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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 mri_open</title> <meta name="keywords" content="mri_open"> <meta name="description" content="mri_open - function to call various mri data tools"> <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> > mri_open.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>mri_open</h1><h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2><div class="box"><strong>mri_open - function to call various mri data tools</strong></div><h2><a name="_synopsis"></a>SYNOPSIS <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2><div class="box"><strong>function [mri] = mri_open(mri) </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"> mri_open - function to call various mri data tools
Useage: [mri] = mri_open(mri)
mri is a parameter structure (see mri_toolbox_defaults for
more details). In this function, it should contain at least
the following string fields:
mri.path - the directory location of the file to load
mri.file - the name of the file to load
mri.type - the file format (Analyze, FreeSurfer)
Analyze is documented in avw_read etc.
FreeSurfer: http://surfer.nmr.mgh.harvard.edu/
The return structure creates or updates mri.data, which contains:
mri.data.hdr struct, eg see avw_hdr_read
mri.data.img 3D matrix of image values
To plot the data returned, set mri.plot = 1 before loading, or use:
avw_view(mri.data)
See also, <a href="avw_img_read.html" class="code" title="function [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine)">avw_img_read</a>, <a href="cor_img_read.html" class="code" title="function [ avw, machine ] = cor_img_read(path,machine)">cor_img_read</a>, <a href="avw_view.html" class="code" title="function [ varargout ] = avw_view(avw,parent,command),">avw_view</a></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_read.html" class="code" title="function [ avw, machine ] = avw_read(fileprefix,IMGorient,machine)">avw_read</a> avw_read - read Analyze format data image (*.img)</li><li><a href="avw_view.html" class="code" title="function [ varargout ] = avw_view(avw,parent,command),">avw_view</a> avw_view - create and navigate ortho views of Analyze 7.5 volume</li><li><a href="cor_img_read.html" class="code" title="function [ avw, machine ] = cor_img_read(path,machine)">cor_img_read</a> COR_IMG_READ - Read Freesurfer format data (COR-001 to COR-256)</li><li><a href="ge_series_read.html" class="code" title="function [ ge, lastfile ] = ge_series_read(examPath, series)">ge_series_read</a> ge_series_read - reads a volume of images from a GE series</li><li><a href="mri_toolbox_defaults.html" class="code" title="function [mri] = mri_toolbox_defaults(command,mri);">mri_toolbox_defaults</a> mri_toolbox_defaults - Create, read, write mri_toolbox defaults</li></ul>This function is called by:<ul style="list-style-image:url(../matlabicon.gif)"><li><a href="convert_mri2brainstorm.html" class="code" title="">convert_mri2brainstorm</a> Script to convert freesurfer analyze files into brainstorm format</li><li><a href="gui_avw_open.html" class="code" title="function [mri] = gui_avw_open(mri,command,parent)">gui_avw_open</a> gui_avw_open - Load & Display Analyze 7.5 data</li><li><a href="gui_cor_open.html" class="code" title="function [mri] = gui_cor_open(mri,command,parent)">gui_cor_open</a> gui_cor_open - Load & Display FreeSurfer COR-??? data</li><li><a href="gui_ge_open.html" class="code" title="function [mri] = gui_ge_open(mri,command,parent)">gui_ge_open</a> gui_ge_open - Load & Display MRI data</li><li><a href="gui_mri_open.html" class="code" title="function [mri] = gui_mri_open(mri,command,parent)">gui_mri_open</a> gui_mri_open - Load & Display MRI data</li></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 <a name="_sub0" href="#_subfunctions" class="code">function [mri] = mri_open(mri)</a>0002 0003 <span class="comment">% mri_open - function to call various mri data tools</span>0004 <span class="comment">%</span>0005 <span class="comment">% Useage: [mri] = mri_open(mri)</span>0006 <span class="comment">%</span>0007 <span class="comment">% mri is a parameter structure (see mri_toolbox_defaults for</span>0008 <span class="comment">% more details). In this function, it should contain at least</span>0009 <span class="comment">% the following string fields:</span>0010 <span class="comment">%</span>0011 <span class="comment">% mri.path - the directory location of the file to load</span>0012 <span class="comment">% mri.file - the name of the file to load</span>0013 <span class="comment">% mri.type - the file format (Analyze, FreeSurfer)</span>0014 <span class="comment">%</span>0015 <span class="comment">% Analyze is documented in avw_read etc.</span>0016 <span class="comment">% FreeSurfer: http://surfer.nmr.mgh.harvard.edu/</span>0017 <span class="comment">%</span>0018 <span class="comment">% The return structure creates or updates mri.data, which contains:</span>0019 <span class="comment">%</span>0020 <span class="comment">% mri.data.hdr struct, eg see avw_hdr_read</span>0021 <span class="comment">% mri.data.img 3D matrix of image values</span>0022 <span class="comment">%</span>0023 <span class="comment">% To plot the data returned, set mri.plot = 1 before loading, or use:</span>0024 <span class="comment">%</span>0025 <span class="comment">% avw_view(mri.data)</span>0026 <span class="comment">%</span>0027 <span class="comment">% See also, avw_img_read, cor_img_read, avw_view</span>0028 <span class="comment">%</span>0029 0030 <span class="comment">% $Revision: 1.2 $ $Date: 2004/02/07 01:41:51 $</span>0031 0032 <span class="comment">% Licence: GNU GPL, no express or implied warranties</span>0033 <span class="comment">% History: 08/2002, Darren.Weber@flinders.edu.au</span>0034 <span class="comment">% 11/2002, Darren.Weber@flinders.edu.au</span>0035 <span class="comment">% corrected some bugs and mistakes on mri.type</span>0036 <span class="comment">%</span>0037 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>0038 0039 version = <span class="string">'$Revision: 1.2 $'</span>;0040 fprintf(<span class="string">'MRI_OPEN [v %s]\n'</span>,version(11:15));0041 0042 <span class="keyword">if</span> ~exist(<span class="string">'mri'</span>,<span class="string">'var'</span>),0043 mri = <a href="mri_toolbox_defaults.html" class="code" title="function [mri] = mri_toolbox_defaults(command,mri);">mri_toolbox_defaults</a>;0044 fprintf(<span class="string">'...creating default mri structure.\n'</span>);0045 <span class="keyword">elseif</span> isempty(mri),0046 mri = <a href="mri_toolbox_defaults.html" class="code" title="function [mri] = mri_toolbox_defaults(command,mri);">mri_toolbox_defaults</a>;0047 fprintf(<span class="string">'...creating default p structure.\n'</span>);0048 <span class="keyword">end</span>0049 0050 [path,name,ext] = fileparts(strcat(mri.path,filesep,mri.file));0051 file = fullfile(path,[name ext]);0052 0053 type = lower(mri.type);0054 0055 <span class="keyword">switch</span> type,0056 0057 <span class="keyword">case</span> <span class="string">'analyze'</span>,0058 0059 fprintf(<span class="string">'...loading Analyze MRI from:\n... %s\n\n'</span>,file);0060 0061 <span class="comment">% see avw_img_read for details about orientation</span>0062 <span class="keyword">switch</span> mri.orient0063 <span class="keyword">case</span> <span class="string">'auto'</span>, mriOrient = <span class="string">''</span>;0064 <span class="keyword">case</span> <span class="string">'axial unflipped'</span>, mriOrient = 0;0065 <span class="keyword">case</span> <span class="string">'coronal unflipped'</span>, mriOrient = 1;0066 <span class="keyword">case</span> <span class="string">'sagittal unflipped'</span>, mriOrient = 2;0067 <span class="keyword">case</span> <span class="string">'axial flipped'</span>, mriOrient = 3;0068 <span class="keyword">case</span> <span class="string">'coronal flipped'</span>, mriOrient = 4;0069 <span class="keyword">case</span> <span class="string">'sagittal flipped'</span>, mriOrient = 5;0070 <span class="keyword">otherwise</span>, mriOrient = <span class="string">''</span>;0071 <span class="keyword">end</span>0072 0073 [ mri.data, mri.IEEEMachine ] = <a href="avw_read.html" class="code" title="function [ avw, machine ] = avw_read(fileprefix,IMGorient,machine)">avw_read</a>(file, mriOrient, mri.IEEEMachine);0074 0075 <span class="keyword">case</span> <span class="string">'brainstorm'</span>,0076 0077 fprintf(<span class="string">'...BrainStorm not supported yet\n\n'</span>);0078 <span class="keyword">return</span>0079 <span class="comment">%fprintf('...loading BrainStorm data from:\n... %s\n',file);</span>0080 0081 <span class="keyword">case</span> {<span class="string">'cor'</span>,<span class="string">'freesurfer'</span>,<span class="string">'freesurfer cor'</span>},0082 0083 <span class="comment">% Get Freesurfer data</span>0084 [ mri.data, mri.IEEEMachine ] = <a href="cor_img_read.html" class="code" title="function [ avw, machine ] = cor_img_read(path,machine)">cor_img_read</a>(path, mri.IEEEMachine);0085 0086 <span class="keyword">case</span> <span class="string">'ge'</span>,0087 0088 <span class="comment">% extract series number from path</span>0089 separators = findstr(mri.path,filesep);0090 seriesPath = mri.path(1:separators(end-1)-1);0091 seriesN = mri.path(separators(end-1)+1:separators(end)-1);0092 0093 <span class="comment">% Get GE data</span>0094 [ mri.data, mri.IEEEMachine ] = <a href="ge_series_read.html" class="code" title="function [ ge, lastfile ] = ge_series_read(examPath, series)">ge_series_read</a>(seriesPath, seriesN);0095 <span class="keyword">if</span> mri.plot,0096 fprintf(<span class="string">'...cannot plot GE data as yet, use ge_series2avw and avw_view\n'</span>);0097 mri.plot = 0;0098 <span class="keyword">end</span>0099 0100 <span class="keyword">otherwise</span>,0101 fprintf(<span class="string">'...MRI format: %s\n'</span>, mri.type);0102 fprintf(<span class="string">'...Sorry, cannot load this data format at present.\n\n'</span>);0103 <span class="keyword">return</span>;0104 <span class="keyword">end</span>0105 0106 <span class="keyword">if</span> mri.plot,0107 <a href="avw_view.html" class="code" title="function [ varargout ] = avw_view(avw,parent,command),">avw_view</a>(mri.data);0108 <span class="keyword">end</span>0109 0110 <span class="keyword">return</span></pre></div><hr><address>Generated on Fri 21-May-2004 12:38:21 by <strong><a href="http://www.artefact.tk/software/matlab/m2html/">m2html</a></strong> © 2003</address></body></html>⌨️ 快捷键说明
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