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

Wed Mar 11 17:03:26 CET 2020

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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