<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">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>
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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>