avw_read - read Analyze format data image (*.img)
[ avw, machine ] = avw_read([fileprefix], [orient], [machine])
This function calls avw_hdr_read and avw_img_read, providing
just a slightly easier command line function call.
fileprefix - a string, the filename without the .img extension.
A gui prompt appears if this argument is missing.
orient - read a specified orientation, integer values:
'', use header history orient field
0, transverse unflipped (LAS*)
1, coronal unflipped (LA*S)
2, sagittal unflipped (L*AS)
3, transverse flipped (LPS*)
4, coronal flipped (LA*I)
5, sagittal flipped (L*AI)
where * follows the slice dimension and letters indicate +XYZ
orientations (L left, R right, A anterior, P posterior,
I inferior, & S superior).
It is rare, but a dataset might be stored in the 3-5
orientations. For more information about orientation, see the
documentation in the mri_toolbox doc directory and the
extensive comments in avw_img_read and avw_hdr_read.
See also the avw_flip function for any orthogonal
reorientation (although this should not be necessary
and must be done with great care, try not to invalidate
the Analyze orientation specifications).
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.
Returned values:
avw.hdr - a struct with image data parameters.
avw.img - a 3D matrix of image data (double precision).
All going well, the returned 3D matrix in avw.img will
correspond with the default ANALYZE coordinate system,
which is a Left-handed coordinate system (radiological
orientation):
X-Y plane is Transverse/Axial
X-Z plane is Coronal
Y-Z plane is Sagittal
X axis runs from patient Right (low X) to patient Left (high X)
Y axis runs from Posterior (low Y) to Anterior (high Y)
Z axis runs from Inferior (low Z) to Superior (high Z)
See also: avw_hdr_read, avw_img_read (both called by this function),
avw_write, avw_img_write, avw_hdr_write,
avw_view, avw_flip0001 function [ avw, machine ] = avw_read(fileprefix,IMGorient,machine) 0002 0003 % avw_read - read Analyze format data image (*.img) 0004 % 0005 % [ avw, machine ] = avw_read([fileprefix], [orient], [machine]) 0006 % 0007 % This function calls avw_hdr_read and avw_img_read, providing 0008 % just a slightly easier command line function call. 0009 % 0010 % fileprefix - a string, the filename without the .img extension. 0011 % A gui prompt appears if this argument is missing. 0012 % 0013 % orient - read a specified orientation, integer values: 0014 % 0015 % '', use header history orient field 0016 % 0, transverse unflipped (LAS*) 0017 % 1, coronal unflipped (LA*S) 0018 % 2, sagittal unflipped (L*AS) 0019 % 3, transverse flipped (LPS*) 0020 % 4, coronal flipped (LA*I) 0021 % 5, sagittal flipped (L*AI) 0022 % 0023 % where * follows the slice dimension and letters indicate +XYZ 0024 % orientations (L left, R right, A anterior, P posterior, 0025 % I inferior, & S superior). 0026 % 0027 % It is rare, but a dataset might be stored in the 3-5 0028 % orientations. For more information about orientation, see the 0029 % documentation in the mri_toolbox doc directory and the 0030 % extensive comments in avw_img_read and avw_hdr_read. 0031 % See also the avw_flip function for any orthogonal 0032 % reorientation (although this should not be necessary 0033 % and must be done with great care, try not to invalidate 0034 % the Analyze orientation specifications). 0035 % 0036 % machine - a string, see machineformat in fread for details. 0037 % The default here is 'ieee-le' but the routine 0038 % will automatically switch between little and big 0039 % endian to read any such Analyze header. It 0040 % reports the appropriate machine format and can 0041 % return the machine value. 0042 % 0043 % Returned values: 0044 % 0045 % avw.hdr - a struct with image data parameters. 0046 % avw.img - a 3D matrix of image data (double precision). 0047 % 0048 % All going well, the returned 3D matrix in avw.img will 0049 % correspond with the default ANALYZE coordinate system, 0050 % which is a Left-handed coordinate system (radiological 0051 % orientation): 0052 % 0053 % X-Y plane is Transverse/Axial 0054 % X-Z plane is Coronal 0055 % Y-Z plane is Sagittal 0056 % 0057 % X axis runs from patient Right (low X) to patient Left (high X) 0058 % Y axis runs from Posterior (low Y) to Anterior (high Y) 0059 % Z axis runs from Inferior (low Z) to Superior (high Z) 0060 % 0061 % See also: avw_hdr_read, avw_img_read (both called by this function), 0062 % avw_write, avw_img_write, avw_hdr_write, 0063 % avw_view, avw_flip 0064 % 0065 0066 0067 % $Revision: 1332 $ $Date:: 2011-02-24 15:57:20 +0900#$ 0068 0069 % Licence: GNU GPL, no express or implied warranties 0070 % History: 07/2003, Darren.Weber_at_radiology.ucsf.edu 0071 % The Analyze format is copyright 0072 % (c) Copyright, 1986-1995 0073 % Biomedical Imaging Resource, Mayo Foundation 0074 % - created this wrapper for avw_img_read, see 0075 % that function for extensive comments 0076 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0077 0078 if ~exist('fileprefix','var'), 0079 [fileprefix, pathname, filterindex] = uigetfile('*.hdr','locate an Analyze .hdr file'); 0080 if pathname, cd(pathname); end 0081 if ~fileprefix, 0082 error('no .hdr file specified'); 0083 end 0084 end 0085 if ~exist('IMGorient','var'), IMGorient = ''; end 0086 if ~exist('machine','var'), machine = 'ieee-le'; end 0087 0088 if findstr('.hdr',fileprefix), 0089 fileprefix = strrep(fileprefix,'.hdr',''); 0090 end 0091 if findstr('.img',fileprefix), 0092 fileprefix = strrep(fileprefix,'.img',''); 0093 end 0094 0095 % MAIN 0096 0097 fid = fopen(sprintf('%s.img',fileprefix),'r',machine); 0098 if fid < 0, 0099 msg = sprintf('...cannot open file %s.img\n\n',fileprefix); 0100 error(msg); 0101 else 0102 % avw_img_read will call avw_hdr_read also 0103 avw = avw_img_read(fileprefix,IMGorient,machine); 0104 end 0105 0106 return