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<div class="moz-cite-prefix">Hi Emanuele,<br>
<br>
I have two comments in addition.<br>
<br>
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>
<br>
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>
<br>
Cheers<br>
Simon<br>
<br>
Le 20/06/2018 à 17:39, tmerlin a écrit :<br>
</div>
<blockquote type="cite"
cite="mid:41b703f9-78c0-8964-f658-3e96b80a148d@univ-brest.fr">
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<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>
</p>
<br>
<br>
<div class="moz-cite-prefix">On 20/06/2018 14:03, Emanuele
Ripiccini wrote:<br>
</div>
<blockquote
cite="mid:008E8963-5356-4B2B-AF43-A61284C140A1@unige.ch"
type="cite"> Dear Thibaut,
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class="">
<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>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">I observed this output</div>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<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>
<div class=""><br class="">
</div>
<div class="">best regards,</div>
<div class=""><br class="">
</div>
<div class="">Emanuele</div>
</div>
<div class="">
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normal; word-spacing: 0px; -webkit-text-stroke-width:
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class="Apple-interchange-newline">
<br class="">
</div>
<div style="color: rgb(0, 0, 0); font-family: Helvetica;
font-size: 12px; font-style: normal;
font-variant-ligatures: normal; font-variant-position:
normal; font-variant-caps: normal;
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normal; font-variant-east-asian: normal; font-weight:
normal; letter-spacing: normal; text-align: start;
text-indent: 0px; text-transform: none; white-space:
normal; word-spacing: 0px; -webkit-text-stroke-width:
0px; word-wrap: break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<div style="font-variant-ligatures: normal;
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normal; font-variant-alternates: normal;
font-variant-east-asian: normal; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
****************************************************************</div>
<div style="font-variant-ligatures: normal;
font-variant-position: normal; font-variant-numeric:
normal; font-variant-alternates: normal;
font-variant-east-asian: normal; word-wrap:
break-word; -webkit-nbsp-mode: space;
-webkit-line-break: after-white-space;" class="">
<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>
</div>
</div>
</div>
</div>
</div>
</div>
<br class="">
</blockquote>
<br>
<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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