COR_IMG_READ - Read Freesurfer format data (COR-001 to COR-256)
[ avw, machine ] = cor_img_read(path, machine)
path - the full path to the COR-??? image files. If empty,
this function uses uigetfile to locate COR-???.
machine - a string, see machineformat in fread for details.
The default here is 'ieee-le' but the routine
will automatically switch between little and big
endian to read any such Analyze header. It
reports the appropriate machine format and can
return the machine value.
This function returns an Analyze data structure, with fields:
avw_hdr - a struct with image data parameters.
avw_img - a 3D matrix of image data (double precision).
See also: AVW_IMAGE_READ, AVW_HEADER_READ0001 function [ avw, machine ] = cor_img_read(path,machine) 0002 0003 % COR_IMG_READ - Read Freesurfer format data (COR-001 to COR-256) 0004 % 0005 % [ avw, machine ] = cor_img_read(path, machine) 0006 % 0007 % path - the full path to the COR-??? image files. If empty, 0008 % this function uses uigetfile to locate COR-???. 0009 % 0010 % machine - a string, see machineformat in fread for details. 0011 % The default here is 'ieee-le' but the routine 0012 % will automatically switch between little and big 0013 % endian to read any such Analyze header. It 0014 % reports the appropriate machine format and can 0015 % return the machine value. 0016 % 0017 % This function returns an Analyze data structure, with fields: 0018 % 0019 % avw_hdr - a struct with image data parameters. 0020 % avw_img - a 3D matrix of image data (double precision). 0021 % 0022 % See also: AVW_IMAGE_READ, AVW_HEADER_READ 0023 % 0024 0025 % $Revision: 1.1 $ $Date: 2004/11/12 01:30:25 $ 0026 0027 % Licence: GNU GPL, no express or implied warranties 0028 % History: 06/2002, Darren.Weber@flinders.edu.au 0029 % 0030 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0031 0032 0033 if ~exist('path','var'), 0034 fprintf('No input path - see help cor_img_read\n'); 0035 [file, path] = uigetfile({'*.*'},'Select COR-001 File'); 0036 end 0037 if ~exist('machine','var'), machine = 'ieee-le'; end 0038 0039 [path,name,ext] = fileparts(strcat(path,filesep,'COR-001')); 0040 file = fullfile(path,[name ext]); 0041 fid = fopen(file,'r',machine); 0042 0043 if fid < 0, 0044 fprintf('Cannot open file %s\n',file); 0045 fclose(fid); 0046 else 0047 fclose(fid); 0048 avw = read_image(path,machine); 0049 end 0050 0051 return 0052 0053 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0054 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0055 function [ avw ] = read_image(path,machine) 0056 0057 0058 % Create the file header, 256^3, 1 mm^3, uchar, etc 0059 avw = avw_hdr_make; 0060 0061 avw.hdr.dime.dim = int16([4 256 256 256 1 0 0 0]); 0062 avw.hdr.dime.pixdim = single([0 1 1 1 0 0 0 0]); 0063 0064 PixelDim = double(avw.hdr.dime.dim(2)); 0065 RowDim = double(avw.hdr.dime.dim(3)); 0066 SliceDim = double(avw.hdr.dime.dim(4)); 0067 0068 % Allocate memory for the image 0069 avw.img = zeros(PixelDim,SliceDim,RowDim); 0070 0071 % Read one file/slice at a time 0072 for y = 1:SliceDim, 0073 0074 file = sprintf('COR-%03d',y); 0075 fprintf('COR_IMAGE_READ: Reading %s %s image.\n',machine,file); 0076 0077 [path,name,ext] = fileparts(strcat(path,filesep,file)); 0078 file = fullfile(path,[name ext]); 0079 0080 % read the whole image into matlab (faster) 0081 fid = fopen(file,'r',machine); fseek(fid,0,'bof'); 0082 tmp = fread(fid,inf,'uchar=>double'); 0083 fclose(fid); 0084 0085 % Arrange image into avw.img xyz matrix 0086 % For Freesurfer COR files the voxels are stored with 0087 % Pixels in 'x' axis (varies fastest) - from patient right to left 0088 % Rows in 'z' axis - from patient superior to inferior 0089 % Slices in 'y' axis - from patient posterior to anterior 0090 0091 n = 1; 0092 for z = RowDim:-1:1, 0093 x = 1:PixelDim; 0094 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0095 n = n + PixelDim; 0096 end 0097 end 0098 0099 0100 avw.hdr.hist.orient = 0; 0101 0102 return