[Gate-users] Voxelized source and phantom in benchImageNavigators

Mon Mar 2 21:29:55 CET 2020

Thanks, Emilie for pointing out the exact problem. There is a problem with
the header file brain_phantom.h33. I don't know whether I have corrupted
the file or it came corrupted. I bypassed it by using amide to
read brain_phantom.i33 and setting its dimension, then export the data as
interfile. Now everything works fine.

Thanks a lot for the help.

On Mon, Mar 2, 2020 at 12:10 PM Zhengzhi Liu <zliu36 at stanford.edu> wrote:

> Thanks, Emilie for your quick reply.
> I am using amide as the viewer. I also doubted the correctness of header
> file brain_phantom.h33 (especially the dimensions). But all these files
> cames with the installation of GATE v8. Meanwhile, brain_phantom.h33 is a
> binary file, I don't know how to convert it into ASCII file to read its
> content inside. Could you please give me any further help? Have you got the
> example work with its own data?
>
> Thanks a lot
> Zhengzhi
>
>
> On Mon, Mar 2, 2020 at 11:44 AM Emilie Gaudin <
> Emilie.Odette.Gaudin at usherbrooke.ca> wrote:
>
>> Hi,
>>
>> Seems you have a problem in the header of your image not in your GATE
>> code.
>> Either the path or the format is wrong
>>
>> Try to debug this first with an image reader application such as imageJ
>> or amide.
>>
>> Emilie
>>
>> Get Outlook for Android <https://aka.ms/ghei36>
>>
>> ------------------------------
>> *From:* Zhengzhi Liu <zliu36 at stanford.edu>
>> *Sent:* Monday, March 2, 2020 2:40:12 PM
>> *To:* Emilie Gaudin <Emilie.Odette.Gaudin at USherbrooke.ca>
>> *Cc:* gate-users at lists.opengatecollaboration.org <
>> gate-users at lists.opengatecollaboration.org>
>> *Subject:* Re: Voxelized source and phantom in benchImageNavigators
>>
>> Dear Emilie,
>>
>> Thank you very much for your help. You are right that *interfileReader*
>> is deprecated now, and using *imageReader* would partially solve
>> the problem in the example
>> <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGate%2Ftree%2Fdevelop%2Fbenchmarks%2FbenchImageNavigators%2Fpet&data=02%7C01%7CEmilie.Odette.Gaudin%40usherbrooke.ca%7C68d48b2e48cc41b1c4cc08d7bee19fe7%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637187748578955552&sdata=ujIvdsBZkOnPYFUlI7uec1hnn8aW1X0nw2czwNjnipM%3D&reserved=0>
>> (Gate/benchmarks/benchImagenvators/pet). However, even after switching to
>> imageReader, I still couldn't get the example work. It failed opening
>> brain_phantom.i33 for reading. Could you please have a look at the attached
>> voxlizedSource.mac and error message to locate my mistake?
>>
>> However, when I used brain_phantom.hmd in the voxlizedSource.mac, then
>> everything worked fine. I attached a 3D rending of the brain_phantom.i33,
>> it does not look like a brain phantom source, does it?
>>
>> Greatly appreciate your help.
>> Sincerely,
>> Zhengzhi
>>
>> On Wed, Feb 26, 2020 at 4:58 PM Emilie Gaudin <
>> Emilie.Odette.Gaudin at usherbrooke.ca> wrote:
>>
>> Dear Zhengzhi ,
>>
>> You are right saying the documentation about voxelized phantom is
>> deprecated, especially for image insertion.
>> Here is some working code for a typical phantom. Be careful of the path
>> in your code and in your image header and everything should be fine.
>>
>> However, I cannot answer for the visu.
>>
>> Cheers,
>>
>> Emilie
>>
>>
>> /gate/source/addSource voxel voxel
>> /gate/source/voxel/reader/insert image
>>
>> /gate/source/voxel/imageReader/translator/insert range
>> /gate/source/voxel/imageReader/rangeTranslator/readTable
>> {path-to-activity-dat-from-this-mac}
>> /gate/source/voxel/imageReader/rangeTranslator/describe 1
>>
>> # The default position of the voxellized source is in the 1^{st}
>> # quarter. So the voxellized source has to be shifted over half its
>> # dimension (dimension = dimImgXYZ * dimVoxXYZ)in the negative direction
>> on each axis
>> /gate/source/voxel/setPosition -90 -90 -90 mm
>> /gate/source/voxel/imageReader/readFile {path-to-header-from-this-mac}
>>
>> /gate/source/voxel/gps/particle e+
>> /gate/source/voxel/gps/energytype Fluor18
>> /gate/source/voxel/setForcedUnstableFlag true
>> /gate/source/voxel/setForcedHalfLife 6586.2 s
>> /gate/source/voxel/gps/angtype iso
>> /gate/source/voxel/dump 1
>> /gate/source/list
>>
>>
>> ------------------------------
>> *De :* Gate-users <gate-users-bounces at lists.opengatecollaboration.org>
>> de la part de Zhengzhi Liu <zliu36 at stanford.edu>
>> *Envoyé :* 26 février 2020 18:59
>> *À :* gate-users at lists.opengatecollaboration.org <
>> gate-users at lists.opengatecollaboration.org>; lomahu at gmail.com <
>> lomahu at gmail.com>; 강한규 <lovehangulp at naver.com>
>> *Objet :* [Gate-users] Voxelized source and phantom in
>> benchImageNavigators
>>
>> Dear Han Gyu, Howard, and Gate users,
>>
>> (I noticed from the previous emails that you two are using voxelized
>> source and phantom, thus I send this email to you. )
>>
>> I tried to import voxelized source and phantom in PET GATE simulation by
>> following the benchImageNavigators
>> <https://can01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGate%2Ftree%2Fdevelop%2Fbenchmarks%2FbenchImageNavigators%2Fpet&data=02%7C01%7CEmilie.Odette.Gaudin%40usherbrooke.ca%7C68d48b2e48cc41b1c4cc08d7bee19fe7%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637187748578965547&sdata=zKu09jeaeGNaE230HanKyYi1nh92EMc3QVUnY1uUSZY%3D&reserved=0>
>> example provided in GATE 8.2 package. However, I can't even get example
>> code work. I have two problems with the example code:
>>
>>    1. Visualization issue:  the qt viewer would automatically close and
>>    leaves me no time to visually check the voxelized source or voxelized
>>    phantom;
>>    2. Running issue: the example can't run and keep throwing the warning
>>    message as shown in the attached screenshot, and no actual output is
>>    generated but an empty root file.
>>
>> I believe importing PET/CT image has become very mature in GATE
>> simulation. Could anyone give any help with running this example code?
>>
>> I am very appreciative of your help.
>> Sincerely,
>>
>> Zhengzhi
>>
>>
>>
>>
>>
>>
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