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<p>Hi Hadi,</p>
<p>Could you share the header of your mumap
(myMapFileName-MuMap.hdr) ? It looks like the problem comes from
some interfile keys.</p>
<p>Best,<br>
Thibaut<br>
</p>
<div class="moz-cite-prefix">On 27/04/2021 20:32, Hadi Rezaei wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAEygHBmjY5F2sLYGYqMci=s8=ch0w9KME7UKCVvQ+_4Mg+oqoQ@mail.gmail.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<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"
moz-do-not-send="true">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>
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</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>
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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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