[Gate-users] implementing MOBY into GATE

Parisa Khateri parisa.khateri at cern.ch
Mon Feb 11 13:25:49 CET 2019

Dear Iván,

Thank you very much for breaking it down into steps. It was very helpful.

I tried my first simulation with the attenuation image as my phantom and placed a point source in the rat body. I resized the image to have very large voxels to accelerate the simulation. It seems to work.

Then I used the activity image (with the same size of the attenuation image) as the source.. again it seems to work. I have to check with smaller voxel size and higher activity for final check.

Thanks again and best regards,


From: Gate-users [gate-users-bounces at lists.opengatecollaboration.org] on behalf of Límbano Iván López Coello [vancoello at gmail.com]
Sent: 06 February 2019 22:20
To: Parisa Khateri
Cc: gate-users at lists.opengatecollaboration.org
Subject: Re: [Gate-users] implementing MOBY into GATE

Hello Parisa

Sure, I will comment my experience:

After generate the MOBY/ROBY Phantom you have to go to the logfile (it is created at the same time that the phantom) to see which attenuation values you have for each tissue an example is below (look for the Linear Attenuation Coefficients):
These values will be useful later for the segmentation and to define sources and detectors, when you create a phantom with the MOBY application, it will generate 3 files, an attenuation image, an activity image and the log file, I used the attenuation image for the simulations.
this attenuation image will be in .bin format, I changed the extension file from .bin to .raw  once you have done this, create a header, an example of my header is presented below:

ObjectType = Image
NDims = 3
DimSize = 256 256 739

ElementType = MET_FLOAT

ElementSpacing = 0.145 0.145 0.145

ElementByteOrderMSB = False
DataFile = MOBY.raw

you can create in a txt file, and when you complete it with the information you need, save it as .mhd extension

until now you will have:

MOBY.raw (attenuation image)
MOBY.mhd ( Meta Image Header)
Attenuation Linear coefficients for the ROI that you want to simulate.

for GATE you can create a macro to confirm if the phantom was imported correctly then use that macro to import disabling the visualization because consumes  a lot of computing resources please see my example below:


/gate/geometry/setMaterialDatabase ../data/GateMaterials.db

/vis/open OGLI

/vis/scene/add/axes 0 0 0 500 mm


/gate/world/geometry/setXLength 50 cm

/gate/world/geometry/setYLength 50 cm

/gate/world/geometry/setZLength 50 cm

/gate/world/setMaterial Air

/gate/world/vis/setVisible 1


# Voxel phantom

/gate/world/daughters/name      mouse
/gate/world/daughters/insert       ImageRegularParametrisedVolume

/gate/mouse/geometry/setRangeToMaterialFile     ../data/Range_MOBY.txt

/gate/mouse/geometry/setImage                   ../data/MOBY.mhd

/gate/mouse/setSkipEqualMaterials 0


the file Range_MOBY was created using the Linear attenuation coefficients as shown below:

19  #number of the structures(tissues)

0       57.5345 Air  ( every tissue is defined in a range of linear attenuation values that you found in the logfile of MOBY)

16.6851 16.6853 Lung

33.3449 33.3451 Adipose

55.1011 55.1013 Pancreas

55.7452 55.7454 Brain

56.5967 56.5969 Intestine

56.6229 56.6231 Muscle

56.7398 56.7400 Heart

56.9961 56.9963 Kidney

57.2666 57.2668 Liver

58.2013 58.2015 Spleen

58.4943 58.4945 Blood

59.1105 59.1107 Body

59.1771 59.1773 Lymph

60.3382 60.3384 Cartilage

65.4576 65.4578 SpineBone

71.8001 71.8003 Skull

82.1753 82.1755 RibBone

doing these steps you will import and see your phantom in the GATE enviroment like this:

Then for the simulation you have to define positioning, source, detectors, etc.

let me know if you need more information.

El mié., 6 feb. 2019 a las 12:06, Parisa Khateri (<parisa.khateri at cern.ch<mailto:parisa.khateri at cern.ch>>) escribió:
Hi Iván,

I was wondering if you could solve this issue. If so, I would really appreciate if you could share your experience with me. I am totally new to Gate voxelized simulation and need some help to import MOBY/ROBY outputs into gate and run a voxelized simulation.

Thank you in advance and kind regards,


From: Gate-users [gate-users-bounces at lists.opengatecollaboration.org<mailto:gate-users-bounces at lists.opengatecollaboration.org>] on behalf of Límbano Iván López Coello [vancoello at gmail.com<mailto:vancoello at gmail.com>]
Sent: 24 October 2017 04:24
To: gate-users at lists.opengatecollaboration.org<mailto:gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] implementing MOBY into GATE

Hello  all
 My name is Iván, I am quite new in this area my final proyect consist in a few experiments using different sizes of MOBY and 67Ga, but I am stuck in how import succesfully the MOBY into GATE

I have a few questions I hope you can help me:

1.- I have checked the forums for this question, but it is still not clear for me, I have created a phantom with the MOBY software, it gave me two files:

Act.bin and Atn.bin, I see that I need to convert them to a 16 bit inter file, but I am using ImageJ to perform the conversion, my steps were:

Import the file then  edit>options>conversions: uncheck scale when converting then I changed the image type to 16 bit and finally save it as a RAW.

I would like to know if that is ok or Do I need to use another software?

2.- I have checked that after the conversion to 16 bit I need to convert again to a i33 with a header h33 with a xmedcon software, I am using Ubuntu 16.04 and I am getting issues during installations of this xmedcon about JAVA JDK 8, so I am not able to perform this conversion yet , I was checking that there is a windows version that I will try to install but in the mean time I would like to know if there is another way to perform the conversion and get my images with a header?

3.- I was trying to do the example that is in GATE webpage that is named pre-clinical dosimetry that has a voxelized mouse phantom, I ran it and looks that it worked but when I enabled the visual mac I can not see the phantom, for now I just want to see a voxelized phantom by just running  the visual mac.. I checked the data folder and I see that the header is in a .iff file and the images are in a .img file. How can I run just the visual mac and see the mouse phantom?

Thank you
Best Regards from México
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