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Dear Simon,
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<div>Thanks for the suggestions. Ok I misunderstood the option of the Gaussian smoothing.</div>
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<div>Regards,</div>
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<div>Emanuele <br>
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<div class="" style="margin: 0px; line-height: normal;"><span style="background-color: rgba(255, 255, 255, 0);">Dr Emanuele Ripiccini </span></div>
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<div class="" style="margin: 0px; line-height: normal;"><span style="background-color: rgba(255, 255, 255, 0);">Université de Genève </span></div>
<div class="" style="margin: 0px; line-height: normal;"><span style="background-color: rgba(255, 255, 255, 0);">Département de physique nucléaire et corpusculaire</span></div>
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Ernest-Ansrmet 24, 1205 Genève</font></a></div>
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<div class="" style="margin: 0px; line-height: normal;"><span style="background-color: rgba(255, 255, 255, 0);">Phone nr : <a href="tel:+41%20223796151" dir="ltr" x-apple-data-detectors="true" x-apple-data-detectors-type="telephone" x-apple-data-detectors-result="2">+41
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Le 20 juin 2018 à 17:55, Simon Stute <<a href="mailto:simon.stute@cea.fr">simon.stute@cea.fr</a>> a écrit :<br>
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<div class="moz-cite-prefix">Hi Emanuele,<br>
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I have two comments in addition.<br>
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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 !<br>
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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.<br>
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Cheers<br>
Simon<br>
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Le 20/06/2018 à 17:39, tmerlin a écrit :<br>
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<blockquote type="cite" cite="mid:41b703f9-78c0-8964-f658-3e96b80a148d@univ-brest.fr">
<p>Dear Emanuele,</p>
<p>You can enable the verbose to see the progression of the sensitivity image generation (add the following option : -vb 2)<br>
</p>
<p>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.<br>
</p>
<p>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.</p>
<p>I will forward this answer to our user mailing-list as this is a question that other users could potentially have.</p>
<p>Best,<br>
Thibaut<br>
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<div class="moz-cite-prefix">On 20/06/2018 14:03, Emanuele Ripiccini wrote:<br>
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<blockquote cite="mid:008E8963-5356-4B2B-AF43-A61284C140A1@unige.ch" type="cite">
Dear Thibaut,
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<div class="">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</div>
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<div class="">./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</div>
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<div class="">I observed this output</div>
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<div class="">sOutputManager::InitOutputDirectory() -> Output path is 'image_test'</div>
<div class="">castor-recon() -> Launch reconstruction from CASToR version 2.0.1.</div>
<div class="">sScannerManager::Initialize() -> From scanner TTPET</div>
<div class="">oProjectorManager::Initialize() -> Initialize projectors and projection lines</div>
<div class="">oOptimizerManager::Initialize() -> Initialize optimizer and penalty</div>
<div class="">oImageConvolverManager::Initialize() -> Initialize image convolvers</div>
<div class="">oSensitivityGenerator::Launch() -> Start the sensitivity computation</div>
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<div class="">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.</div>
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<div class="">best regards,</div>
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<div class="">Emanuele</div>
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<div style="margin: 0px; line-height: normal;" class="">Dr Emanuele Ripiccini </div>
<div style="margin: 0px; line-height: normal;" class="">Assistant Post-doctorant</div>
<div style="margin: 0px; line-height: normal;" class=""><br class="">
</div>
<div style="margin: 0px; line-height: normal;" class="">Université de Genève </div>
<div style="margin: 0px; line-height: normal;" class="">Département de physique nucléaire et corpusculaire</div>
<div style="margin: 0px; line-height: normal;" class="">Quai Ernest-Ansrmet 24, 1205 Genève</div>
<div style="margin: 0px; line-height: normal;" class=""><br class="">
</div>
<div style="margin: 0px; line-height: normal;" class="">Phone nr : +41 223796151</div>
<div style="margin: 0px; line-height: normal;" class="">Pavillon des isotopes</div>
<div style="margin: 0px; line-height: normal;" class="">Office nr : 124</div>
<div style="margin: 0px; line-height: normal;" class="">****************************************************************</div>
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<pre class="moz-signature" cols="72">--
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</pre>
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