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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 avw2cor</title> <meta name="keywords" content="avw2cor"> <meta name="description" content="avw2cor - converts an avw struct to FreeSurfer COR-* files"> <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> > avw2cor.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>avw2cor</h1><h2><a name="_name"></a>PURPOSE <a href="#_top"><img alt="^" border="0" src="../up.png"></a></h2><div class="box"><strong>avw2cor - converts an avw struct to FreeSurfer COR-* files</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 avw2cor(avw,CORpath) </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"> avw2cor - converts an avw struct to FreeSurfer COR-* files
avw2cor(avw,CORpath)
avw - Analyze volume, see avw_read
CORpath - full path to FreeSurfer directory
This function will translate an 8-bit
uchar AVW file to a series of MGH-style
COR files that also have an 8-bit uchar
datatype.
Example: avw2cor(avw,'/data/subjects/bert/mri/orig')
will use the workspace avw struct and output files
named /data/subjects/bert/mri/orig/COR-[0-256]
However, it is probably best to use the FreeSurfer
command line tool, mri_convert, as it will handle
various datatypes and it will reslice Analyze
volumes that are not 256^3 mm FOV and 1^3 mm
voxels.</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="avw2cor.html" class="code" title="function avw2cor(avw,CORpath)">avw2cor</a> avw2cor - converts an avw struct to FreeSurfer COR-* files</li></ul>This function is called by:<ul style="list-style-image:url(../matlabicon.gif)"><li><a href="avw2cor.html" class="code" title="function avw2cor(avw,CORpath)">avw2cor</a> avw2cor - converts an avw struct to FreeSurfer COR-* files</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 avw2cor(avw,CORpath)</a>0002 0003 <span class="comment">% avw2cor - converts an avw struct to FreeSurfer COR-* files</span>0004 <span class="comment">%</span>0005 <span class="comment">% avw2cor(avw,CORpath)</span>0006 <span class="comment">%</span>0007 <span class="comment">% avw - Analyze volume, see avw_read</span>0008 <span class="comment">%</span>0009 <span class="comment">% CORpath - full path to FreeSurfer directory</span>0010 <span class="comment">%</span>0011 <span class="comment">% This function will translate an 8-bit</span>0012 <span class="comment">% uchar AVW file to a series of MGH-style</span>0013 <span class="comment">% COR files that also have an 8-bit uchar</span>0014 <span class="comment">% datatype.</span>0015 <span class="comment">%</span>0016 <span class="comment">% Example: avw2cor(avw,'/data/subjects/bert/mri/orig')</span>0017 <span class="comment">% will use the workspace avw struct and output files</span>0018 <span class="comment">% named /data/subjects/bert/mri/orig/COR-[0-256]</span>0019 <span class="comment">%</span>0020 <span class="comment">% However, it is probably best to use the FreeSurfer</span>0021 <span class="comment">% command line tool, mri_convert, as it will handle</span>0022 <span class="comment">% various datatypes and it will reslice Analyze</span>0023 <span class="comment">% volumes that are not 256^3 mm FOV and 1^3 mm</span>0024 <span class="comment">% voxels.</span>0025 <span class="comment">%</span>0026 0027 <span class="comment">% An AFNI BRIK volume may be formed from the resulting</span>0028 <span class="comment">% COR files by using the AFNI command:</span>0029 <span class="comment">% to3d -anat -prefix raw -session $SUBJECTS_DIR/$subjname/afni \</span>0030 <span class="comment">% -view orig -datum byte -orient LSP \</span>0031 <span class="comment">% $SUBJECTS_DIR/$subjname/mri/orig/COR-\[0-256]\*</span>0032 0033 0034 <span class="comment">% $Revision: 1.3 $ $Date: 2004/02/07 01:41:51 $</span>0035 0036 <span class="comment">% Licence: GNU GPL, no express or implied warranties</span>0037 <span class="comment">% History: 1/21/99: Timothy M. Ellmore, LBC/NIMH</span>0038 <span class="comment">% Aug 2003, Darren.Weber_at_radiology.ucsf.edu</span>0039 <span class="comment">% Adapted to mri_toolbox</span>0040 <span class="comment">%</span>0041 <span class="comment">%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</span>0042 0043 version = <span class="string">'[$Revision: 1.3 $]'</span>;0044 fprintf(<span class="string">'\nAVW2COR [v%s]\n'</span>,version(12:16)); tic;0045 0046 <span class="keyword">if</span> ~exist(<span class="string">'avw'</span>,<span class="string">'var'</span>),0047 doc <a href="avw2cor.html" class="code" title="function avw2cor(avw,CORpath)">avw2cor</a>;0048 msg = sprintf(<span class="string">'...no input avw\n'</span>);0049 error(msg);0050 <span class="keyword">elseif</span> isempty(avw),0051 doc <a href="avw2cor.html" class="code" title="function avw2cor(avw,CORpath)">avw2cor</a>;0052 msg = sprintf(<span class="string">'...empty input avw\n'</span>);0053 error(msg);0054 <span class="keyword">end</span>0055 0056 <span class="comment">% MGH COR files have these dimensions</span>0057 xdim = 256;0058 ydim = 256;0059 zdim = 256;0060 0061 <span class="comment">% datatype is always 8-bit uchar for MGH COR files</span>0062 type = <span class="string">'uchar'</span>;0063 0064 <span class="comment">% this function used to read in an avwfile, but</span>0065 <span class="comment">% it now takes a workspace avw struct, so the</span>0066 <span class="comment">% conversion process requires avw_read first</span>0067 <span class="comment">%avw = avw_read(AVWfile);</span>0068 0069 0070 <span class="comment">% check that avw.img is the right dimensions</span>0071 dim = avw.hdr.dime.dim(2:4);0072 <span class="keyword">if</span> (dim(1) == xdim) & (dim(2) == ydim) & (dim(3) == zdim),0073 <span class="comment">% OK we have the right dimensions</span>0074 <span class="keyword">else</span>0075 <span class="comment">%should try to reslice the volume, but not sure if</span>0076 <span class="comment">%this works properly, as meshgrid is a strange beast.</span>0077 <span class="comment">%[xi,yi,zi] = meshgrid(1:1:256,1:1:256,1:1:256);</span>0078 <span class="comment">%reslice = interp3(avw.img,xi,yi,zi);</span>0079 error(<span class="string">'...avw.img is not 256x256x256 voxels, reslice it.\n'</span>);0080 <span class="keyword">end</span>0081 0082 0083 <span class="comment">% extract sliceplanes and write COR files</span>0084 0085 <span class="keyword">for</span> i = 1:ydim,0086 0087 <span class="comment">% COR files are coronal slices, so we assume</span>0088 <span class="comment">% the analyze file was read correctly by avw_read</span>0089 <span class="comment">% and we use the ydim to loop over coronal slices</span>0090 0091 <span class="comment">% create zero sliceplane</span>0092 CORfile = zeros(xdim,zdim);0093 0094 <span class="comment">% extract the current sliceplane</span>0095 CORfile(:,:) = avw.img(:,i,:);0096 0097 <span class="comment">% create the CORfile name</span>0098 CORfname = [CORpath,filesep,sprintf(<span class="string">'COR-%03d'</span>,i)];0099 0100 <span class="keyword">if</span> i > 1,0101 backspaces = repmat(<span class="string">'\b'</span>,1,7);0102 <span class="keyword">else</span>0103 backspaces = <span class="string">''</span>;0104 <span class="keyword">end</span>0105 fprintf([backspaces,<span class="string">'%s image.'</span>],sprintf(<span class="string">'COR-%03d'</span>,i));0106 0107 fid = fopen(CORfname, <span class="string">'w'</span>);0108 fwrite(fid, CORfile(:), type);0109 fclose(fid);0110 0111 <span class="keyword">end</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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