[Gate-users] Importing DICOM CT data
Bryan McIntosh
mcintoshster at gmail.com
Sun Dec 27 16:46:48 CET 2020
Hello everyone,
I finally got some time to spend yesterday working on my problem with
importing DICOM CT volumes. Here's a quick update:
-Rukiah's suggestion of checking the HU calibration files was a good one,
and was the first thing that I checked. My file's minimum value was -1000
(verified by loading the DICOM data into AMIDE), and my calibration went
down to -1030 so that was not causing my particular problem. It was a good
thing to check, though!
-Replacing "setRangeToMaterialFile" with "setHUToMaterialFile" worked. Now
I can actually start working through the simulation that I want to run in
the phantom. I did some quick benchmarking, and for reference I am seeing a
tiny bit under 2 million decays per real-time second using all eight
threads of my Ryzen 3700X. I'd love to get my hands on a 5800X, but right
now getting one of those is about as likely as purchasing a new GPU or
video game console. :P
Have the best holiday that you can, and all the best in 2021!
-Bryan McIntosh
On Thu, Dec 24, 2020 at 11:42 PM <
gate-users-request at lists.opengatecollaboration.org> wrote:
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> Today's Topics:
>
> 1. Re: Importing DICOM CT data (David Boersma & Rukiah)
> (Bryan McIntosh)
> 2. GATE tutoring material (Xuzhi He)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 23 Dec 2020 07:50:19 -0600
> From: Bryan McIntosh <mcintoshster at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] Importing DICOM CT data (David Boersma &
> Rukiah)
> Message-ID:
> <CAC6uAtDaHD6yU78njkQzOC6ZKMmEkekb=NsXdbUAtc2jt=
> y9tQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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 <
> gate-users-request at lists.opengatecollaboration.org> wrote:
>
> > Send Gate-users mailing list submissions to
> > gate-users at lists.opengatecollaboration.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > or, via email, send a message with subject or body 'help' to
> > gate-users-request at lists.opengatecollaboration.org
> >
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> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Gate-users digest..."
> >
> >
> > 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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> Message: 2
> Date: Thu, 24 Dec 2020 01:17:54 -0800
> From: Xuzhi He <xzhe at ucdavis.edu>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] GATE tutoring material
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> Hi Gate Users
>
> I am new to GATE. Could someone recommend GATE tutoring videos or some
> other tutoring material? Thanks in advance.
>
> Happy Holidays
> Xuzhi
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