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</o:shapelayout></xml><![endif]--></head><body lang=EN-GB link=blue vlink=purple><div class=WordSection1><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Hi Emmanuel<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Lipids I believe. It’s all in the file.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>As in the excoef.txt file:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>HbO</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>deoxyHb</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>Water</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>Lipids</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>LuTex</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>GdTex</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'> 6.0000000e+02 7.3696000e-01 3.3801592e+00 2.3000000e-04 4.6600000e-04 NaN NaN</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'> 6.0100000e+02 6.7523960e-01 3.2586989e+00 2.3400000e-04 4.7100000e-04 NaN NaN</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>You don’t need all columns of the excoef.txt. See ‘load_mesh.m’ on how excoef.txt file is handled.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>A hint:<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>The excoef.txt file saves any and any number of spectra. I.e. you can use/define your own spectra!<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>Not all spectra from the ‘excoef.txt’ are used. The ‘*.param’ file is used to set spectra in use. E.g. ‘cylinder_spec.param’ sets only haemoglobins and water:<o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>spec</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>HbO</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>deoxyHb</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>Water</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>S-Amplitude</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>S-Power</span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>0.01 0.01 0.4 1 1 </span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>0.01 0.01 0.4 1 1 </span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal style='text-autospace:none'><span style='font-size:10.0pt;font-family:"Courier New";color:black'>0.01 0.01 0.4 1 1 </span><span style='font-family:"Courier New"'><o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'>S.<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Regards<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Stanislaw Wojtkiewicz, PhD<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'><o:p> </o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>---<o:p></o:p></span></p><p class=MsoNormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>School of Computer Science<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>University of Birmingham<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>B15 2TT<o:p></o:p></span></p></div><p class=MsoNormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US'><o:p> </o:p></span></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=MsoNormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> emmanuel.cosnard@outlook.fr <emmanuel.cosnard@outlook.fr> <br><b>Sent:</b> 19 March 2019 12:00<br><b>To:</b> nirfast@public.kitware.com; s.wojtkiewicz@cs.bham.ac.uk<br><b>Subject:</b> RE: [Nirfast] Extinction parameters<o:p></o:p></span></p></div></div><p class=MsoNormal><o:p> </o:p></p><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>Hi Stanislas, <o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>Thank you very much for your answer. There is still a fourth column for each line of the .excoef file, and I don't understand to what it corresponds. Do you know what is the last column about, and how I can fill it?<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>Thank you,<o:p></o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'><o:p> </o:p></span></p></div><div><p class=MsoNormal><span style='font-family:"Calibri",sans-serif;color:black'>Emmanuel<o:p></o:p></span></p></div><div class=MsoNormal align=center style='text-align:center'><hr size=2 width="98%" align=center></div><div id=divRplyFwdMsg><p class=MsoNormal><b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'>De :</span></b><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'> Stanislaw Wojtkiewicz <</span><a href="mailto:s.wojtkiewicz@cs.bham.ac.uk"><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>s.wojtkiewicz@cs.bham.ac.uk</span></a><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'>><br><b>Envoyé :</b> mardi 19 mars 2019 11:13<br><b>À :</b> </span><a href="mailto:emmanuel.cosnard@outlook.fr"><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>emmanuel.cosnard@outlook.fr</span></a><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'>; </span><a href="mailto:nirfast@public.kitware.com"><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>nirfast@public.kitware.com</span></a><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:black'><br><b>Objet :</b> RE: [Nirfast] Extinction parameters</span> <o:p></o:p></p><div><p class=MsoNormal> <o:p></o:p></p></div></div><div><div><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Hi Emmanuel</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>NIRFAST values are expressed in ln(10)*mm^-1mM^-1 (mM - milli molar (molar - moles/liter)) for haemoglobins and in mm^-1 for water.</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Compare with </span><a href="https://omlc.org/spectra/hemoglobin/summary.html"><span style='font-size:11.0pt;font-family:"Calibri",sans-serif'>https://omlc.org/spectra/hemoglobin/summary.html</span></a><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>It’s the same. Also, this website gives you all information needed.</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>Cheers,</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'>S.</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><div><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Regards</span><o:p></o:p></p><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>Stanislaw Wojtkiewicz, PhD</span><o:p></o:p></p><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'> </span><o:p></o:p></p><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>---</span><o:p></o:p></p><p class=xmsonormal><span lang=EN-US style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>School of Computer Science</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>University of Birmingham</span><o:p></o:p></p><p class=xmsonormal><span style='font-size:11.0pt;font-family:Consolas;color:#1F497D'>B15 2TT</span><o:p></o:p></p></div><p class=xmsonormal><span style='font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D'> </span><o:p></o:p></p><div><div style='border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm'><p class=xmsonormal><b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>From:</span></b><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> </span><a href="mailto:emmanuel.cosnard@outlook.fr"><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>emmanuel.cosnard@outlook.fr</span></a><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'> <</span><a href="mailto:emmanuel.cosnard@outlook.fr"><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>emmanuel.cosnard@outlook.fr</span></a><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>> <br><b>Sent:</b> 19 March 2019 10:41<br><b>To:</b> </span><a href="mailto:nirfast@public.kitware.com"><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'>nirfast@public.kitware.com</span></a><span lang=EN-US style='font-size:11.0pt;font-family:"Calibri",sans-serif'><br><b>Subject:</b> [Nirfast] Extinction parameters</span><o:p></o:p></p></div></div><p class=xmsonormal> <o:p></o:p></p><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>Hello,</span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>I would like to know how exactly do we compute the extinction parameters for each wavelength, that are stored in the excoef file? </span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>Thank you and regards,</span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'> </span><o:p></o:p></p></div><div><p class=xmsonormal><span style='font-family:"Calibri",sans-serif;color:black'>Emmanuel</span><o:p></o:p></p></div></div><div id="x_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2"><p class=MsoNormal style='margin-bottom:12.0pt'><o:p> </o:p></p><div class=MsoNormal align=center style='text-align:center'><hr size=1 width="99%" noshade style='color:#909090' align=center></div><table class=MsoNormalTable border=0 cellspacing=0 cellpadding=0 style='border-collapse:collapse'><tr><td style='padding:0cm 11.25pt 0cm 6.0pt'><p class=MsoNormal><a href="https://www.avast.com/antivirus"><span style='text-decoration:none'><img border=0 width=90 height=33 style='width:.9375in;height:.3437in' id="_x0000_i1027" src="http://static.avast.com/emails/avast-mail-stamp.png" alt="Avast logo"></span></a><o:p></o:p></p></td><td style='padding:.75pt .75pt .75pt .75pt'><p><span style='font-family:"Calibri",sans-serif;color:#3D4D5A'>This email has been checked for viruses by Avast antivirus software. <br></span><a href="https://www.avast.com/antivirus"><span style='font-family:"Calibri",sans-serif'>www.avast.com</span></a><span style='font-family:"Calibri",sans-serif;color:#3D4D5A'> <o:p></o:p></span></p></td></tr></table><p class=MsoNormal><br><br><o:p></o:p></p></div></div></div></body></html>