[Gate-users] Voxelized source and phantom in benchImageNavigators

Emilie Gaudin Emilie.Odette.Gaudin at USherbrooke.ca
Mon Mar 2 20:44:02 CET 2020


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.


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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.

On Wed, Feb 26, 2020 at 4:58 PM Emilie Gaudin <Emilie.Odette.Gaudin at usherbrooke.ca<mailto: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.



/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

De : Gate-users <gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>> de la part de Zhengzhi Liu <zliu36 at stanford.edu<mailto:zliu36 at stanford.edu>>
Envoyé : 26 février 2020 18:59
À : gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org> <gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>>; lomahu at gmail.com<mailto:lomahu at gmail.com> <lomahu at gmail.com<mailto:lomahu at gmail.com>>; 강한규 <lovehangulp at naver.com<mailto: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.


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