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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Hojjat,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Extremely grateful for your co-operation. ImageJ and Amide worked properly. But for MATLAB, I am getting -1 for fid and then the second command i.e. fread is
not working and obviously rest of the commands are not working . Am I supposed to get the fid as -1 ? I am just wondering if you would like to have a look on the gate.sin file with your provided code.<br>
And is there any software or open source code you know to get reconstruction image from .sin file?<br>
Please let me know.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Good wishes.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Smita<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> gate-users-bounces@lists.opengatecollaboration.org [mailto:gate-users-bounces@lists.opengatecollaboration.org]
<b>On Behalf Of </b>Hojjat Mahani<br>
<b>Sent:</b> Friday, 31 January 2014 5:00 AM<br>
<b>To:</b> GATErs<br>
<b>Subject:</b> Re: [Gate-users] About Output File<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="text-align:justify;background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">Hi Smita,<o:p></o:p></span></p>
<p class="MsoNormal" style="text-align:justify;background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">The '.sin' file is simply a set of 2D projection images. It can be analysed by MATLAB, using the following commands: <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">fid = fopen ('[your output name]', 'r');<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">projection = fread (fid, 'uint16');<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">fclose (fid);<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">projection = reshape (projection, dim1, dim2, dim3); % dim1, dim2 and dim3 are dimensions of the .sin file<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">Alternatives are completely free tools: ImageJ and Amide. In both tools, once the image is selected, you must select the image type
as 16-bit unsigned, little Endian.<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">Please have a look at the following links which direct you to the ImageJ and Amide web-sites, respectively:<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">ImageJ:
<a href="http://rsbweb.nih.gov/ij/">http://rsbweb.nih.gov/ij/</a><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">Amide: <a href="http://amide.sourceforge.net/index.html">http://amide.sourceforge.net/index.html</a><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">The '.hdr' file is also a header-file which contains GATE interfile-output information. Such a file will help you to identify .sin
file specifications such as height, width and number of projection images (dim1, dim2 and dim3, respectively). <o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black">Good work,<o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="background:white"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:black">Hojjat </span></b><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt;background:white"><span style="font-size:10.0pt;font-family:"Helvetica","sans-serif";color:black"><o:p> </o:p></span></p>
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