avw_img_read - read Analyze format data image (*.img)
[ avw, machine ] = avw_img_read(fileprefix,[orient],[machine],[verbose])
fileprefix - a string, the filename without the .img extension
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).
Some files may contain data in the 3-5 orientations, but this
is unlikely. For more information about orientation, see the
documentation at the end of this .m file. See also the
AVW_FLIP function for orthogonal reorientation.
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.
verbose - the default is to output processing information to the command
window. If verbose = 0, this will not happen.
Returned values:
avw.hdr - a struct with image data parameters.
avw.img - a 3D matrix of image data (double precision).
A returned 3D matrix will correspond with the
default ANALYZE coordinate system, which
is Left-handed:
X-Y plane is Transverse
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)
The function can read a 4D Analyze volume, but only if it is in the
axial unflipped orientation.
See also: avw_hdr_read (called by this function),
avw_view, avw_write, avw_img_write, avw_flip0001 function [ avw, machine ] = avw_img_read(fileprefix,IMGorient,machine,verbose) 0002 0003 % avw_img_read - read Analyze format data image (*.img) 0004 % 0005 % [ avw, machine ] = avw_img_read(fileprefix,[orient],[machine],[verbose]) 0006 % 0007 % fileprefix - a string, the filename without the .img extension 0008 % 0009 % orient - read a specified orientation, integer values: 0010 % 0011 % '', use header history orient field 0012 % 0, transverse unflipped (LAS*) 0013 % 1, coronal unflipped (LA*S) 0014 % 2, sagittal unflipped (L*AS) 0015 % 3, transverse flipped (LPS*) 0016 % 4, coronal flipped (LA*I) 0017 % 5, sagittal flipped (L*AI) 0018 % 0019 % where * follows the slice dimension and letters indicate +XYZ 0020 % orientations (L left, R right, A anterior, P posterior, 0021 % I inferior, & S superior). 0022 % 0023 % Some files may contain data in the 3-5 orientations, but this 0024 % is unlikely. For more information about orientation, see the 0025 % documentation at the end of this .m file. See also the 0026 % AVW_FLIP function for orthogonal reorientation. 0027 % 0028 % machine - a string, see machineformat in fread for details. 0029 % The default here is 'ieee-le' but the routine 0030 % will automatically switch between little and big 0031 % endian to read any such Analyze header. It 0032 % reports the appropriate machine format and can 0033 % return the machine value. 0034 % 0035 % verbose - the default is to output processing information to the command 0036 % window. If verbose = 0, this will not happen. 0037 % 0038 % Returned values: 0039 % 0040 % avw.hdr - a struct with image data parameters. 0041 % avw.img - a 3D matrix of image data (double precision). 0042 % 0043 % A returned 3D matrix will correspond with the 0044 % default ANALYZE coordinate system, which 0045 % is Left-handed: 0046 % 0047 % X-Y plane is Transverse 0048 % X-Z plane is Coronal 0049 % Y-Z plane is Sagittal 0050 % 0051 % X axis runs from patient right (low X) to patient Left (high X) 0052 % Y axis runs from posterior (low Y) to Anterior (high Y) 0053 % Z axis runs from inferior (low Z) to Superior (high Z) 0054 % 0055 % The function can read a 4D Analyze volume, but only if it is in the 0056 % axial unflipped orientation. 0057 % 0058 % See also: avw_hdr_read (called by this function), 0059 % avw_view, avw_write, avw_img_write, avw_flip 0060 % 0061 0062 0063 % $Revision: 1.1 $ $Date: 2004/11/12 01:30:25 $ 0064 0065 % Licence: GNU GPL, no express or implied warranties 0066 % History: 05/2002, Darren.Weber@flinders.edu.au 0067 % The Analyze format is copyright 0068 % (c) Copyright, 1986-1995 0069 % Biomedical Imaging Resource, Mayo Foundation 0070 % 01/2003, Darren.Weber@flinders.edu.au 0071 % - adapted for matlab v5 0072 % - revised all orientation information and handling 0073 % after seeking further advice from AnalyzeDirect.com 0074 % 03/2003, Darren.Weber@flinders.edu.au 0075 % - adapted for -ve pixdim values (non standard Analyze) 0076 % 07/2004, chodkowski@kennedykrieger.org, added ability to 0077 % read volumes with dimensionality greather than 3. 0078 % a >3D volume cannot be flipped. and error is thrown if a volume of 0079 % greater than 3D (ie, avw.hdr.dime.dim(1) > 3) requests a data flip 0080 % (ie, avw.hdr.hist.orient ~= 0 ). i pulled the transfer of read-in 0081 % data (tmp) to avw.img out of any looping mechanism. looping is not 0082 % necessary as the data is already in its correct orientation. using 0083 % 'reshape' rather than looping should be faster but, more importantly, 0084 % it allows the reading in of N-D volumes. See lines 270-280. 0085 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0086 0087 if ~exist('IMGorient','var'), IMGorient = ''; end 0088 if ~exist('machine','var'), machine = 'ieee-le'; end 0089 if ~exist('verbose','var'), verbose = 1; end 0090 0091 if isempty(IMGorient), IMGorient = ''; end 0092 if isempty(machine), machine = 'ieee-le'; end 0093 if isempty(verbose), verbose = 1; end 0094 0095 if ~exist('fileprefix','var'), 0096 msg = sprintf('...no input fileprefix - see help avw_img_read\n\n'); 0097 error(msg); 0098 end 0099 if findstr('.hdr',fileprefix), 0100 fileprefix = strrep(fileprefix,'.hdr',''); 0101 end 0102 if findstr('.img',fileprefix), 0103 fileprefix = strrep(fileprefix,'.img',''); 0104 end 0105 0106 % MAIN 0107 0108 % Read the file header 0109 [ avw, machine ] = avw_hdr_read(fileprefix,machine,verbose); 0110 0111 avw = read_image(avw,IMGorient,machine,verbose); 0112 0113 return 0114 0115 0116 0117 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0118 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0119 function [ avw ] = read_image(avw,IMGorient,machine,verbose) 0120 0121 fid = fopen(sprintf('%s.img',avw.fileprefix),'r',machine); 0122 if fid < 0, 0123 msg = sprintf('...cannot open file %s.img\n\n',avw.fileprefix); 0124 error(msg); 0125 end 0126 0127 if verbose, 0128 ver = '[$Revision: 1.1 $]'; 0129 fprintf('\nAVW_IMG_READ [v%s]\n',ver(12:16)); tic; 0130 end 0131 0132 % short int bitpix; /* Number of bits per pixel; 1, 8, 16, 32, or 64. */ 0133 % short int datatype /* Datatype for this image set */ 0134 % /*Acceptable values for datatype are*/ 0135 % #define DT_NONE 0 0136 % #define DT_UNKNOWN 0 /*Unknown data type*/ 0137 % #define DT_BINARY 1 /*Binary ( 1 bit per voxel)*/ 0138 % #define DT_UNSIGNED_CHAR 2 /*Unsigned character ( 8 bits per voxel)*/ 0139 % #define DT_SIGNED_SHORT 4 /*Signed short (16 bits per voxel)*/ 0140 % #define DT_SIGNED_INT 8 /*Signed integer (32 bits per voxel)*/ 0141 % #define DT_FLOAT 16 /*Floating point (32 bits per voxel)*/ 0142 % #define DT_COMPLEX 32 /*Complex (64 bits per voxel; 2 floating point numbers)/* 0143 % #define DT_DOUBLE 64 /*Double precision (64 bits per voxel)*/ 0144 % #define DT_RGB 128 /*A Red-Green-Blue datatype*/ 0145 % #define DT_ALL 255 /*Undocumented*/ 0146 0147 switch double(avw.hdr.dime.bitpix), 0148 case 1, precision = 'bit1'; 0149 case 8, precision = 'uchar'; 0150 case 16, precision = 'int16'; 0151 case 32, 0152 if isequal(avw.hdr.dime.datatype, 8), precision = 'int32'; 0153 else precision = 'single'; 0154 end 0155 case 64, precision = 'double'; 0156 otherwise, 0157 precision = 'uchar'; 0158 if verbose, fprintf('...precision undefined in header, using ''uchar''\n'); end 0159 end 0160 0161 % read the whole .img file into matlab (faster) 0162 if verbose, 0163 fprintf('...reading %s Analyze %s image format.\n',machine,precision); 0164 end 0165 fseek(fid,0,'bof'); 0166 % adjust for matlab version 0167 ver = version; 0168 ver = str2num(ver(1)); 0169 if ver < 6, 0170 tmp = fread(fid,inf,sprintf('%s',precision)); 0171 else, 0172 tmp = fread(fid,inf,sprintf('%s=>double',precision)); 0173 end 0174 fclose(fid); 0175 0176 % Update the global min and max values 0177 avw.hdr.dime.glmax = max(double(tmp)); 0178 avw.hdr.dime.glmin = min(double(tmp)); 0179 0180 0181 %--------------------------------------------------------------- 0182 % Now partition the img data into xyz 0183 0184 % --- first figure out the size of the image 0185 0186 % short int dim[ ]; /* Array of the image dimensions */ 0187 % 0188 % dim[0] Number of dimensions in database; usually 4. 0189 % dim[1] Image X dimension; number of pixels in an image row. 0190 % dim[2] Image Y dimension; number of pixel rows in slice. 0191 % dim[3] Volume Z dimension; number of slices in a volume. 0192 % dim[4] Time points; number of volumes in database. 0193 0194 PixelDim = double(avw.hdr.dime.dim(2)); 0195 RowDim = double(avw.hdr.dime.dim(3)); 0196 SliceDim = double(avw.hdr.dime.dim(4)); 0197 TimeDim = double(avw.hdr.dime.dim(5)); 0198 0199 PixelSz = double(avw.hdr.dime.pixdim(2)); 0200 RowSz = double(avw.hdr.dime.pixdim(3)); 0201 SliceSz = double(avw.hdr.dime.pixdim(4)); 0202 TimeSz = double(avw.hdr.dime.pixdim(5)); 0203 0204 0205 0206 0207 % ---- NON STANDARD ANALYZE... 0208 0209 % Some Analyze files have been found to set -ve pixdim values, eg 0210 % the MNI template avg152T1_brain in the FSL etc/standard folder, 0211 % perhaps to indicate flipped orientation? If so, this code below 0212 % will NOT handle the flip correctly! 0213 if PixelSz < 0, 0214 warning('X pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(2))'); 0215 PixelSz = abs(PixelSz); 0216 avw.hdr.dime.pixdim(2) = single(PixelSz); 0217 end 0218 if RowSz < 0, 0219 warning('Y pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(3))'); 0220 RowSz = abs(RowSz); 0221 avw.hdr.dime.pixdim(3) = single(RowSz); 0222 end 0223 if SliceSz < 0, 0224 warning('Z pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(4))'); 0225 SliceSz = abs(SliceSz); 0226 avw.hdr.dime.pixdim(4) = single(SliceSz); 0227 end 0228 0229 % ---- END OF NON STANDARD ANALYZE 0230 0231 0232 0233 0234 0235 % --- check the orientation specification and arrange img accordingly 0236 if ~isempty(IMGorient), 0237 if ischar(IMGorient), 0238 avw.hdr.hist.orient = uint8(str2num(IMGorient)); 0239 else 0240 avw.hdr.hist.orient = uint8(IMGorient); 0241 end 0242 end, 0243 0244 if isempty(avw.hdr.hist.orient), 0245 msg = [ '...unspecified avw.hdr.hist.orient, using default 0\n',... 0246 ' (check image and try explicit IMGorient option).\n']; 0247 fprintf(msg); 0248 avw.hdr.hist.orient = uint8(0); 0249 end 0250 0251 % --- check if the orientation is to be flipped for a volume with more 0252 % --- than 3 dimensions. this logic is currently unsupported so throw 0253 % --- an error. volumes of any dimensionality may be read in *only* as 0254 % --- unflipped, ie, avw.hdr.hist.orient == 0 0255 if ( TimeDim > 1 ) && (avw.hdr.hist.orient ~= 0 ), 0256 msg = [ 'ERROR: This volume has more than 3 dimensions *and* ', ... 0257 'requires flipping the data. Flipping is not supported ', ... 0258 'for volumes with dimensionality greater than 3. Set ', ... 0259 'avw.hdr.hist.orient = 0 and flip your volume after ', ... 0260 'calling this function' ]; 0261 msg = sprintf( '%s (%s).', msg, mfilename ); 0262 error( msg ); 0263 end 0264 0265 switch double(avw.hdr.hist.orient), 0266 0267 case 0, % transverse unflipped 0268 0269 % orient = 0: The primary orientation of the data on disk is in the 0270 % transverse plane relative to the object scanned. Most commonly, the fastest 0271 % moving index through the voxels that are part of this transverse image would 0272 % span the right-left extent of the structure imaged, with the next fastest 0273 % moving index spanning the posterior-anterior extent of the structure. This 0274 % 'orient' flag would indicate to Analyze that this data should be placed in 0275 % the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension 0276 % being the slice direction. 0277 0278 % For the 'transverse unflipped' type, the voxels are stored with 0279 % Pixels in 'x' axis (varies fastest) - from patient right to left 0280 % Rows in 'y' axis - from patient posterior to anterior 0281 % Slices in 'z' axis - from patient inferior to superior 0282 0283 if verbose, fprintf('...reading axial unflipped orientation\n'); end 0284 0285 % -- This code will handle nD files 0286 dims = double( avw.hdr.dime.dim(2:end) ); 0287 % replace dimensions of 0 with 1 to be used in reshape 0288 idx = find( dims == 0 ); 0289 dims( idx ) = 1; 0290 avw.img = reshape( tmp, dims ); 0291 0292 % -- The code above replaces this 0293 % avw.img = zeros(PixelDim,RowDim,SliceDim); 0294 % 0295 % n = 1; 0296 % x = 1:PixelDim; 0297 % for z = 1:SliceDim, 0298 % for y = 1:RowDim, 0299 % % load Y row of X values into Z slice avw.img 0300 % avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0301 % n = n + PixelDim; 0302 % end 0303 % end 0304 0305 0306 % no need to rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0307 0308 0309 case 1, % coronal unflipped 0310 0311 % orient = 1: The primary orientation of the data on disk is in the coronal 0312 % plane relative to the object scanned. Most commonly, the fastest moving 0313 % index through the voxels that are part of this coronal image would span the 0314 % right-left extent of the structure imaged, with the next fastest moving 0315 % index spanning the inferior-superior extent of the structure. This 'orient' 0316 % flag would indicate to Analyze that this data should be placed in the X-Z 0317 % plane of the 3D Analyze Coordinate System, with the Y dimension being the 0318 % slice direction. 0319 0320 % For the 'coronal unflipped' type, the voxels are stored with 0321 % Pixels in 'x' axis (varies fastest) - from patient right to left 0322 % Rows in 'z' axis - from patient inferior to superior 0323 % Slices in 'y' axis - from patient posterior to anterior 0324 0325 if verbose, fprintf('...reading coronal unflipped orientation\n'); end 0326 0327 avw.img = zeros(PixelDim,SliceDim,RowDim); 0328 0329 n = 1; 0330 x = 1:PixelDim; 0331 for y = 1:SliceDim, 0332 for z = 1:RowDim, 0333 % load Z row of X values into Y slice avw.img 0334 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0335 n = n + PixelDim; 0336 end 0337 end 0338 0339 % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0340 avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]); 0341 avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]); 0342 0343 0344 case 2, % sagittal unflipped 0345 0346 % orient = 2: The primary orientation of the data on disk is in the sagittal 0347 % plane relative to the object scanned. Most commonly, the fastest moving 0348 % index through the voxels that are part of this sagittal image would span the 0349 % posterior-anterior extent of the structure imaged, with the next fastest 0350 % moving index spanning the inferior-superior extent of the structure. This 0351 % 'orient' flag would indicate to Analyze that this data should be placed in 0352 % the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension 0353 % being the slice direction. 0354 0355 % For the 'sagittal unflipped' type, the voxels are stored with 0356 % Pixels in 'y' axis (varies fastest) - from patient posterior to anterior 0357 % Rows in 'z' axis - from patient inferior to superior 0358 % Slices in 'x' axis - from patient right to left 0359 0360 if verbose, fprintf('...reading sagittal unflipped orientation\n'); end 0361 0362 avw.img = zeros(SliceDim,PixelDim,RowDim); 0363 0364 n = 1; 0365 y = 1:PixelDim; % posterior to anterior (fastest) 0366 0367 for x = 1:SliceDim, % right to left (slowest) 0368 for z = 1:RowDim, % inferior to superior 0369 0370 % load Z row of Y values into X slice avw.img 0371 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0372 n = n + PixelDim; 0373 end 0374 end 0375 0376 % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0377 avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]); 0378 avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]); 0379 0380 0381 %-------------------------------------------------------------------------------- 0382 % Orient values 3-5 have the second index reversed in order, essentially 0383 % 'flipping' the images relative to what would most likely become the vertical 0384 % axis of the displayed image. 0385 %-------------------------------------------------------------------------------- 0386 0387 case 3, % transverse/axial flipped 0388 0389 % orient = 3: The primary orientation of the data on disk is in the 0390 % transverse plane relative to the object scanned. Most commonly, the fastest 0391 % moving index through the voxels that are part of this transverse image would 0392 % span the right-left extent of the structure imaged, with the next fastest 0393 % moving index spanning the *anterior-posterior* extent of the structure. This 0394 % 'orient' flag would indicate to Analyze that this data should be placed in 0395 % the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension 0396 % being the slice direction. 0397 0398 % For the 'transverse flipped' type, the voxels are stored with 0399 % Pixels in 'x' axis (varies fastest) - from patient right to Left 0400 % Rows in 'y' axis - from patient anterior to Posterior * 0401 % Slices in 'z' axis - from patient inferior to Superior 0402 0403 if verbose, fprintf('...reading axial flipped (+Y from Anterior to Posterior)\n'); end 0404 0405 avw.img = zeros(PixelDim,RowDim,SliceDim); 0406 0407 n = 1; 0408 x = 1:PixelDim; 0409 for z = 1:SliceDim, 0410 for y = RowDim:-1:1, % flip in Y, read A2P file into P2A 3D matrix 0411 0412 % load a flipped Y row of X values into Z slice avw.img 0413 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0414 n = n + PixelDim; 0415 end 0416 end 0417 0418 % no need to rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0419 0420 0421 case 4, % coronal flipped 0422 0423 % orient = 4: The primary orientation of the data on disk is in the coronal 0424 % plane relative to the object scanned. Most commonly, the fastest moving 0425 % index through the voxels that are part of this coronal image would span the 0426 % right-left extent of the structure imaged, with the next fastest moving 0427 % index spanning the *superior-inferior* extent of the structure. This 'orient' 0428 % flag would indicate to Analyze that this data should be placed in the X-Z 0429 % plane of the 3D Analyze Coordinate System, with the Y dimension being the 0430 % slice direction. 0431 0432 % For the 'coronal flipped' type, the voxels are stored with 0433 % Pixels in 'x' axis (varies fastest) - from patient right to Left 0434 % Rows in 'z' axis - from patient superior to Inferior* 0435 % Slices in 'y' axis - from patient posterior to Anterior 0436 0437 if verbose, fprintf('...reading coronal flipped (+Z from Superior to Inferior)\n'); end 0438 0439 avw.img = zeros(PixelDim,SliceDim,RowDim); 0440 0441 n = 1; 0442 x = 1:PixelDim; 0443 for y = 1:SliceDim, 0444 for z = RowDim:-1:1, % flip in Z, read S2I file into I2S 3D matrix 0445 0446 % load a flipped Z row of X values into Y slice avw.img 0447 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0448 n = n + PixelDim; 0449 end 0450 end 0451 0452 % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0453 avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]); 0454 avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]); 0455 0456 0457 case 5, % sagittal flipped 0458 0459 % orient = 5: The primary orientation of the data on disk is in the sagittal 0460 % plane relative to the object scanned. Most commonly, the fastest moving 0461 % index through the voxels that are part of this sagittal image would span the 0462 % posterior-anterior extent of the structure imaged, with the next fastest 0463 % moving index spanning the *superior-inferior* extent of the structure. This 0464 % 'orient' flag would indicate to Analyze that this data should be placed in 0465 % the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension 0466 % being the slice direction. 0467 0468 % For the 'sagittal flipped' type, the voxels are stored with 0469 % Pixels in 'y' axis (varies fastest) - from patient posterior to Anterior 0470 % Rows in 'z' axis - from patient superior to Inferior* 0471 % Slices in 'x' axis - from patient right to Left 0472 0473 if verbose, fprintf('...reading sagittal flipped (+Z from Superior to Inferior)\n'); end 0474 0475 avw.img = zeros(SliceDim,PixelDim,RowDim); 0476 0477 n = 1; 0478 y = 1:PixelDim; 0479 0480 for x = 1:SliceDim, 0481 for z = RowDim:-1:1, % flip in Z, read S2I file into I2S 3D matrix 0482 0483 % load a flipped Z row of Y values into X slice avw.img 0484 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0485 n = n + PixelDim; 0486 end 0487 end 0488 0489 % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0490 avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]); 0491 avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]); 0492 0493 otherwise 0494 0495 error('unknown value in avw.hdr.hist.orient, try explicit IMGorient option.'); 0496 0497 end 0498 0499 if verbose, t=toc; fprintf('...done (%5.2f sec).\n\n',t); end 0500 0501 return 0502 0503 0504 0505 0506 % This function attempts to read the orientation of the 0507 % Analyze file according to the hdr.hist.orient field of the 0508 % header. Unfortunately, this field is optional and not 0509 % all programs will set it correctly, so there is no guarantee, 0510 % that the data loaded will be correctly oriented. If necessary, 0511 % experiment with the 'orient' option to read the .img 0512 % data into the 3D matrix of avw.img as preferred. 0513 % 0514 0515 % (Conventions gathered from e-mail with support@AnalyzeDirect.com) 0516 % 0517 % 0 transverse unflipped 0518 % X direction first, progressing from patient right to left, 0519 % Y direction second, progressing from patient posterior to anterior, 0520 % Z direction third, progressing from patient inferior to superior. 0521 % 1 coronal unflipped 0522 % X direction first, progressing from patient right to left, 0523 % Z direction second, progressing from patient inferior to superior, 0524 % Y direction third, progressing from patient posterior to anterior. 0525 % 2 sagittal unflipped 0526 % Y direction first, progressing from patient posterior to anterior, 0527 % Z direction second, progressing from patient inferior to superior, 0528 % X direction third, progressing from patient right to left. 0529 % 3 transverse flipped 0530 % X direction first, progressing from patient right to left, 0531 % Y direction second, progressing from patient anterior to posterior, 0532 % Z direction third, progressing from patient inferior to superior. 0533 % 4 coronal flipped 0534 % X direction first, progressing from patient right to left, 0535 % Z direction second, progressing from patient superior to inferior, 0536 % Y direction third, progressing from patient posterior to anterior. 0537 % 5 sagittal flipped 0538 % Y direction first, progressing from patient posterior to anterior, 0539 % Z direction second, progressing from patient superior to inferior, 0540 % X direction third, progressing from patient right to left. 0541 0542 0543 %---------------------------------------------------------------------------- 0544 % From ANALYZE documentation... 0545 % 0546 % The ANALYZE coordinate system has an origin in the lower left 0547 % corner. That is, with the subject lying supine, the coordinate 0548 % origin is on the right side of the body (x), at the back (y), 0549 % and at the feet (z). This means that: 0550 % 0551 % +X increases from right (R) to left (L) 0552 % +Y increases from the back (posterior,P) to the front (anterior, A) 0553 % +Z increases from the feet (inferior,I) to the head (superior, S) 0554 % 0555 % The LAS orientation is the radiological convention, where patient 0556 % left is on the image right. The alternative neurological 0557 % convention is RAS (also Talairach convention). 0558 % 0559 % A major advantage of the Analzye origin convention is that the 0560 % coordinate origin of each orthogonal orientation (transverse, 0561 % coronal, and sagittal) lies in the lower left corner of the 0562 % slice as it is displayed. 0563 % 0564 % Orthogonal slices are numbered from one to the number of slices 0565 % in that orientation. For example, a volume (x, y, z) dimensioned 0566 % 128, 256, 48 has: 0567 % 0568 % 128 sagittal slices numbered 1 through 128 (X) 0569 % 256 coronal slices numbered 1 through 256 (Y) 0570 % 48 transverse slices numbered 1 through 48 (Z) 0571 % 0572 % Pixel coordinates are made with reference to the slice numbers from 0573 % which the pixels come. Thus, the first pixel in the volume is 0574 % referenced p(1,1,1) and not at p(0,0,0). 0575 % 0576 % Transverse slices are in the XY plane (also known as axial slices). 0577 % Sagittal slices are in the ZY plane. 0578 % Coronal slices are in the ZX plane. 0579 % 0580 %---------------------------------------------------------------------------- 0581 0582 0583 %---------------------------------------------------------------------------- 0584 % E-mail from support@AnalyzeDirect.com 0585 % 0586 % The 'orient' field in the data_history structure specifies the primary 0587 % orientation of the data as it is stored in the file on disk. This usually 0588 % corresponds to the orientation in the plane of acquisition, given that this 0589 % would correspond to the order in which the data is written to disk by the 0590 % scanner or other software application. As you know, this field will contain 0591 % the values: 0592 % 0593 % orient = 0 transverse unflipped 0594 % 1 coronal unflipped 0595 % 2 sagittal unflipped 0596 % 3 transverse flipped 0597 % 4 coronal flipped 0598 % 5 sagittal flipped 0599 % 0600 % It would be vary rare that you would ever encounter any old Analyze 7.5 0601 % files that contain values of 'orient' which indicate that the data has been 0602 % 'flipped'. The 'flipped flag' values were really only used internal to 0603 % Analyze to precondition data for fast display in the Movie module, where the 0604 % images were actually flipped vertically in order to accommodate the raster 0605 % paint order on older graphics devices. The only cases you will encounter 0606 % will have values of 0, 1, or 2. 0607 % 0608 % As mentioned, the 'orient' flag only specifies the primary orientation of 0609 % data as stored in the disk file itself. It has nothing to do with the 0610 % representation of the data in the 3D Analyze coordinate system, which always 0611 % has a fixed representation to the data. The meaning of the 'orient' values 0612 % should be interpreted as follows: 0613 % 0614 % orient = 0: The primary orientation of the data on disk is in the 0615 % transverse plane relative to the object scanned. Most commonly, the fastest 0616 % moving index through the voxels that are part of this transverse image would 0617 % span the right-left extent of the structure imaged, with the next fastest 0618 % moving index spanning the posterior-anterior extent of the structure. This 0619 % 'orient' flag would indicate to Analyze that this data should be placed in 0620 % the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension 0621 % being the slice direction. 0622 % 0623 % orient = 1: The primary orientation of the data on disk is in the coronal 0624 % plane relative to the object scanned. Most commonly, the fastest moving 0625 % index through the voxels that are part of this coronal image would span the 0626 % right-left extent of the structure imaged, with the next fastest moving 0627 % index spanning the inferior-superior extent of the structure. This 'orient' 0628 % flag would indicate to Analyze that this data should be placed in the X-Z 0629 % plane of the 3D Analyze Coordinate System, with the Y dimension being the 0630 % slice direction. 0631 % 0632 % orient = 2: The primary orientation of the data on disk is in the sagittal 0633 % plane relative to the object scanned. Most commonly, the fastest moving 0634 % index through the voxels that are part of this sagittal image would span the 0635 % posterior-anterior extent of the structure imaged, with the next fastest 0636 % moving index spanning the inferior-superior extent of the structure. This 0637 % 'orient' flag would indicate to Analyze that this data should be placed in 0638 % the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension 0639 % being the slice direction. 0640 % 0641 % Orient values 3-5 have the second index reversed in order, essentially 0642 % 'flipping' the images relative to what would most likely become the vertical 0643 % axis of the displayed image. 0644 % 0645 % Hopefully you understand the difference between the indication this 'orient' 0646 % flag has relative to data stored on disk and the full 3D Analyze Coordinate 0647 % System for data that is managed as a volume image. As mentioned previously, 0648 % the orientation of patient anatomy in the 3D Analyze Coordinate System has a 0649 % fixed orientation relative to each of the orthogonal axes. This orientation 0650 % is completely described in the information that is attached, but the basics 0651 % are: 0652 % 0653 % Left-handed coordinate system 0654 % 0655 % X-Y plane is Transverse 0656 % X-Z plane is Coronal 0657 % Y-Z plane is Sagittal 0658 % 0659 % X axis runs from patient right (low X) to patient left (high X) 0660 % Y axis runs from posterior (low Y) to anterior (high Y) 0661 % Z axis runs from inferior (low Z) to superior (high Z) 0662 % 0663 %---------------------------------------------------------------------------- 0664 0665 0666 0667 %---------------------------------------------------------------------------- 0668 % SPM2 NOTES from spm2 webpage: One thing to watch out for is the image 0669 % orientation. The proper Analyze format uses a left-handed co-ordinate 0670 % system, whereas Talairach uses a right-handed one. In SPM99, images were 0671 % flipped at the spatial normalisation stage (from one co-ordinate system 0672 % to the other). In SPM2b, a different approach is used, so that either a 0673 % left- or right-handed co-ordinate system is used throughout. The SPM2b 0674 % program is told about the handedness that the images are stored with by 0675 % the spm_flip_analyze_images.m function and the defaults.analyze.flip 0676 % parameter that is specified in the spm_defaults.m file. These files are 0677 % intended to be customised for each site. If you previously used SPM99 0678 % and your images were flipped during spatial normalisation, then set 0679 % defaults.analyze.flip=1. If no flipping took place, then set 0680 % defaults.analyze.flip=0. Check that when using the Display facility 0681 % (possibly after specifying some rigid-body rotations) that: 0682 % 0683 % The top-left image is coronal with the top (superior) of the head displayed 0684 % at the top and the left shown on the left. This is as if the subject is viewed 0685 % from behind. 0686 % 0687 % The bottom-left image is axial with the front (anterior) of the head at the 0688 % top and the left shown on the left. This is as if the subject is viewed from above. 0689 % 0690 % The top-right image is sagittal with the front (anterior) of the head at the 0691 % left and the top of the head shown at the top. This is as if the subject is 0692 % viewed from the left. 0693 %----------------------------------------------------------------------------