<div dir="ltr">Hi Tmerlin<div>Thank you for your answer.</div><div>I provided an attenuation map using mu map actor in GATE using the following commands:</div><div>#</div><div>/gate/actor/addActor MuMapActor getMuMap<br>/gate/actor/getMuMap/attachTo world<br>/gate/actor/getMuMap/save mhdoutput/myMapFileName.hdr<br>/gate/actor/getMuMap/setPosition 0 0 0 mm<br>/gate/actor/getMuMap/setVoxelSize 2.344 2.344 2.344 mm<br>/gate/actor/getMuMap/setResolution 300 300 900<br>/gate/actor/getMuMap/setEnergy 511 keV<br>/gate/actor/getMuMap/setMuUnit 1 1/cm<br></div><div>and the hdr/image file was provided. But after I added this hdr file to castor-recon (./castor-recon -df myfile_df.Cdh -dout output -opti MLEM -it 10:20 -th 40 -dim 256,256,827 -fov 600,600,1940 -atn myMapFileName-MuMap.hdr) I found some error as follow: </div><div><b>"oOptimizerManager::Initialize() -> Initialize optimizer and penalty<br>***** IntfCheckConsistency()-> Error : some mandatory keys not initialized. Cannot read the interfile image !<br> Error when trying to read path to image data<br> Error when trying to read matrix size (image dimensions) : x= 0, y= 0, z= 1<br>***** oInterfileIO::IntfReadImage() -> A error occurred while checking consistencies between reconstruction parameters and interfile keys in the header '../../GATE_9/gate/Gate/benchmarks/benchPET/Hadi/mhdoutput/myMapFileName-SourceMap.hdr' !<br>***** oImageSpace::InitAttenuationImage() -> An error occurred while reading from file '../../GATE_9/gate/Gate/benchmarks/benchPET/Hadi/mhdoutput/myMapFileName-SourceMap.hdr' !<br>***** oSensitivityGenerator::Initialize() -> A problem occurred while initializing the attenuation image into the image space !<br>***** oSensitivityGenerator::Initialize() -> A problem occurred while initializing the attenuation files !<br>***** castor-recon() -> A problem occurred while initializing the sensitivity generator !<br>***** Exit function called. Abort with code 1."</b><br></div><div>any suggestion to fix it would be appreciated.</div><div>Best,</div><div>Hadi</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, Apr 26, 2021 at 2:58 PM tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr">Thibaut.Merlin@univ-brest.fr</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<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>On 24/04/2021 12:23, Hadi Rezaei wrote:<br>
</div>
<blockquote type="cite">
<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>
<fieldset></fieldset>
<pre>_______________________________________________
Castor-users mailing list
<a href="mailto:Castor-users@lists.castor-project.org" target="_blank">Castor-users@lists.castor-project.org</a>
<a href="https://lists.castor-project.org/mailman/listinfo/castor-users" target="_blank">https://lists.castor-project.org/mailman/listinfo/castor-users</a>
To look for something in the mailing-list archives, use the search box at:
<a href="https://castor-project.org/mailing-list" target="_blank">https://castor-project.org/mailing-list</a></pre>
</blockquote>
<pre 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>
</div>
_______________________________________________<br>
Castor-users mailing list<br>
<a href="mailto:Castor-users@lists.castor-project.org" target="_blank">Castor-users@lists.castor-project.org</a><br>
<a href="https://lists.castor-project.org/mailman/listinfo/castor-users" rel="noreferrer" target="_blank">https://lists.castor-project.org/mailman/listinfo/castor-users</a><br>
<br>
To look for something in the mailing-list archives, use the search box at:<br>
<a href="https://castor-project.org/mailing-list" rel="noreferrer" target="_blank">https://castor-project.org/mailing-list</a></blockquote></div>