<div dir="ltr">Thank you very much. <br></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 3, 2021 at 2:47 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>Here is a umap example.</p>
<p>Best,<br>
Thibaut<br>
</p>
<p><br>
</p>
<div>On 03/05/2021 11:01, Hadi Rezaei wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Thibaut
<div>I am sorry for the delay.<br>
<div>Could you share a sample of the header (.hdr) file ??</div>
<div>Thank you so much.</div>
</div>
<div>Hadi</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Thu, Apr 29, 2021 at 6:27
PM tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr" target="_blank">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>Could you check if there is an issue with the file ? I
couldn't open it using regular text editors.</p>
<p>Best,<br>
Thibaut<br>
</p>
<div>On 28/04/2021 20:57, Hadi Rezaei wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Thibaut</div>
<div>Thank you for your answer. <br>
</div>
<div>I shared it. I got it from GATE directly.<br>
</div>
<div>Thank you <br>
</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Wed, Apr 28, 2021
at 9:02 PM tmerlin <<a href="mailto:Thibaut.Merlin@univ-brest.fr" target="_blank">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>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>On 27/04/2021 20:32, Hadi Rezaei wrote:<br>
</div>
<blockquote type="cite">
<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" target="_blank">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>_______________________________________________
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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>
</div>
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</div>
</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>
</blockquote>
</div>
</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>
</blockquote>
</div>
</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>
</blockquote></div>