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<p>Hi Hadi,</p>
<p>You can provide an attenuation map to castor-recon if you use
list-mode format with the -atn option (or directly to
castor-GATERootToCastor if you want to get an histogram) .<br>
</p>
<p>castor-GATERootToCastor doesn't perform normalization correction,
so normalization correction coefficients would have to be computed
manually and inserted directly in the datafiles, as indicated in
the documentation section 6.1.</p>
<p>Looking at your image, it is not easy to know what is wrong
without details about the simulation and the image values, but it
seems it was reconstructed from a simulation with very low
statistics.<br>
</p>
<p>Hope this helps,<br>
Thibaut<br>
</p>
<div class="moz-cite-prefix">On 24/04/2021 12:23, Hadi Rezaei wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAEygHB=wm70Y1KrFgaqjaLxNdyQyLD1UvS=6QdfuKsS2oF0==w@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr"><font face="arial, sans-serif">Dear CASToR users<br>
</font>
<div><font face="arial, sans-serif">I simulated an IEC NEMA
phantom on a PET using GATE and reconstructed it using
CASTOR without any correction (random, scatter, attenuation
and normalization). The reconstructed image was undesirable.
I found that for random and scatter correction I can write
"-t" on the castor-GATERootToCastor to convert only
trues (is it right?). But, how can I perform the attenuation
correction (and also normalization)? </font></div>
<div><font face="arial, sans-serif">I used bellow commands for
convert to CASTOR and reconstructed it.</font></div>
<div><font face="arial, sans-serif"> ./castor-GATERootToCastor
-i output.root -m mymacfile.mac -o IEC -s IEC -geo -k</font></div>
<font face="arial, sans-serif">./castor-recon -df IEC_df.Cdh
-dout IEC -opti MLEM -it 10:20 -th 40 -dim 512,512,1655 -fov
600,600,1940</font>
<div><font face="arial, sans-serif">I attached the reconstructed
image here.
<span style="color:rgb(0,0,0)">I would therefore
appreciate it if anyone could help me to apply any
correction on it.</span></font></div>
<div><font face="arial, sans-serif"><font color="#000000">Best
regards</font></font></div>
<div><font face="arial, sans-serif"><font color="#000000">Hadi<br>
</font></font>
<div><font face="arial, sans-serif"> </font><br>
</div>
</div>
</div>
<br>
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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)
Institut Brestois de recherche en Bio-Santé (IBRBS)
12 Avenue Foch, 29200 Brest, FRANCE
Tel: 06.75.12.24.90</pre>
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