[Castor-users] few questions about castor

[Simon Stute]

Hi Emanuele,

I have two comments in addition.

First, I strongly suggest to compile CASToR with multi-threading support 
(with CASTOR_OMP, see the documentation). Then you can use the option 
"-th 0" to tell CASToR to use as many cores as available in your 
computer, so a good improvement !

Second, beware of the gaussian filter parameterization ! When you set 
"gaussian,0.7,0.7,1.::psf", I suppose that you expect a gaussian with 
0.7 FWHM in X, 0.7 in Y and 1 in Z. So then you should use 
"gaussian,0.7,1.,3.::psf", because the first parameter is for transaxial 
FWHM (so both for X and Y), the second parameter is for axial FWHM, and 
the third parameter is the number of sigmas of the gaussian filter that 
are kept into the integral of it in the convolution kernel. For the 
latter, we suggest 3 sigmas.

Cheers
Simon

Le 20/06/2018 à 17:39, tmerlin a écrit :
>
> Dear Emanuele,
>
> You can enable the verbose to see the progression of the sensitivity 
> image generation (add the following option : -vb 2)
>
> This computation performs a dual loop on all the detector elements to 
> compute all possible lines of response, depending on the potential 
> angle restrictions in the geometry file and datafile. So the duration 
> will mostly depend on the total number of detectors and the image 
> dimensions.
>
> Once the sensitivity image is computed, it could be re-used for other 
> reconstructions (provided these reconstructions use the same 
> dimensions, projectors and image-based operations such as psf, etc..) 
> using the option -sens sensitivity_file.hdr.
>
> I will forward this answer to our user mailing-list as this is a 
> question that other users could potentially have.
>
> Best,
> Thibaut
>
>
>
> On 20/06/2018 14:03, Emanuele Ripiccini wrote:
>> Dear Thibaut,
>>
>> many thanks again for your precious answers. I successfully created 
>> the geometry LUT, the geometry header, the binary data file and the 
>> header data file. I executed castor using my geometry and my data 
>> with this command
>>
>> ./castor-recon -df 
>> /Users/emanuele/Desktop/example_ttpet/TTPETdata.cdh -opti MLEM -it 
>> 5:1 -proj joseph -conv gaussian,0.7,0.7,1.::psf -dim 200,200,200 -vox 
>> 0.25,0.25,0.25 -dout image_test
>>
>>
>> I observed this output
>>
>> sOutputManager::InitOutputDirectory() -> Output path is 'image_test'
>> castor-recon() -> Launch reconstruction from CASToR version 2.0.1.
>> sScannerManager::Initialize() -> From scanner TTPET
>> oProjectorManager::Initialize() -> Initialize projectors and 
>> projection lines
>> oOptimizerManager::Initialize() -> Initialize optimizer and penalty
>> oImageConvolverManager::Initialize() -> Initialize image convolvers
>> oSensitivityGenerator::Launch() -> Start the sensitivity computation
>>
>> but after this it has been 3 hours and half more or less. You told me 
>> that it would take time given our geometry, but I don’t know if it is 
>> normal or not and I should see some output to follow the status.
>>
>> best regards,
>>
>> Emanuele
>>
>>
>> ****************************************************************
>> Dr Emanuele Ripiccini
>> Assistant Post-doctorant
>>
>> Université de Genève
>> Département de physique nucléaire et corpusculaire
>> Quai Ernest-Ansrmet 24, 1205 Genève
>>
>> Phone nr : +41 223796151
>> Pavillon des isotopes
>> Office nr : 124
>> ****************************************************************
>>
>
> -- 
> 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
>
>
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