> ===========================================================================================================================
> *Problem*: *No coincidence* in the "*PETscanner*" when *genericRepeater *was
> used.
> *Solution*: *Modify the GATEv8.2 source code* using a *git patch file*
>  and *re-compile*.
>
> GATE mailing list (Christian Pommranz <pommranz at astro.uni-tuebingen.de>)
>
> http://lists.opengatecollaboration.org/pipermail/gate-users/2019-February/010729.html
>
> *STEP1*> Download the git patch file in the mailing list.
> Filename: *coincidences_for_generic_repeater.patch*
>
> *STEP2*> Apply the git patch file.
> >cd /home/kanghg2/program/Gate-8.2
> >git apply --ignore-space-change --ignore-whitespace
> coincidences_for_generic_repeater.patch
>
> *STEP3*> Re-compile GATEv8.2
> >cd /home/kanghg2/program/Gate-8.2-build
> >ccmake ../Gate-8.2
> [c] configure
> [g] generate
>
> >make
>
> *STEP4*> Run the GATE PETscanner with genericRepeater.
> *Now coincidence output will be generated!*
>
>
> ===========================================================================================================================
>
>
>
> Hopefully, you will be able to obtain coincidence output with
> genericRepeater.
>
>
> Best regards,
>
>
>
> Han Gyu Kang, Ph.D.
>
>
>
> Imaging Physics Group, NIRS-QST, Japan.
>

On Fri, Mar 6, 2020 at 5:57 PM Matthew Strugari <matthew.strugari at dal.ca>
wrote:

> Hi Zhengzhi,
>
>
>
> According to the user manual (Section 1.5.1
> https://opengate.readthedocs.io/en/latest/defining_a_system_scanner_ct_pet_spect_optical.html#defining-the-systems),
> the system name must be one of those available in Table 1.1. In the image
> you provided, this would be Table 4.1. I’m not sure which version of the
> user manual you are referring to, but the most up to date information can
> be found on readthedocs. Nonetheless, your error of COMMAND NOT FOUND shows
> that you defined the system name to be PETscanner which is not a valid
> system name. Replace “PETscanner” with “scanner” and you should be able to
> assign level5 with the defined functionality.
>
>
>
> Regards,
>
> Matthew
>
>
>
> *From: *Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
> on behalf of Zhengzhi Liu <zliu36 at stanford.edu>
> *Date: *Friday, March 6, 2020 at 7:30 PM
> *To: *gate-users <gate-users at lists.opengatecollaboration.org>
> *Subject: *Re: [Gate-users] Report of GATEv8.2 bugs
>
>
>
> According to the user manual, 5 levels can be attached. However, I am not
> able to attach any 5th level. Please share your thoughts if you have some
> experience.  Thanks a lot.
>
>
>
>
>
>
>
> On Fri, Mar 6, 2020 at 3:17 PM Zhengzhi Liu <zliu36 at stanford.edu> wrote:
>
> Report of a potential bug:
>
>
>
> It looks PETScanner only allows 4 layers to be attached, whenever I tried
> to attach the 5th layer (no matter what the geometry is), it throws the
> errormsg.  Has anyone been able to attach a 5 level to PETScanner?  My
> understanding is Gate doesn't recognize the keyword *level5*.
>
>
>
> Thanks for reading.
>
>
>
> Sincere greetings,
>
> Zhengzhi
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200306/2b81e7a4/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 110290 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200306/2b81e7a4/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.png
Type: image/png
Size: 75696 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200306/2b81e7a4/attachment-0005.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screenshot from 2020-03-06 19-16-16.png
Type: image/png
Size: 34488 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200306/2b81e7a4/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: 1580185151205.png
Type: image/png
Size: 52132 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20200306/2b81e7a4/attachment-0007.png>