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

Wed Mar 11 18:07:31 CET 2020

I have achieved my goal by averaging the location of hits in each crystal.
But just wondering if there is a deterministic way to get the spatial
position of crystals.

On Wed, Mar 11, 2020 at 9:03 AM Zhengzhi Liu <zliu36 at stanford.edu> wrote:

> Hi Maxime,
>
> Thanks for reading my email and looking into it. Thanks for confirming the
> legitimacy of my doubt. I wish it would allow users to
> use TakeEnergyCentroid.
>
> Please allow me to rephrase my sentences as follows:
> In my system, each crystal is coupled to a single readout channel. In
> order to align my simulated system with my real system, I wanted to
> register the center of each crystal in Gate then to compare it with that of
> my real system, for which I have already got the data.  The way I can think
> of to achieve the measurement of crystal center location in Gate is by
> using TakeEnergyCentroid and setting readout depth to crystal level.
>
> To be short, Yes, I want the spatial position of my crystals.
>
>
> Thanks for your time and wisdom.
>
> Warmest regards,
> Zhengzhi
>
>
>
> On Wed, Mar 11, 2020 at 8:43 AM Maxime Toussaint <
> Maxime.Toussaint at usherbrooke.ca> wrote:
>
>> Greetings,
>>
>> The documentation claim that this policy is applied relative to a
>> "crystal" component. Since PetScanner configuration do not possess that
>> component, it make sense that it will not work. When in doupt, the code
>> can't(Most of the time) lie. In [1], you can see that the "crystal"
>> component is required. I have no idea why, however.
>>
>> Also, i am not sure I understand the following: "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." You want to know the spatial position of your crystals?
>>
>> Have a nice day,
>> Maxime Toussaint
>>
>>
>> [1]
>> https://github.com/OpenGATE/Gate/blob/f2d9a5e19d568c71fe11b64a05d4f6037a208841/source/digits_hits/src/GateReadout.cc
>>
>> ------------------------------
>> *De :* Zhengzhi Liu <zliu36 at stanford.edu>
>> *Envoyé :* 9 mars 2020 20:34
>> *À :* 강한규 <lovehangulp at naver.com>; Maxime Toussaint
>> <Maxime.Toussaint at USherbrooke.ca>
>> *Cc :* gate-users <gate-users at lists.opengatecollaboration.org>
>> *Objet :* Re: [Gate-users] Report of GATEv8.2 bugs (PETscanner "level5"
>> is NOT working)
>>
>> 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%7C7c194e0ad8b8458980d208d7c48ae8d6%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637193973212126017&sdata=L%2B6wmzXNj%2BY5CEAxtwyT9T5QLqOgteVaFv3O%2FhIfdcA%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%7C7c194e0ad8b8458980d208d7c48ae8d6%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637193973212126017&sdata=pKVc7m0txcRWujIUCIAbhUzqmwyonTNuM9ToKD7MbFo%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
>>
>> _______________________________________________
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>>
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>
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