[Gate-users] Importing DICOM CT data (David Boersma & Rukiah)
Bryan McIntosh
mcintoshster at gmail.com
Wed Dec 23 14:50:19 CET 2020
Hi David and Rukiah,
Thank you for the responses! I will try David's suggestion of using
setHUtoMaterialFile first, and then Rukiah's idea of expanding the range of
my density calibration file. Once I'm finished with that, I'll let the
mailing list know what happened; I am sure it will help someone else.
Thanks for the help!
-Bryan
On Wed, Dec 23, 2020 at 5:32 AM <
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> Today's Topics:
>
> 1. Bain CT Image (HU ranges and corresponding material
> definitions) (Atiq Ur Rahman)
> 2. Re: Importing DICOM CT data (David Boersma)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 23 Dec 2020 15:28:50 +0800
> From: Atiq Ur Rahman <atiqchep at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Bain CT Image (HU ranges and corresponding
> material definitions)
> Message-ID:
> <
> CAEQ5BgcK06a47u9BgXO0CZtiYSQo55tAwnFVDA9mQjKP-NYNpA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Users,
> I have been dealing with brain CT Dicom image. To read it in Gate, we write
> a material file that specifies the HU ranges and corresponding material.
> For a certain brain image, how can I specify the realistic HU range of the
> organs and their corresponding compositions (To define material
> definitions)? I have seen that some organ compositions are already defined
> in GateMaterial.db (Liver Saleen, bones, kidneys) files. If someone has
> preliminarily defined some HU ranges of organs and material definitions,
> your sharing will be much appreciated OR can point how to prepare such
> files.
> Regards
> Atiq
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> Message: 2
> Date: Wed, 23 Dec 2020 10:06:22 +0000
> From: David Boersma <david.boersma at acmit.at>
> To: "gate-users at lists.opengatecollaboration.org"
> <gate-users at lists.opengatecollaboration.org>, Bryan McIntosh
> <mcintoshster at gmail.com>, Rukiah <katoshka_7880 at yahoo.com>
> Subject: Re: [Gate-users] Importing DICOM CT data
> Message-ID:
> <
> VI1P190MB03515910D67B1C7BBDED25AC86DE0 at VI1P190MB0351.EURP190.PROD.OUTLOOK.COM
> >
>
> Content-Type: text/plain; charset="utf-8"
>
> Hi!
>
> Bryan, what happens if you replace "setRangeToMaterialFile" with
> "setHUToMaterialFile" in the nested voxelized image configuration?
>
> (I think that the range-to-material command is intended for a different
> kind of input image, I think, images in which the voxel values are not HU
> values. If I understood your problem correctly and if my solution works for
> you, then the lesson for us is to improve the error message, to make it
> more clear to the user what is going wrong in such a situation...)
>
> /David
>
>
> ________________________________
> From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> on
> behalf of Rukiah <katoshka_7880 at yahoo.com>
> Sent: Wednesday, December 23, 2020 5:10 AM
> To: gate-users at lists.opengatecollaboration.org <
> gate-users at lists.opengatecollaboration.org>; Bryan McIntosh <
> mcintoshster at gmail.com>
> Subject: Re: [Gate-users] Importing DICOM CT data
>
> Hi,
> This response might be late. And I am not sure if you found the solution.
> I just want to share my experience on creating voxelized phantom from CT
> image, using GATE 7.2 back then. I experienced the same error and thought
> that was nothing to do with the image format since GATE 7.2 accept the uint
> or int image. I was using Analyze or Interfile format during that time
> since 7.2 version was not able to accept Dicom.
>
> The error occurred because the CT image and the HU calibration txt does
> not have the same min or max HU. In your case, GATE detected the HU of
> -1000, however, in HU calibration txt, the min HU started at higher than
> -1000. Therefore, GATE was not able to define and calibrate the HU less
> than -1000.
> Whether you can rescale back the CT image according to the HU calibration
> txt or vice versa, the problem will be solved.
>
> Good luck.
>
>
>
>
>
>
> On Friday, December 18, 2020, 06:39:01 AM GMT+8, Bryan McIntosh <
> mcintoshster at gmail.com> wrote:
>
>
> 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/SetMaterialTable
> data/Schneider2000MaterialsTable.txt
> #/gate/HounsfieldMaterialGenerator/SetDensityTable
> data/Schneider2000DensitiesTable.txt
> #/gate/HounsfieldMaterialGenerator/SetDensityTolerance 0.1
> g/cm3
> #/gate/HounsfieldMaterialGenerator/SetOutputMaterialDatabaseFilename
> data/patient-HUmaterials.db
> #/gate/HounsfieldMaterialGenerator/SetOutputHUMaterialFilename
> data/patient-HU2mat.txt
> #/gate/HounsfieldMaterialGenerator/Generate
>
> # Voxelized prostate phantom
> # VOXELIZED PHANTOM BASED ON PATIENT DATA
> /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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