[Gate-users] Voxelized source and phantom in benchImageNavigators

Emilie Gaudin Emilie.Odette.Gaudin at USherbrooke.ca
Thu Feb 27 01:58:40 CET 2020

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> 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%7C5a0fdfecb92f41327dee08d7bb181412%7C3a5a8744593545f99423b32c3a5de082%7C0%7C0%7C637183584400280037&sdata=EWD5fXak7Z6BJEkq10UUv3BD%2F4r6eNyw3caHQrS9C7w%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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