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<p class="MsoNormal"><span style="font-size:11.0pt">This is outstanding. Thanks!
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">By dark and flood field, I was referring to the files in the Calibration folder (e.g. GainImage.xim, OffsetImage.xim). But it appears the xim files are indeed corrected.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">-Greg<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Simon Rit <simon.rit@creatis.insa-lyon.fr>
<br>
<b>Sent:</b> Monday, March 16, 2026 6:25 PM<br>
<b>To:</b> Sharp, Gregory C. <gcsharp@mgb.org><br>
<b>Cc:</b> rtk-users <rtk-users@openrtk.org><br>
<b>Subject:</b> Re: [Rtk-users] Questions about xim / fdk<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
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<p class="MsoNormal">Hi Greg,<o:p></o:p></p>
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<p class="MsoNormal">- rtk can convert these files in any ITK file format. Run<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">rtkprojections -p DIRECTORY -r FILENAME -o test.mha --nolineint</span><o:p></o:p></p>
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<p class="MsoNormal">- They are not already dark and flood corrected. See the converting class<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://secure-web.cisco.com/11Ab1IGr-lFK3XBotE4RuLXuERQtAXKQf3CkhfVQQ9iZT-KkC2_n6MGFVomQqfRUVPYVHoyjIMhJPWxr8hHKi-8YBVaeeGcbq2H63ARZVqGLOMtZiq_yWchaEt4rJcg_NIM3VMl-cjcyokmoyRKA974QvcFP8j1hvBP2j6gJbupfgIfkYlNecEpd4oU-sm86qjuaLipQElHPYBS2NWBQuKIegbBC72jAiPFu88hj9rKWwNxjX_1BB70jX1bIJTp_JS_PJCGeaEjHPFKH5p4Aef7LeMUMpl2pBl8k47bGhz7KWlcqpAWQFbPKwjSEX_P8x/https%3A%2F%2Fgithub.com%2FRTKConsortium%2FRTK%2Fblob%2Fmain%2Finclude%2FrtkVarianObiRawImageFilter.h%23L35-L38">https://github.com/RTKConsortium/RTK/blob/main/include/rtkVarianObiRawImageFilter.h#L35-L38</a><o:p></o:p></p>
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<p class="MsoNormal">- The FDK output are in 1/length unit. The length unit are a user choice, so if you set all ditances (spacings in image meta information and lengths in RTK geometry) in mm, then you reconstruct in 1/mm.<o:p></o:p></p>
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<p class="MsoNormal">- Conversion to HU requires a linear conversion after calibrating the value for air and water. We don't do that usually but I believe there is an ITK filter for this conversion.<o:p></o:p></p>
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<p class="MsoNormal">- If you want to use a subset of projections, you can use our tool rtksubselect :<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-family:"Courier New"">srit@srit-Precision-5480:~$ rtksubselect -h<br>
RTK 2.7.0, git hash 5e5929a510fc5940dccba9a96eec70aa6597f2fc<br>
<br>
Subselects a few projections from a list of projection files and a geometry <br>
file.<br>
<br>
Usage: RTK [OPTIONS]... [FILES]...<br>
<br>
-h, --help Print help and exit<br>
-V, --version Print version and exit<br>
-v, --verbose Verbose execution (default=off)<br>
-g, --geometry=STRING XML geometry file name<br>
--out_geometry=STRING Output geometry file name<br>
--out_proj=STRING Output projections stack file name<br>
-f, --first=INT First projection index (default=`0')<br>
-l, --last=INT Last projection index<br>
-s, --step=INT Step between projections (default=`1')<br>
--list=INT List of projection indices to keep (0-based)</span><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Good luck with all this,<o:p></o:p></p>
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<p class="MsoNormal">Simon<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Mon, Mar 16, 2026 at 7:51<span style="font-family:"Arial",sans-serif"> </span>PM Sharp, Gregory C. <<a href="mailto:gcsharp@mgb.org">gcsharp@mgb.org</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi all, I have a few questions:<br>
<br>
Is there any viewer for these files and/or can I convert them into mha?<br>
<br>
Are the xim files already dark and flood corrected?<br>
<br>
What are the units for the fdk output? Can they be scaled into something like HU?<br>
<br>
Is there a way to specify subsets of gantry angles to be used in the fdk recon?<br>
<br>
Thank you,<br>
Greg<br>
<br>
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