[Gate-users] Importing DICOM CT data

Bryan McIntosh mcintoshster at gmail.com
Thu Dec 17 23:38:40 CET 2020

Hi everyone,

I am working on a side project to do some HDR brachytherapy dosimetry in
GATE 8.2, and am having a very difficult time creating a voxelized phantom
based on the DICOM CT data of our prostate phantom. However, as my
simulation starts I get the following error as the voxelized phantom is
turned into an image volume:

"GateVImageVolume.cc (l.742):  I find R=-1000 in the image, while range
stop at -1001"

The only reference I could find in the mailing list archives to this was
back in 2016, before GATE had DICOM import capability. The same issue
happens if I try to import the volume split across multiple files (the
default from our planning CT system) or as a single file (using AMIDE to
export the multi-file data). I'd rather not change the data to an Interfile
format, since GATE won't import Interfile data unless it's an unsigned INT;
that would make it pretty difficult to have CT data for the air-equivalent
part of the phantom that represents the colon!

So, has anyone found a way to work around this? Is this fixed in GATE 9.0
and I just need to install the new version, or is there some other fix i
need to go through? I'll post the beginning of my macro and system
configuration below.

Thanks for your time,

-Bryan McIntosh

My configuration:
Linux Mint 19.3
GATE 8.2, GEANT4 10.5.p01, root 6.14, ITK 5.1.2
Ryzen 7 3700X, 16 GB RAM, Gigabyte X470

Phantom-defining macro content
/gate/geometry/setMaterialDatabase GateMaterials.db

# World
/gate/world/geometry/setXLength 3 m
/gate/world/geometry/setYLength 3 m
/gate/world/geometry/setZLength 3 m
/gate/world/setMaterial Air

#Generate Hounsfield unit table (commented out after 1st run)
#/gate/HounsfieldMaterialGenerator/SetDensityTolerance               0.1

# Voxelized prostate phantom
/gate/world/daughters/name prostate

/gate/world/daughters/insert ImageNestedParametrisedVolume
/gate/prostate/geometry/setImage                data/CT.T111112.1.dcm
/gate/geometry/setMaterialDatabase     data/patient-HUmaterials.db
/gate/prostate/geometry/setRangeToMaterialFile  data/patient-HU2mat.dat
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