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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>
<br>
<div class="moz-cite-prefix">On 04/18/2017 04:36 PM, Michael
Ljungberg wrote:<br>
</div>
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<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"><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">Didier Benoit
<a class="moz-txt-link-rfc2396E" 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 class="moz-txt-link-rfc2396E" href="mailto:michael.ljungberg@med.lu.se"><michael.ljungberg@med.lu.se></a>,
<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","serif""><o:p> </o:p></span></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>
<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","serif""> </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>
<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>
<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>
<pre><a moz-do-not-send="true" href="http://lists.castor-project.org/listinfo/castor-users">http://lists.castor-project.org/listinfo/castor-users</a><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","serif";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>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
-------------------------------------------------------------------------------
Didier BENOIT, PhD,
Laboratoire de Traitement de l'Information Médicale (LaTIM - INSERM UMR 1101)
CHRU Morvan, bâtiment 1, étage 1
5 Avenue Foch
29609 Brest
FRANCE
E-mail:
<a class="moz-txt-link-abbreviated" href="mailto:didier.benoit@univ-brest.fr">didier.benoit@univ-brest.fr</a>
<a class="moz-txt-link-abbreviated" href="mailto:didier.benoit@inserm.fr">didier.benoit@inserm.fr</a>
Tél: +33 (0)2 98 01 81 96
-------------------------------------------------------------------------------</pre>
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