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<p>Dear Michael,</p>
<p><br>
</p>
<p>The attenuation coefficient is in cm-1 as explicitly specified in
the manual. The attenuation map was extracted directly from the
Siemens computation which uses (as you assume) a wide beam
approach. The correct value should be the one you mention for the
methodology used by CASToR. I apologize for this misunderstanding
and a correct mu-map will be uploaded soon.</p>
<p>Thanks for pointing out this small error.<br>
</p>
<p><br>
</p>
<p>Best regards</p>
<p><br>
</p>
<p>Thomas Carlier<br>
</p>
<br>
<div class="moz-cite-prefix">Le 19/04/2017 à 16:42, Michael
Ljungberg a écrit :<br>
</div>
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<p class="MsoNormal">Dear Simon and Didier<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you for your comments and
information. I have now written a conversion program between
simind interfiles and castor and I can reconstruct images :-)
. I have a final question for the moment and that concerns the
units of the mu map. I assume it is mu (cm-1) for the current
photon energy. When I looked at the SPECT benchmark file the
average value in a ROI is however, around 0.128 cm-1 instead
of 0.154 which is this the linear attenuation coefficient for
water. Is this an ‘effective attenuation coefficient map’ with
lower values with the purpose of compensate for presence of
scatter? I just want to be clear about what values the mu-map
should reflect.<o:p></o:p></p>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Hälsningar
/ Best regards<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Michael<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="color:black">From: </span></b><span
style="color:black">Castor-users <a
class="moz-txt-link-rfc2396E"
href="mailto:castor-users-bounces@lists.castor-project.org"><castor-users-bounces@lists.castor-project.org></a>
on behalf of Simon Stute <a class="moz-txt-link-rfc2396E"
href="mailto:simon.stute@cea.fr"><simon.stute@cea.fr></a><br>
<b>Date: </b>Tuesday, 18 April 2017 at 17:26<br>
<b>To: </b><a class="moz-txt-link-rfc2396E"
href="mailto:castor-users@lists.castor-project.org">"castor-users@lists.castor-project.org"</a>
<a class="moz-txt-link-rfc2396E"
href="mailto:castor-users@lists.castor-project.org"><castor-users@lists.castor-project.org></a><br>
<b>Subject: </b>Re: [Castor-users] SPECT reading
Interfile</span><span
style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times New
Roman""><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal">Hello,<br>
<br>
The castor configuration folder also contains other
configuration files, so it is not only related to the
scanner geometries.<br>
<br>
However, a third possibility is to copy the whole 'config'
folder (it is light) into your working directory, put your
geom files inside the 'scanner' sub-folder and then you can
use the '-conf ./your_config_folder' option to overload the
path of the configuration directory at run-time.<br>
<br>
The '-conf' option is described when calling 'castor-recon
-help-misc'.<br>
<br>
Regards<br>
Simon<br>
<br>
<br>
Le 18/04/2017 à 17:13, Didier Benoit a écrit :<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal" style="margin-bottom:12.0pt">In our
software, we didn't plan to read the .geom files in 2 or
more folders. I think you have 2 solutions :<br>
<br>
1- You can copy all your .geom files for each different kind
of scanners in the CASTOR_CONFIG folder<br>
<br>
2- Or creating a "castor_test" folder, where you write all
your .geom files (and the .geom files provided by CASToR)
and set CASTOR_CONFIG to the location of "castor_test"
during the installation.<br>
<br>
Kind regards,<br>
Didier<br>
<br>
<o:p></o:p></p>
<div>
<p class="MsoNormal">On 04/18/2017 04:36 PM, Michael
Ljungberg wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Sorry Didier<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I meant the CASTOR_CONFIG folder. That
was my question - if it would be possible for your
software to search first in the local directory for a
scanner name before looking in the CASTOR_CONFIG folder.
Sometimes one do simulations as function of different
camera geometries and I can then imagine I would need one
.geom file for each of them. If the search for the scanner
name is first made in the local directory and then in the
CASTOR_CONFIG folder then these local .geom files could be
isolated from the more permanent scanner system files,
stored in the CASTOR_CONFIG folder.<o:p></o:p></p>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Hälsningar
/ Best regards</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Michael</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="color:black">From: </span></b><span
style="color:black">Didier Benoit <a
moz-do-not-send="true"
href="mailto:didier.benoit@inserm.fr"><didier.benoit@inserm.fr></a><br>
<b>Date: </b>Tuesday, 18 April 2017 at 16:07<br>
<b>To: </b>Michael Ljungberg <a
moz-do-not-send="true"
href="mailto:michael.ljungberg@med.lu.se"><michael.ljungberg@med.lu.se></a>,
<a moz-do-not-send="true"
href="mailto:castor-users@lists.castor-project.org">"castor-users@lists.castor-project.org"</a>
<a moz-do-not-send="true"
href="mailto:castor-users@lists.castor-project.org"><castor-users@lists.castor-project.org></a><br>
<b>Subject: </b>Re: [Castor-users] SPECT reading
Interfile</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="font-family:"Times
New Roman""> </span><o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">With a
time value set to 0, the SPECT reconstruction should work.<br>
<br>
In your second question, what do you exactly mean by
"SYSTEM location" ? I'm not sure to understand. Is it your
scanner system location defined by "CASTOR_CONFIG" during
the compilation ? If it's the case you can't add a path in
the Cdf file for the tag " Scanner name". If you want to
create a custom scanner file you have to save it in the
"CASTOR_CONFIG" directory.<br>
<br>
Kind Regards,<br>
Didier<br>
<br>
<br>
<br>
<o:p></o:p></p>
<div>
<p class="MsoNormal">On 04/18/2017 03:26 PM, Michael
Ljungberg wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Dear Didier<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thank you for your explanation. I
think it will not be a major problem to implement. For
SPECT reconstructions, does the Time value be clearly
defined? <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Another related question regards the
files for the system. I wonder if it would be possible
to allow castor-recon program to first look in the local
folder for a geometry file before looking in the
standard SYSTEM location? If I implement direct writing
to the caster format in the simind program, I can
foresee that the SYSTEM folder can be quickly filled
with files. Alternatively, is it possible to add a path
to the system name in the cdh file?<o:p></o:p></p>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Hälsningar
/ Best regards</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Michael</span><o:p></o:p></p>
</div>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<div style="border:none;border-top:solid #B5C4DF
1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="color:black">From:
</span></b><span style="color:black">Castor-users <a
moz-do-not-send="true"
href="mailto:castor-users-bounces@lists.castor-project.org"><castor-users-bounces@lists.castor-project.org></a>
on behalf of Didier Benoit <a
moz-do-not-send="true"
href="mailto:didier.benoit@inserm.fr"><didier.benoit@inserm.fr></a><br>
<b>Date: </b>Tuesday, 18 April 2017 at 14:52<br>
<b>To: </b><a moz-do-not-send="true"
href="mailto:castor-users@lists.castor-project.org">"castor-users@lists.castor-project.org"</a>
<a moz-do-not-send="true"
href="mailto:castor-users@lists.castor-project.org"><castor-users@lists.castor-project.org></a><br>
<b>Subject: </b>Re: [Castor-users] SPECT reading
Interfile</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span
style="font-family:"Times New Roman""> </span><o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt">Dear
Michael,<span style="color:#222222"><br>
<br>
Thanks for your interest. Interfile format is only
used as input/output format for image (not projection
data). As you have seen, input data for SPECT (and
also for PET) is composed of 2 files: a header file
(*.Cdh) and a binary file (*.Cdf) storing the data
from a machine or a Monte Carlo simulation. Here is
some information about this Cdf file. This file is not
a pure histogram (a successive number of counts by
bin). The Data should (must) be arrange as described
in the “CASToR general documentation” page 30.</span><br>
<br>
For instance, in the case of a 64x64 float matrix for 64
angles (and I consider you don't have both normalization
and scatter informations), your Cdf file should contain
262 144 events (64x64x64) with the following format:<br>
<br>
EVENT 0:<br>
time: 0 (uint32_t)<br>
data: 32 (float/double) it's your data for a specific
bin<br>
projection ID: 0 (uint32_t) it's the angle ID between 0
and 63 in this example<br>
binID: 0 (uint32_t) it's the bin ID between 0 and (64x64
– 1) in this example<br>
<br>
We don't provide a SPECT/PET data converter, but the
easiest way to create a correct Cdf file (I consider you
are using C/C++) is to create a struct like this:<br>
<br>
struct SPECT_CASTOR_EVENT_FORMAT {<br>
uint32_t time;<br>
float data;<br>
uint32_t projectionID;<br>
uint32_t binID;<br>
};<br>
<br>
and store each bin from your data in the CASToR event
format.<br>
<br>
Kind Regards,<br>
Didier Benoit<br>
<br>
<br>
<br>
<o:p></o:p></p>
<div>
<p class="MsoNormal">On 04/14/2017 05:34 PM, Michael
Ljungberg wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Dear Castor developers<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">I ran into this release a week ago
and it is really a nice contribution you have made. I
have been working with Monte Carlo simulations for
many years developing the program simind and often I
get this question of supplying reconstruction software
since simind only produce projections. So being able
to direct to your webpage would be natural. <o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">However, I dont understand how to
read data into castor-recon. I also use Interfile and
float values so when reading in the manual at you are
using interfile for both input data and output gave me
confidence for a smooth connection. But I dont see how
to actual do this. I checked the spect benchmark file
but the cdh format is different. So my question is how
I can read in for example a 64x64 float matrices for
64 angles stored in a data file and with an associated
interfile header file.<o:p></o:p></p>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"> </span><o:p></o:p></p>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Hälsningar
/ Best regards</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"> </span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Michael
Ljungberg</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Lund
University</span><o:p></o:p></p>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">Sweden</span><o:p></o:p></p>
</div>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal"><br>
<br>
<br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Castor-users mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:Castor-users@lists.castor-project.org">Castor-users@lists.castor-project.org</a><o:p></o:p></pre>
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</blockquote>
<p class="MsoNormal"><br>
<br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>-------------------------------------------------------------------------------<o:p></o:p></pre>
<pre>Didier BENOIT, PhD,<o:p></o:p></pre>
<pre>Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)<o:p></o:p></pre>
<pre>CHRU Morvan, bâtiment 1, étage 1<o:p></o:p></pre>
<pre>5 Avenue Foch<o:p></o:p></pre>
<pre>29609 Brest<o:p></o:p></pre>
<pre>FRANCE<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>E-mail:<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:didier.benoit@univ-brest.fr">didier.benoit@univ-brest.fr</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:didier.benoit@inserm.fr">didier.benoit@inserm.fr</a><o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Tél: +33 (0)2 98 01 81 96<o:p></o:p></pre>
<pre>-------------------------------------------------------------------------------<o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>-------------------------------------------------------------------------------<o:p></o:p></pre>
<pre>Didier BENOIT, PhD,<o:p></o:p></pre>
<pre>Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)<o:p></o:p></pre>
<pre>CHRU Morvan, bâtiment 1, étage 1<o:p></o:p></pre>
<pre>5 Avenue Foch<o:p></o:p></pre>
<pre>29609 Brest<o:p></o:p></pre>
<pre>FRANCE<o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>E-mail:<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:didier.benoit@univ-brest.fr">didier.benoit@univ-brest.fr</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:didier.benoit@inserm.fr">didier.benoit@inserm.fr</a><o:p></o:p></pre>
<pre> <o:p></o:p></pre>
<pre>Tél: +33 (0)2 98 01 81 96<o:p></o:p></pre>
<pre>-------------------------------------------------------------------------------<o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><span style="font-family:"Times New
Roman";mso-fareast-language:EN-GB"><br>
<br>
<o:p></o:p></span></p>
<pre>-- <o:p></o:p></pre>
<pre>-------------------------------------------------------------------------------<o:p></o:p></pre>
<pre>Didier BENOIT, PhD,<o:p></o:p></pre>
<pre>Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)<o:p></o:p></pre>
<pre>CHRU Morvan, bâtiment 1, étage 1<o:p></o:p></pre>
<pre>5 Avenue Foch<o:p></o:p></pre>
<pre>29609 Brest<o:p></o:p></pre>
<pre>FRANCE<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>E-mail:<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:didier.benoit@univ-brest.fr">didier.benoit@univ-brest.fr</a><o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:didier.benoit@inserm.fr">didier.benoit@inserm.fr</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Tél: +33 (0)2 98 01 81 96<o:p></o:p></pre>
<pre>-------------------------------------------------------------------------------<o:p></o:p></pre>
<p class="MsoNormal"><span style="font-family:"Times New
Roman";mso-fareast-language:EN-GB"><br>
<br>
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<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Castor-users mailing list<o:p></o:p></pre>
<pre><a moz-do-not-send="true" href="mailto:Castor-users@lists.castor-project.org">Castor-users@lists.castor-project.org</a><o:p></o:p></pre>
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Roman";mso-fareast-language:EN-GB"><br>
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<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
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