[Castor-users] SPECT reconstruction with scatter

Wed Aug 2 20:18:20 CEST 2017

Dear CASToR community,

I am appealing for some help getting CASToR to reconstruct some SPECT projection data with scatter correction.

I have attached the Matlab code we’re using to convert SPECT projection data from Interfile into CASToR .cdh/.cdf files.  I also attach the result of this code when we feed it three interfiles (photopeak and upper/lower scatter windows).  The code estimates the scatter component (in counts/sec) using the Triple Energy Window method.

When we run the resulting datafiles through castor-recon.exe, we get the attached error message.  As there is a mismatch between the expected and actual sizes, I suspect the problem relates to the bit depth of the variables as I write them to the .cdf file, or a problem with the header and CASToR not recognising the fact that I’ve included normalisation factors.  As we are using the pre-compiled binaries, we haven’t changed the default FLTNMDATA variable, so I am writing variables of this type as 32-bit floats.

I can’t spot any other issues with the conversion code, but I’m obviously missing something.  I would appreciate any help anyone can offer.  I have already had some very helpful email exchanges with Michael Ljungberg in Lund, who has already got this working.  But rather than continue to hassle Michael, I thought I would give him a break and appeal to the wider community!

Kind regards,

James.

James Scuffham, MSc, PhD, MIPEM
Deputy Head of Section
Nuclear Medicine Physics
Royal Surrey County Hospital
Egerton Road, Guildford, GU2 7XX
T: 01483 406708

Associate Tutor
Department of Physics
University of Surrey
Guildford, GU2 7XH

From: Castor-users [mailto:castor-users-bounces at lists.castor-project.org] On Behalf Of Kajal Aggarwal
Sent: 02 August 2017 10:10
To: tmerlin
Cc: castor-users at lists.castor-project.org
Subject: Re: [Castor-users] Query related to castor-GateMacToGeom

Hello,
Thank you for the detailed explanation. I am having troubles to reconstruct an image for a cylindrical PET system simulated using Gate. I am generating .geom file and .cdh and .cdf files (attached in this email) for my .mac file and for the output root file. But the image generated has some problem (see the screen-shot below). Please guide me where I am going wrong.
Thank you very much for all your support.
Regards,
Kajal

[Inline image 1]

[Inline image 2]

On Tue, Aug 1, 2017 at 9:00 PM, tmerlin <Thibaut.Merlin at univ-brest.fr<mailto:Thibaut.Merlin at univ-brest.fr>> wrote:

Hello Kajal,

F.O.V variables are arbitrary computed as scanner_radius(mm)/4 for the transaxial component, and the axial dimension (mm) of the rsector/block for the axial component. The transaxial/axial number of voxels are calculated from these values in order to get (large) isotropic 4mm voxels.

The sole purpose of these variables is to be used as default for reconstruction dimensions/voxel sizes when using this scanner, in the case no dimensions have been initialized in command-line options. In practice, they are overwritten by the parameters entered in command line options (-dim for number of voxels, -fov /-vox for field of view and voxel dimensions initializations ).

Best regards,

Thibaut

On 01/08/2017 16:54, Kajal Aggarwal wrote:
Hello everyone,
I am trying to create .geom file from a .mac file for PET scanner system. In the .geom file created, I would like to know how the voxels number transaxial, voxels number axial, field of view transaxial, field of view axial are being calculated.

--
Thanking you.

Yours sincerely,
Kajal Aggarwal

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--

Thibaut MERLIN -- PhD

Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)

Bâtiment 1

CHRU Morvan - 2, Av. Foch

29609 Brest CEDEX - FRANCE

Tel: 06.75.12.24.90

--
Thanking you.

Yours sincerely,
Kajal Aggarwal

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