[Gate-users] Report of GATEv8.2 bugs (PETscanner "level5" is NOT working)

Tue Mar 10 01:34:27 CET 2020

A follow-up question, does PETScanner work with TakeEnergyCentroid policy?

In my simulation using the PETScanner system, everything works fine and it
has been validated to a certain degree. However, soon as I switched to
TakeEnergyCentroid policy, no matter what the readout depth is, the core
dumped. The error message is shown in the screenshot below. According to
the error message, it looks like it was trying to find the system component
"crystal", however, "crystal" is not defined in the PETScanner/scanner as
shown in its hierarchy below.

Basically, what I am trying to achieve is to measure the location of each
crystal center since each crystal is coupled to a single readout
PMT/readout channel in my design. The way I can think of is setting the
readout depth to crystal level and using TakeEnergyCentroid policy,
however, it crashes in the PETScanner system.

Any suggestions? Is PETScanner compatible with akeEnergyCentroid policy? Or
I have messed something up.

Thank you very much for help.

Zhengzhi

On Sat, Mar 7, 2020 at 2:48 PM Zhengzhi Liu <zliu36 at stanford.edu> wrote:

> Dr. Han Gyu,
>
> Thank you for your detailed explanation and for showing us your excellent
> work. You have been a great help to many GATE users (like me) in this
> community.
> Thank you very much and look forward to meeting you in person in future
> conferences.
>
> Sincerely,
> Zhengzhi
>
> On Fri, Mar 6, 2020 at 10:25 PM 강한규 <lovehangulp at naver.com> wrote:
>
>> Dear Zhengzhi and Maxime,
>>
>>
>>
>> Recently, I have been busy so I was not able to answer your questions.
>>
>>
>>
>> I also experienced that the *"level5" is NOT working for "PETscanner" in
>> GATEv6.2*.(slide#3-4)
>>
>> The solution was *to attach the "layer1"* to the 4th layer crystal as
>> Maxime mentioned.
>>
>>
>>
>> Attached is my work about GATEv6.2 simulation for *staggered 4-layer DOI
>> PET scanner*.
>>
>>
>>
>>
>>
>>
>>
>> After GATE simulation and image reconstruction, I obtained the PET image
>> successfully.(slide#5-11)
>>
>> The GATE output and crystal ID information are summarized.(slide#12-18)
>>
>>
>>
>> By the way, if you want more layers, then you can use just
>> "genericRepeater".
>>
>> In doing so you can place the crystal array whatever you like.
>>
>> In this case, you need two system attachments as below.
>>
>> -level1 (for PET block)
>>
>> -level2 (for crystal with genericRepeater)
>>
>>
>>
>> Hopefully, my answer would be helpful for your works.
>>
>>
>>
>> Best regards,
>>
>>
>>
>> Han Gyu
>>
>>
>>
>>
>> --------Han Gyu Kang, Ph.D, Researcher
>>
>> National Institute of Radiological Sciences (NIRS)
>> National Institutes for Quantum and Radiological Science and Technology
>> (QST)
>>  4-9-1 Anagawa, Inage-ku, Chiba 263-8555, JAPAN
>>
>>
>>
>> -----Original Message-----
>> *From:* "Maxime Toussaint"<Maxime.Toussaint at USherbrooke.ca>
>> *To:* "gate-users at lists.opengatecollaboration.org"<
>> gate-users at lists.opengatecollaboration.org>;
>> *Cc:*
>> *Sent:* 2020-03-07 (토) 12:46:38 (GMT+09:00)
>> *Subject:* Re: [Gate-users] Report of GATEv8.2 bugs
>>
>> Greetings,
>>
>> Sorry, I explained myself poorly. level1 to level4 are okay. What I meant
>> was to change level5 to either layer0 or layer1.
>>
>> Bests,
>> Maxime Toussaint
>> ------------------------------
>> *De :* Zhengzhi Liu <zliu36 at stanford.edu>
>> *Envoyé :* 6 mars 2020 22:39
>> *À :* Maxime Toussaint <Maxime.Toussaint at USherbrooke.ca>
>> *Objet :* Re: [Gate-users] Report of GATEv8.2 bugs
>>
>> Hi Maxime,
>>
>> Thank you very much as well. I tried your suggestion of replacing level1
>> to level5 with layer0 to layer4 in PETScaner. It failed at layer2 and does
>> not allow me to add layer2 and later layers. It worked fine with 2layers.
>> Could you please verify this with your code by adding some simple dummy
>> layers to your code?
>> Here is the errormsg:
>> [image: Screenshot from 2020-03-06 19-37-02.png]
>>
>> Thank you very much sincerely.
>>
>> Zhengzhi
>>
>> On Fri, Mar 6, 2020 at 7:04 PM Maxime Toussaint <
>> Maxime.Toussaint at usherbrooke.ca> wrote:
>>
>> Greetings,
>>
>> I quickly looked at the code and I think I found the problem. In short,
>> the documentation is correct for the current version of the Gate code on
>> github but not for Gate 8.2.
>>
>> If we look at [1], we see that a change was made from having
>> PETscanner/scanner system with components called layer0/layer1 to one
>> called level5. That change was committed the 9th of May 2019 while Gate 8.2
>> seems to be a Februray 2019 version of the code.
>>
>> I tried using layer0 (and later layer1) and Gate did not produce any
>> warning nor bug. Note that this does not prove that the resulting system
>> work.
>>
>> Also, "PETscanner" is a valid system definition. I will propose a
>> modification of the table 1.2 to make it more explicit.
>>
>> This situation does highlight a little problem. From my understanding,
>> the current version of the user guide follow the code on github but it is
>> also used for the current stable version of Gate (8.2 at the moment). If I
>> am correct, I would propose that a version of the user guide, extracted at
>> the same time as the official version, be saved separately from the
>> "latest" and a note added saying something like "correction to the user
>> guide are only applied on the latest version". After all, we can't expect
>> anyone to adapt all versions of the user guide each time the user guide is
>> enhanced.
>>
>> Hope that I could help and have a nice day,
>> Maxime Toussaint
>>
>>
>> [1]
>> https://github.com/OpenGATE/Gate/blame/cbe7ffb1c3222b5c1801eb7bc8b703253540e6b1/source/geometry/src/GateScannerSystem.cc
>> <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGate%2Fblame%2Fcbe7ffb1c3222b5c1801eb7bc8b703253540e6b1%2Fsource%2Fgeometry%2Fsrc%2FGateScannerSystem.cc&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7Ca971d6afd43c4d17ddde08d7c24949ce%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637191492338352392&sdata=0tnuCu9tvsChRVm3SDxUCDOJ9SpRttb70TPFsZ5VJaM%3D&reserved=0>
>> ------------------------------
>> *De :* Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
>> de la part de Matthew Strugari <matthew.strugari at dal.ca>
>> *Envoyé :* 6 mars 2020 20:57
>> *À :* Zhengzhi Liu <zliu36 at stanford.edu>; gate-users <
>> gate-users at lists.opengatecollaboration.org>
>> *Objet :* Re: [Gate-users] Report of GATEv8.2 bugs
>>
>>
>> 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
>> <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fopengate.readthedocs.io%2Fen%2Flatest%2Fdefining_a_system_scanner_ct_pet_spect_optical.html%23defining-the-systems&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7Ca971d6afd43c4d17ddde08d7c24949ce%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637191492338352392&sdata=%2BOyRHqqtKsH6tb6OA12YUa9MelxQnO%2B2Od%2FVliHcntM%3D&reserved=0>),
>> 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
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>> <https://can01.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fmailman%2Flistinfo%2Fgate-users&data=02%7C01%7CMaxime.Toussaint%40usherbrooke.ca%7Ca971d6afd43c4d17ddde08d7c24949ce%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637191492338362384&sdata=UfD8AWEjo0llrSZP6b%2FJNn3sNzMRQk2vlbRjtr4F4b4%3D&reserved=0>
>>
>>
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