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<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/REC-html40/loose.dtd"><html><head> <title>Description of mesh_3shell_script</title> <meta name="keywords" content="mesh_3shell_script"> <meta name="description" content="mesh_3shell_script"> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta name="generator" content="m2html © 2003 Guillaume Flandin"> <meta name="robots" content="index, follow"> <link type="text/css" rel="stylesheet" href="../m2html.css"></head><body><a name="_top"></a><div><a href="../index.html">Home</a> > <a href="index.html">mri_toolbox</a> > mesh_3shell_script.m</div><!--<table width="100%"><tr><td align="left"><a href="../index.html"><img alt="<" border="0" src="../left.png"> Master index</a></td><td align="right"><a href="index.html">Index for mri_toolbox <img alt=">" border="0" src="../right.png"></a></td></tr></table>--><h1>mesh_3shell_script</h1><h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2><div class="box"><strong>mesh_3shell_script</strong></div><h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2><div class="box"><strong>This is a script file. </strong></div><h2><a name="_description"></a>DESCRIPTION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2><div class="fragment"><pre class="comment"> mesh_3shell_script
Assumes preprocessing of MRI with
FreeSurfer http://surfer.nmr.mgh.harvard.edu/
FSL tools (BET & FAST) http://fmrib.ox.ac.uk/
An example FSL script can be found at the end of this script</pre></div><!-- crossreference --><h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2>This function calls:<ul style="list-style-image:url(../matlabicon.gif)"><li><a href="avw_img_read.html" class="code" title="function [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine)">avw_img_read</a> avw_img_read - read Analyze format data image (*.img)</li><li><a href="avw_shrinkwrap.html" class="code" title="function [FV, Edges] = avw_shrinkwrap(avw,FV,interpVal,fitval,fittol,fititer,fitchange,fitvattr)">avw_shrinkwrap</a> avw_shrinkwrap - Tesselate the surface of a 3D Analyze 7.5 avw struct</li></ul>This function is called by:<ul style="list-style-image:url(../matlabicon.gif)"></ul><!-- crossreference --><h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2><div class="fragment"><pre>0001 0002 <span class="comment">% mesh_3shell_script</span>0003 <span class="comment">%</span>0004 <span class="comment">% Assumes preprocessing of MRI with</span>0005 <span class="comment">% FreeSurfer http://surfer.nmr.mgh.harvard.edu/</span>0006 <span class="comment">% FSL tools (BET & FAST) http://fmrib.ox.ac.uk/</span>0007 <span class="comment">%</span>0008 <span class="comment">% An example FSL script can be found at the end of this script</span>0009 <span class="comment">%</span>0010 0011 <span class="comment">% Licence: GNU GPL, no implied or express warranties</span>0012 <span class="comment">% History: 08/2002, Darren.Weber@flinders.edu.au</span>0013 <span class="comment">% 08/2003, Darren.Weber_at_radiology.ucsf.edu</span>0014 <span class="comment">% added more control variables and the FSL script</span>0015 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>0016 0017 plot = 0;0018 0019 doScalp = 0;0020 doIskull = 0;0021 doOskull = 0;0022 doCortex = 0;0023 0024 doCorrection = 0;0025 0026 doOutputEMSE = 0;0027 doOutputBrainStorm = 1;0028 0029 0030 <span class="comment">%IMG.path = 'D:\freesurfer\subjects\ucsf_morgan\mri\analyze';</span>0031 IMG.path = <span class="string">'/data/ucsf/mri/ucsf_morgan/mri/analyze'</span>;0032 IMG.meshpath = <span class="string">'/data/ucsf/mri/ucsf_morgan/surf'</span>;0033 0034 IMG.scalp = <span class="string">'morgan_orig_axial_las_smooth'</span>;0035 IMG.oskull = <span class="string">'morgan_orig_axial_las_skull'</span>;0036 IMG.iskull = <span class="string">'morgan_orig_axial_las_brain'</span>;0037 0038 IMG.intensity.scalp = 60;0039 IMG.tolerance.scalp = 20;0040 IMG.intensity.oskull = 15;0041 IMG.tolerance.oskull = 10;0042 IMG.intensity.iskull = 80;0043 IMG.tolerance.iskull = 40;0044 0045 0046 0047 <span class="keyword">if</span> ~exist(<span class="string">'p'</span>,<span class="string">'var'</span>),0048 p = eeg_toolbox_defaults;0049 <span class="keyword">end</span>0050 0051 <span class="keyword">if</span> plot,0052 0053 <span class="comment">% plot scalp surface (index 4), in red</span>0054 <span class="keyword">if</span> ~isempty(p.mesh.data.vertices{4}),0055 patch(<span class="string">'vertices'</span>,p.mesh.data.vertices{4},<span class="string">'faces'</span>,p.mesh.data.faces{4},<span class="keyword">...</span>0056 <span class="string">'FaceColor'</span>,[.6 0 0],<span class="string">'Edgecolor'</span>,<span class="string">'none'</span>,<span class="string">'FaceAlpha'</span>,.2);0057 <span class="keyword">end</span>0058 <span class="comment">% plot outer skull surface (index 3), in green</span>0059 <span class="keyword">if</span> ~isempty(p.mesh.data.vertices{3}),0060 patch(<span class="string">'vertices'</span>,p.mesh.data.vertices{3},<span class="string">'faces'</span>,p.mesh.data.faces{3},<span class="keyword">...</span>0061 <span class="string">'FaceColor'</span>,[.0 .6 .0],<span class="string">'Edgecolor'</span>,[.8 .8 .8],<span class="string">'FaceAlpha'</span>,.4);0062 <span class="keyword">end</span>0063 <span class="comment">% plot inner skull surface (index 2), in blue</span>0064 <span class="keyword">if</span> ~isempty(p.mesh.data.vertices{2}),0065 patch(<span class="string">'vertices'</span>,p.mesh.data.vertices{2},<span class="string">'faces'</span>,p.mesh.data.faces{2},<span class="keyword">...</span>0066 <span class="string">'FaceColor'</span>,[.0 .0 .6],<span class="string">'Edgecolor'</span>,[.8 .8 .8],<span class="string">'FaceAlpha'</span>,.6);0067 <span class="keyword">end</span>0068 <span class="comment">% plot cortex surface (index 1), in black</span>0069 <span class="keyword">if</span> ~isempty(p.mesh.data.vertices{1}),0070 patch(<span class="string">'vertices'</span>,p.mesh.data.vertices{1},<span class="string">'faces'</span>,p.mesh.data.faces{1},<span class="keyword">...</span>0071 <span class="string">'FaceColor'</span>,[.0 .0 .0],<span class="string">'Edgecolor'</span>,[.8 .8 .8],<span class="string">'FaceAlpha'</span>,1);0072 <span class="keyword">end</span>0073 0074 camlight; mouse_rotate;0075 axis tight; hold on0076 0077 <span class="comment">% FV = ISkull;</span>0078 <span class="comment">% patch('vertices',FV.vertices,'faces',FV.faces,'FaceColor',[.6 .0 .0],'Edgecolor','none','FaceAlpha',.2); axis tight; hold on</span>0079 <span class="comment">% x = FV.vertices(1,1);</span>0080 <span class="comment">% y = FV.vertices(1,2);</span>0081 <span class="comment">% z = FV.vertices(1,3);</span>0082 <span class="comment">% plot3(x,y,z,'ro')</span>0083 <span class="comment">%</span>0084 <span class="keyword">return</span>0085 <span class="keyword">end</span>0086 0087 0088 0089 <span class="comment">% TESSELATE SKULL/SCALP SURFACES</span>0090 0091 0092 <span class="comment">% Image files to process</span>0093 0094 <span class="comment">% These images were created with the freesurfer mri_convert command, eg:</span>⌨️ 快捷键说明
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