[Gate-users] Voxelized source and phantom in benchImageNavigators

Zhengzhi Liu zliu36 at stanford.edu
Mon Mar 2 20:40:12 CET 2020

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
(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> 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%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.
> Sincerely,
> Zhengzhi
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