<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns:mv="http://macVmlSchemaUri" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Title" content="">
<meta name="Keywords" content="">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<!--[if !mso]><style>v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style><![endif]--><style><!--
/* Font Definitions */
@font-face
{font-family:"Courier New";
panose-1:2 7 3 9 2 2 5 2 4 4;}
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman";}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Courier;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:Calibri;
color:windowtext;}
span.msoIns
{mso-style-type:export-only;
mso-style-name:"";
text-decoration:underline;
color:teal;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style>
</head>
<body bgcolor="white" lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Hi Vince,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">I have seen this before and there is an easy fix. Some of the GUI programs have dummy/blank rectangular panels just to keep things looking organized. The input fields should lay on top
of these panels, so you have a border around the fields. For whatever reason, in later versions of matlab on Mac OS, the panel is shown on top of the input fields, blocking them from view. The fix is to type “guide” at the matlab command prompt and then
open the matlab figure file (NIRFAST/gui/gui_set_values.fig in this case) in GUIDE. Once in edit mode, you can select the panel and right click and select “Send to back” (much like in powerpoint) and should then see all of the fields. Save your edited file
and you should be set.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">I thought I had gone through and fixed all of these before we released the latest version of NIRFASTmatlab. If you don’t have NIRFASTMatlab 9, you can try downloading it. If you do have
it and are still seeing this error, follow the steps above. <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">FYI, For command line work:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">To see the regions of a mesh, type “plotimage(mesh,mesh.region)”, where “mesh” is your mesh workspace variable.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">Then, to change an optical property for a given region (region 2 in the case), type “mesh.mua(mesh.region==2) = yourvalue”.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri">I hope this helps!<br>
Scott<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">From: </span>
</b><span style="font-family:Calibri;color:black">Nirfast <nirfast-bounces@public.kitware.com> on behalf of Hamid Dehghani <h.dehghani@cs.bham.ac.uk><br>
<b>Date: </b>Sunday, June 26, 2016 at 2:55 PM<br>
<b>To: </b>"nirfast@public.kitware.com" <nirfast@public.kitware.com><br>
<b>Subject: </b>Re: [Nirfast] Change Optical Properties<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<p>Hi Vince<o:p></o:p></p>
<p>Yet another issue of MATLAB not being fully compatible with latest MAC OSand on how MAC OS sets screen resolution.
<o:p></o:p></p>
<p>To set optical properties on command line, you can either run NIRFAST on a different OS to see the commands we use, or just type:<o:p></o:p></p>
<p>help add_blob<o:p></o:p></p>
<p>Regards<o:p></o:p></p>
<p>Hamid<o:p></o:p></p>
<p><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<p class="MsoNormal">On 24/06/2016 18:58, Vincent Kitsmiller wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<div>
<p class="MsoNormal"><span style="font-size:9.5pt">I am having an issue when attempting to change optical properties. When I attempt to change optical properties I get a mostly blank screen like this<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.5pt"><img width="534" height="198" id="_x0000_i1025" src="cid:image001.png@01D1D11A.51CC8D90" alt="nline
image 1"><o:p></o:p></span></p>
<div>
<p class="MsoNormal"><span style="font-size:9.5pt">I don't get any errors however and did see a populated or partially populated screen at some point. I know you can also change optical properties by region with a script or the nirfast command window but I
am not sure how nirfast assigns the region numbers. Thanks in advance for the help.<o:p></o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.5pt"><o:p> </o:p></span></p>
</div>
<div>
<p class="MsoNormal"><span style="font-size:9.5pt">-Vince<o:p></o:p></span></p>
</div>
</div>
</div>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Nirfast mailing list<o:p></o:p></pre>
<pre><a href="mailto:Nirfast@public.kitware.com">Nirfast@public.kitware.com</a><o:p></o:p></pre>
<pre><a href="http://public.kitware.com/mailman/listinfo/nirfast">http://public.kitware.com/mailman/listinfo/nirfast</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>--------------------------<o:p></o:p></pre>
<pre>Hamid Dehghani, PhD, MIPEM<o:p></o:p></pre>
<pre>School of Computer Science<o:p></o:p></pre>
<pre>Acting Director, Physical Sciences for Health Doctoral Training Centre<o:p></o:p></pre>
<pre>University of Birmingham<o:p></o:p></pre>
<pre>B15 2TT<o:p></o:p></pre>
<pre>0121 414 8728 <o:p></o:p></pre>
</div>
</div>
</div>
</body>
</html>