avw_img_read - read Analyze format data image (*.img)
[ avw, machine ] = avw_img_read(fileprefix, [volIndex], [orient], [machine])
fileprefix - a string, the filename without the .img extension
volIndex - the volume to read from a 4D file, where the first volume
has index 1 (the default)
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.
Returned values:
avw.hdr - a struct with image data parameters.
avw.img - a 3D matrix of image data (double precision)
from a volume of a 4D Analyze file
The 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)
See also: avw_hdr_read (called by this function),
avw_view, avw_write, avw_img_write, avw_flip0001 function [ avw, machine ] = avw_img_read_4d(fileprefix,volIndex,IMGorient,machine) 0002 0003 % avw_img_read - read Analyze format data image (*.img) 0004 % 0005 % [ avw, machine ] = avw_img_read(fileprefix, [volIndex], [orient], [machine]) 0006 % 0007 % fileprefix - a string, the filename without the .img extension 0008 % 0009 % volIndex - the volume to read from a 4D file, where the first volume 0010 % has index 1 (the default) 0011 % 0012 % orient - read a specified orientation, integer values: 0013 % 0014 % '', use header history orient field 0015 % 0, transverse unflipped (LAS*) 0016 % 1, coronal unflipped (LA*S) 0017 % 2, sagittal unflipped (L*AS) 0018 % 3, transverse flipped (LPS*) 0019 % 4, coronal flipped (LA*I) 0020 % 5, sagittal flipped (L*AI) 0021 % 0022 % where * follows the slice dimension and letters indicate +XYZ 0023 % orientations (L left, R right, A anterior, P posterior, 0024 % I inferior, & S superior). 0025 % 0026 % Some files may contain data in the 3-5 orientations, but this 0027 % is unlikely. For more information about orientation, see the 0028 % documentation at the end of this .m file. See also the 0029 % AVW_FLIP function for orthogonal reorientation. 0030 % 0031 % machine - a string, see machineformat in fread for details. 0032 % The default here is 'ieee-le' but the routine 0033 % will automatically switch between little and big 0034 % endian to read any such Analyze header. It 0035 % reports the appropriate machine format and can 0036 % return the machine value. 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 % from a volume of a 4D Analyze file 0043 % 0044 % The returned 3D matrix will correspond with the 0045 % default ANALYZE coordinate system, which 0046 % is Left-handed: 0047 % 0048 % X-Y plane is Transverse 0049 % X-Z plane is Coronal 0050 % Y-Z plane is Sagittal 0051 % 0052 % X axis runs from patient right (low X) to patient Left (high X) 0053 % Y axis runs from posterior (low Y) to Anterior (high Y) 0054 % Z axis runs from inferior (low Z) to Superior (high Z) 0055 % 0056 % See also: avw_hdr_read (called by this function), 0057 % avw_view, avw_write, avw_img_write, avw_flip 0058 % 0059 0060 0061 % $Revision: 1.1 $ $Date: 2004/11/12 01:30:25 $ 0062 0063 % Licence: GNU GPL, no express or implied warranties 0064 % History: 05/2002, Darren.Weber@flinders.edu.au 0065 % The Analyze format is copyright 0066 % (c) Copyright, 1986-1995 0067 % Biomedical Imaging Resource, Mayo Foundation 0068 % 01/2003, Darren.Weber@flinders.edu.au 0069 % - adapted for matlab v5 0070 % - revised all orientation information and handling 0071 % after seeking further advice from AnalyzeDirect.com 0072 % 03/2003, Darren.Weber@flinders.edu.au 0073 % - adapted for -ve pixdim values (non standard Analyze) 0074 % 11/2003, Darren.Weber_at_radiology.ucsf.edu 0075 % - adapted for 4D Analyze files 0076 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0077 0078 0079 error('in development'); 0080 0081 0082 if ~exist('fileprefix','var'), 0083 msg = sprintf('...no input fileprefix - see help avw_img_read\n\n'); 0084 error(msg); 0085 end 0086 if ~exist('volIndex','var'), volIndex = 1; end 0087 if ~exist('IMGorient','var'), IMGorient = ''; end 0088 if ~exist('machine','var'), machine = 'ieee-le'; end 0089 0090 if findstr('.hdr',fileprefix), 0091 fileprefix = strrep(fileprefix,'.hdr',''); 0092 end 0093 if findstr('.img',fileprefix), 0094 fileprefix = strrep(fileprefix,'.img',''); 0095 end 0096 0097 % MAIN 0098 0099 % Read the file header 0100 [ avw, machine ] = avw_hdr_read(fileprefix,machine); 0101 0102 avw = read_image(avw,volIndex,IMGorient,machine); 0103 0104 return 0105 0106 0107 0108 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0109 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0110 function [ avw ] = read_image(avw,volIndex,IMGorient,machine) 0111 0112 fid = fopen(sprintf('%s.img',avw.fileprefix),'r',machine); 0113 if fid < 0, 0114 msg = sprintf('...cannot open file %s.img\n\n',avw.fileprefix); 0115 error(msg); 0116 end 0117 0118 version = '[$Revision: 1.1 $]'; 0119 fprintf('\nAVW_IMG_READ [v%s]\n',version(12:16)); tic; 0120 0121 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0122 % check data precision 0123 0124 % short int bitpix; /* Number of bits per pixel; 1, 8, 16, 32, or 64. */ 0125 % short int datatype /* Datatype for this image set */ 0126 % /*Acceptable values for datatype are*/ 0127 % #define DT_NONE 0 0128 % #define DT_UNKNOWN 0 /*Unknown data type*/ 0129 % #define DT_BINARY 1 /*Binary ( 1 bit per voxel)*/ 0130 % #define DT_UNSIGNED_CHAR 2 /*Unsigned character ( 8 bits per voxel)*/ 0131 % #define DT_SIGNED_SHORT 4 /*Signed short (16 bits per voxel)*/ 0132 % #define DT_SIGNED_INT 8 /*Signed integer (32 bits per voxel)*/ 0133 % #define DT_FLOAT 16 /*Floating point (32 bits per voxel)*/ 0134 % #define DT_COMPLEX 32 /*Complex (64 bits per voxel; 2 floating point numbers)/* 0135 % #define DT_DOUBLE 64 /*Double precision (64 bits per voxel)*/ 0136 % #define DT_RGB 128 /*A Red-Green-Blue datatype*/ 0137 % #define DT_ALL 255 /*Undocumented*/ 0138 0139 switch double(avw.hdr.dime.bitpix), 0140 case 1, precision = 'bit1'; 0141 case 8, precision = 'uchar'; 0142 case 16, precision = 'int16'; 0143 case 32, 0144 if isequal(avw.hdr.dime.datatype, 8), precision = 'int32'; 0145 else precision = 'single'; 0146 end 0147 case 64, precision = 'double'; 0148 otherwise, 0149 precision = 'uchar'; 0150 fprintf('...precision undefined in header, using ''uchar''\n'); 0151 end 0152 0153 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0154 % calculate the byte index range for a volume to be read 0155 % In general, voxel(a,b,c) will be stored as byte N where 0156 % N = a + Nx(b + Ny*c), given the first voxel of the image 0157 % is (0,0,0). Matlab fseek command indexes the first voxel 0158 % as (0,0,0), so this formula should work. 0159 0160 Nx = double(avw.hdr.dime.dim(2)); 0161 Ny = double(avw.hdr.dime.dim(3)); 0162 Nz = double(avw.hdr.dime.dim(4)); 0163 Nt = double(avw.hdr.dime.dim(5)); 0164 0165 readPixels = Nx * Ny * Nz; 0166 0167 bitpix = double(avw.hdr.dime.bitpix); 0168 0169 if Nt == 1, 0170 fprintf('...reading volume %d of %d\n',1,Nt); 0171 avw.offset = 0; 0172 else 0173 if volIndex <= Nt, 0174 fprintf('...reading volume %d of %d\n',volIndex,Nt); 0175 avw.offset = (readPixels * volIndex) - readPixels; 0176 % this the offset in pixels, but we need bytes for fseek! 0177 avw.offset = (avw.offset * bitpix) / 8; 0178 0179 else 0180 msg = sprintf('volIndex > 4D volume (%d vols)',Nt); 0181 error(msg); 0182 end 0183 end 0184 0185 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0186 % read a volume from the .img file into matlab 0187 fprintf('...reading %s Analyze %s image format.\n',machine,precision); 0188 fseek(fid,avw.offset,'bof'); 0189 % adjust for matlab version 0190 ver = version; 0191 ver = str2num(ver(1)); 0192 if ver < 6, 0193 tmp = fread(fid,readPixels,sprintf('%s',precision)); 0194 else, 0195 0196 ftell(fid) 0197 0198 0199 [tmp, count] = fread(fid,readPixels,sprintf('%s=>double',precision)); 0200 0201 0202 ftell(fid) 0203 0204 avw.offset = (readPixels * [volIndex + 1]) - readPixels; 0205 avw.offset = (avw.offset * bitpix) / 8 0206 0207 0208 if count ~= readPixels, 0209 msg = sprintf('only read %d of %d total pixels',count,readPixels); 0210 error(msg); 0211 end 0212 end 0213 fclose(fid); 0214 0215 % Update the global min and max values 0216 avw.hdr.dime.glmax = max(double(tmp)); 0217 avw.hdr.dime.glmin = min(double(tmp)); 0218 0219 0220 %--------------------------------------------------------------- 0221 % Now partition the img data into xyz 0222 0223 % --- first figure out the size of the image 0224 0225 % short int dim[ ]; /* Array of the image dimensions */ 0226 % 0227 % dim[0] Number of dimensions in database; usually 4. 0228 % dim[1] Image X dimension; number of pixels in an image row. 0229 % dim[2] Image Y dimension; number of pixel rows in slice. 0230 % dim[3] Volume Z dimension; number of slices in a volume. 0231 % dim[4] Time points; number of volumes in database. 0232 0233 PixelDim = double(avw.hdr.dime.dim(2)); 0234 RowDim = double(avw.hdr.dime.dim(3)); 0235 SliceDim = double(avw.hdr.dime.dim(4)); 0236 0237 PixelSz = double(avw.hdr.dime.pixdim(2)); 0238 RowSz = double(avw.hdr.dime.pixdim(3)); 0239 SliceSz = double(avw.hdr.dime.pixdim(4)); 0240 0241 0242 0243 0244 0245 % ---- NON STANDARD ANALYZE... 0246 0247 % Some Analyze files have been found to set -ve pixdim values, eg 0248 % the MNI template avg152T1_brain in the FSL etc/standard folder, 0249 % perhaps to indicate flipped orientation? If so, this code below 0250 % will NOT handle the flip correctly! 0251 if PixelSz < 0, 0252 warning('X pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(2))'); 0253 PixelSz = abs(PixelSz); 0254 avw.hdr.dime.pixdim(2) = single(PixelSz); 0255 end 0256 if RowSz < 0, 0257 warning('Y pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(3))'); 0258 RowSz = abs(RowSz); 0259 avw.hdr.dime.pixdim(3) = single(RowSz); 0260 end 0261 if SliceSz < 0, 0262 warning('Z pixdim < 0 !!! resetting to abs(avw.hdr.dime.pixdim(4))'); 0263 SliceSz = abs(SliceSz); 0264 avw.hdr.dime.pixdim(4) = single(SliceSz); 0265 end 0266 0267 % ---- END OF NON STANDARD ANALYZE 0268 0269 0270 0271 0272 0273 % --- check the orientation specification and arrange img accordingly 0274 if ~isempty(IMGorient), 0275 if ischar(IMGorient), 0276 avw.hdr.hist.orient = uint8(str2num(IMGorient)); 0277 else 0278 avw.hdr.hist.orient = uint8(IMGorient); 0279 end 0280 end, 0281 0282 if isempty(avw.hdr.hist.orient), 0283 msg = [ '...unspecified avw.hdr.hist.orient, using default 0\n',... 0284 ' (check image and try explicit IMGorient option).\n']; 0285 fprintf(msg); 0286 avw.hdr.hist.orient = uint8(0); 0287 end 0288 0289 switch double(avw.hdr.hist.orient), 0290 0291 case 0, % transverse unflipped 0292 0293 % orient = 0: The primary orientation of the data on disk is in the 0294 % transverse plane relative to the object scanned. Most commonly, the fastest 0295 % moving index through the voxels that are part of this transverse image would 0296 % span the right->left extent of the structure imaged, with the next fastest 0297 % moving index spanning the posterior->anterior extent of the structure. This 0298 % 'orient' flag would indicate to Analyze that this data should be placed in 0299 % the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension 0300 % being the slice direction. 0301 0302 % For the 'transverse unflipped' type, the voxels are stored with 0303 % Pixels in 'x' axis (varies fastest) - from patient right to left 0304 % Rows in 'y' axis - from patient posterior to anterior 0305 % Slices in 'z' axis - from patient inferior to superior 0306 0307 fprintf('...reading axial unflipped orientation\n'); 0308 0309 avw.img = zeros(PixelDim,RowDim,SliceDim); 0310 0311 n = 1; 0312 x = 1:PixelDim; 0313 for z = 1:SliceDim, 0314 for y = 1:RowDim, 0315 % load Y row of X values into Z slice avw.img 0316 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0317 n = n + PixelDim; 0318 end 0319 end 0320 0321 % no need to rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0322 0323 0324 case 1, % coronal unflipped 0325 0326 % orient = 1: The primary orientation of the data on disk is in the coronal 0327 % plane relative to the object scanned. Most commonly, the fastest moving 0328 % index through the voxels that are part of this coronal image would span the 0329 % right->left extent of the structure imaged, with the next fastest moving 0330 % index spanning the inferior->superior extent of the structure. This 'orient' 0331 % flag would indicate to Analyze that this data should be placed in the X-Z 0332 % plane of the 3D Analyze Coordinate System, with the Y dimension being the 0333 % slice direction. 0334 0335 % For the 'coronal unflipped' type, the voxels are stored with 0336 % Pixels in 'x' axis (varies fastest) - from patient right to left 0337 % Rows in 'z' axis - from patient inferior to superior 0338 % Slices in 'y' axis - from patient posterior to anterior 0339 0340 fprintf('...reading coronal unflipped orientation\n'); 0341 0342 avw.img = zeros(PixelDim,SliceDim,RowDim); 0343 0344 n = 1; 0345 x = 1:PixelDim; 0346 for y = 1:SliceDim, 0347 for z = 1:RowDim, 0348 % load Z row of X values into Y slice avw.img 0349 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0350 n = n + PixelDim; 0351 end 0352 end 0353 0354 % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0355 avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]); 0356 avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]); 0357 0358 0359 case 2, % sagittal unflipped 0360 0361 % orient = 2: The primary orientation of the data on disk is in the sagittal 0362 % plane relative to the object scanned. Most commonly, the fastest moving 0363 % index through the voxels that are part of this sagittal image would span the 0364 % posterior->anterior extent of the structure imaged, with the next fastest 0365 % moving index spanning the inferior->superior extent of the structure. This 0366 % 'orient' flag would indicate to Analyze that this data should be placed in 0367 % the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension 0368 % being the slice direction. 0369 0370 % For the 'sagittal unflipped' type, the voxels are stored with 0371 % Pixels in 'y' axis (varies fastest) - from patient posterior to anterior 0372 % Rows in 'z' axis - from patient inferior to superior 0373 % Slices in 'x' axis - from patient right to left 0374 0375 fprintf('...reading sagittal unflipped orientation\n'); 0376 0377 avw.img = zeros(SliceDim,PixelDim,RowDim); 0378 0379 n = 1; 0380 y = 1:PixelDim; % posterior to anterior (fastest) 0381 0382 for x = 1:SliceDim, % right to left (slowest) 0383 for z = 1:RowDim, % inferior to superior 0384 0385 % load Z row of Y values into X slice avw.img 0386 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0387 n = n + PixelDim; 0388 end 0389 end 0390 0391 % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0392 avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]); 0393 avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]); 0394 0395 0396 %-------------------------------------------------------------------------------- 0397 % Orient values 3-5 have the second index reversed in order, essentially 0398 % 'flipping' the images relative to what would most likely become the vertical 0399 % axis of the displayed image. 0400 %-------------------------------------------------------------------------------- 0401 0402 case 3, % transverse/axial flipped 0403 0404 % orient = 3: The primary orientation of the data on disk is in the 0405 % transverse plane relative to the object scanned. Most commonly, the fastest 0406 % moving index through the voxels that are part of this transverse image would 0407 % span the right->left extent of the structure imaged, with the next fastest 0408 % moving index spanning the *anterior->posterior* extent of the structure. This 0409 % 'orient' flag would indicate to Analyze that this data should be placed in 0410 % the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension 0411 % being the slice direction. 0412 0413 % For the 'transverse flipped' type, the voxels are stored with 0414 % Pixels in 'x' axis (varies fastest) - from patient right to Left 0415 % Rows in 'y' axis - from patient anterior to Posterior * 0416 % Slices in 'z' axis - from patient inferior to Superior 0417 0418 fprintf('...reading axial flipped (+Y from Anterior to Posterior)\n'); 0419 0420 avw.img = zeros(PixelDim,RowDim,SliceDim); 0421 0422 n = 1; 0423 x = 1:PixelDim; 0424 for z = 1:SliceDim, 0425 for y = RowDim:-1:1, % flip in Y, read A2P file into P2A 3D matrix 0426 0427 % load a flipped Y row of X values into Z slice avw.img 0428 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0429 n = n + PixelDim; 0430 end 0431 end 0432 0433 % no need to rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0434 0435 0436 case 4, % coronal flipped 0437 0438 % orient = 4: The primary orientation of the data on disk is in the coronal 0439 % plane relative to the object scanned. Most commonly, the fastest moving 0440 % index through the voxels that are part of this coronal image would span the 0441 % right->left extent of the structure imaged, with the next fastest moving 0442 % index spanning the *superior->inferior* extent of the structure. This 'orient' 0443 % flag would indicate to Analyze that this data should be placed in the X-Z 0444 % plane of the 3D Analyze Coordinate System, with the Y dimension being the 0445 % slice direction. 0446 0447 % For the 'coronal flipped' type, the voxels are stored with 0448 % Pixels in 'x' axis (varies fastest) - from patient right to Left 0449 % Rows in 'z' axis - from patient superior to Inferior* 0450 % Slices in 'y' axis - from patient posterior to Anterior 0451 0452 fprintf('...reading coronal flipped (+Z from Superior to Inferior)\n'); 0453 0454 avw.img = zeros(PixelDim,SliceDim,RowDim); 0455 0456 n = 1; 0457 x = 1:PixelDim; 0458 for y = 1:SliceDim, 0459 for z = RowDim:-1:1, % flip in Z, read S2I file into I2S 3D matrix 0460 0461 % load a flipped Z row of X values into Y slice avw.img 0462 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0463 n = n + PixelDim; 0464 end 0465 end 0466 0467 % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0468 avw.hdr.dime.dim(2:4) = int16([PixelDim,SliceDim,RowDim]); 0469 avw.hdr.dime.pixdim(2:4) = single([PixelSz,SliceSz,RowSz]); 0470 0471 0472 case 5, % sagittal flipped 0473 0474 % orient = 5: The primary orientation of the data on disk is in the sagittal 0475 % plane relative to the object scanned. Most commonly, the fastest moving 0476 % index through the voxels that are part of this sagittal image would span the 0477 % posterior->anterior extent of the structure imaged, with the next fastest 0478 % moving index spanning the *superior->inferior* extent of the structure. This 0479 % 'orient' flag would indicate to Analyze that this data should be placed in 0480 % the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension 0481 % being the slice direction. 0482 0483 % For the 'sagittal flipped' type, the voxels are stored with 0484 % Pixels in 'y' axis (varies fastest) - from patient posterior to Anterior 0485 % Rows in 'z' axis - from patient superior to Inferior* 0486 % Slices in 'x' axis - from patient right to Left 0487 0488 fprintf('...reading sagittal flipped (+Z from Superior to Inferior)\n'); 0489 0490 avw.img = zeros(SliceDim,PixelDim,RowDim); 0491 0492 n = 1; 0493 y = 1:PixelDim; 0494 0495 for x = 1:SliceDim, 0496 for z = RowDim:-1:1, % flip in Z, read S2I file into I2S 3D matrix 0497 0498 % load a flipped Z row of Y values into X slice avw.img 0499 avw.img(x,y,z) = tmp(n:n+(PixelDim-1)); 0500 n = n + PixelDim; 0501 end 0502 end 0503 0504 % rearrange avw.hdr.dime.dim or avw.hdr.dime.pixdim 0505 avw.hdr.dime.dim(2:4) = int16([SliceDim,PixelDim,RowDim]); 0506 avw.hdr.dime.pixdim(2:4) = single([SliceSz,PixelSz,RowSz]); 0507 0508 otherwise 0509 0510 error('unknown value in avw.hdr.hist.orient, try explicit IMGorient option.'); 0511 0512 end 0513 0514 t=toc; fprintf('...done (%5.2f sec).\n\n',t); 0515 0516 return 0517 0518 0519 0520 0521 % This function attempts to read the orientation of the 0522 % Analyze file according to the hdr.hist.orient field of the 0523 % header. Unfortunately, this field is optional and not 0524 % all programs will set it correctly, so there is no guarantee, 0525 % that the data loaded will be correctly oriented. If necessary, 0526 % experiment with the 'orient' option to read the .img 0527 % data into the 3D matrix of avw.img as preferred. 0528 % 0529 0530 % (Conventions gathered from e-mail with support@AnalyzeDirect.com) 0531 % 0532 % 0 transverse unflipped 0533 % X direction first, progressing from patient right to left, 0534 % Y direction second, progressing from patient posterior to anterior, 0535 % Z direction third, progressing from patient inferior to superior. 0536 % 1 coronal unflipped 0537 % X direction first, progressing from patient right to left, 0538 % Z direction second, progressing from patient inferior to superior, 0539 % Y direction third, progressing from patient posterior to anterior. 0540 % 2 sagittal unflipped 0541 % Y direction first, progressing from patient posterior to anterior, 0542 % Z direction second, progressing from patient inferior to superior, 0543 % X direction third, progressing from patient right to left. 0544 % 3 transverse flipped 0545 % X direction first, progressing from patient right to left, 0546 % Y direction second, progressing from patient anterior to posterior, 0547 % Z direction third, progressing from patient inferior to superior. 0548 % 4 coronal flipped 0549 % X direction first, progressing from patient right to left, 0550 % Z direction second, progressing from patient superior to inferior, 0551 % Y direction third, progressing from patient posterior to anterior. 0552 % 5 sagittal flipped 0553 % Y direction first, progressing from patient posterior to anterior, 0554 % Z direction second, progressing from patient superior to inferior, 0555 % X direction third, progressing from patient right to left. 0556 0557 0558 %---------------------------------------------------------------------------- 0559 % From ANALYZE documentation... 0560 % 0561 % The ANALYZE coordinate system has an origin in the lower left 0562 % corner. That is, with the subject lying supine, the coordinate 0563 % origin is on the right side of the body (x), at the back (y), 0564 % and at the feet (z). This means that: 0565 % 0566 % +X increases from right (R) to left (L) 0567 % +Y increases from the back (posterior,P) to the front (anterior, A) 0568 % +Z increases from the feet (inferior,I) to the head (superior, S) 0569 % 0570 % The LAS orientation is the radiological convention, where patient 0571 % left is on the image right. The alternative neurological 0572 % convention is RAS (also Talairach convention). 0573 % 0574 % A major advantage of the Analzye origin convention is that the 0575 % coordinate origin of each orthogonal orientation (transverse, 0576 % coronal, and sagittal) lies in the lower left corner of the 0577 % slice as it is displayed. 0578 % 0579 % Orthogonal slices are numbered from one to the number of slices 0580 % in that orientation. For example, a volume (x, y, z) dimensioned 0581 % 128, 256, 48 has: 0582 % 0583 % 128 sagittal slices numbered 1 through 128 (X) 0584 % 256 coronal slices numbered 1 through 256 (Y) 0585 % 48 transverse slices numbered 1 through 48 (Z) 0586 % 0587 % Pixel coordinates are made with reference to the slice numbers from 0588 % which the pixels come. Thus, the first pixel in the volume is 0589 % referenced p(1,1,1) and not at p(0,0,0). 0590 % 0591 % Transverse slices are in the XY plane (also known as axial slices). 0592 % Sagittal slices are in the ZY plane. 0593 % Coronal slices are in the ZX plane. 0594 % 0595 %---------------------------------------------------------------------------- 0596 0597 0598 %---------------------------------------------------------------------------- 0599 % E-mail from support@AnalyzeDirect.com 0600 % 0601 % The 'orient' field in the data_history structure specifies the primary 0602 % orientation of the data as it is stored in the file on disk. This usually 0603 % corresponds to the orientation in the plane of acquisition, given that this 0604 % would correspond to the order in which the data is written to disk by the 0605 % scanner or other software application. As you know, this field will contain 0606 % the values: 0607 % 0608 % orient = 0 transverse unflipped 0609 % 1 coronal unflipped 0610 % 2 sagittal unflipped 0611 % 3 transverse flipped 0612 % 4 coronal flipped 0613 % 5 sagittal flipped 0614 % 0615 % It would be vary rare that you would ever encounter any old Analyze 7.5 0616 % files that contain values of 'orient' which indicate that the data has been 0617 % 'flipped'. The 'flipped flag' values were really only used internal to 0618 % Analyze to precondition data for fast display in the Movie module, where the 0619 % images were actually flipped vertically in order to accommodate the raster 0620 % paint order on older graphics devices. The only cases you will encounter 0621 % will have values of 0, 1, or 2. 0622 % 0623 % As mentioned, the 'orient' flag only specifies the primary orientation of 0624 % data as stored in the disk file itself. It has nothing to do with the 0625 % representation of the data in the 3D Analyze coordinate system, which always 0626 % has a fixed representation to the data. The meaning of the 'orient' values 0627 % should be interpreted as follows: 0628 % 0629 % orient = 0: The primary orientation of the data on disk is in the 0630 % transverse plane relative to the object scanned. Most commonly, the fastest 0631 % moving index through the voxels that are part of this transverse image would 0632 % span the right-left extent of the structure imaged, with the next fastest 0633 % moving index spanning the posterior-anterior extent of the structure. This 0634 % 'orient' flag would indicate to Analyze that this data should be placed in 0635 % the X-Y plane of the 3D Analyze Coordinate System, with the Z dimension 0636 % being the slice direction. 0637 % 0638 % orient = 1: The primary orientation of the data on disk is in the coronal 0639 % plane relative to the object scanned. Most commonly, the fastest moving 0640 % index through the voxels that are part of this coronal image would span the 0641 % right-left extent of the structure imaged, with the next fastest moving 0642 % index spanning the inferior-superior extent of the structure. This 'orient' 0643 % flag would indicate to Analyze that this data should be placed in the X-Z 0644 % plane of the 3D Analyze Coordinate System, with the Y dimension being the 0645 % slice direction. 0646 % 0647 % orient = 2: The primary orientation of the data on disk is in the sagittal 0648 % plane relative to the object scanned. Most commonly, the fastest moving 0649 % index through the voxels that are part of this sagittal image would span the 0650 % posterior-anterior extent of the structure imaged, with the next fastest 0651 % moving index spanning the inferior-superior extent of the structure. This 0652 % 'orient' flag would indicate to Analyze that this data should be placed in 0653 % the Y-Z plane of the 3D Analyze Coordinate System, with the X dimension 0654 % being the slice direction. 0655 % 0656 % Orient values 3-5 have the second index reversed in order, essentially 0657 % 'flipping' the images relative to what would most likely become the vertical 0658 % axis of the displayed image. 0659 % 0660 % Hopefully you understand the difference between the indication this 'orient' 0661 % flag has relative to data stored on disk and the full 3D Analyze Coordinate 0662 % System for data that is managed as a volume image. As mentioned previously, 0663 % the orientation of patient anatomy in the 3D Analyze Coordinate System has a 0664 % fixed orientation relative to each of the orthogonal axes. This orientation 0665 % is completely described in the information that is attached, but the basics 0666 % are: 0667 % 0668 % Left-handed coordinate system 0669 % 0670 % X-Y plane is Transverse 0671 % X-Z plane is Coronal 0672 % Y-Z plane is Sagittal 0673 % 0674 % X axis runs from patient right (low X) to patient left (high X) 0675 % Y axis runs from posterior (low Y) to anterior (high Y) 0676 % Z axis runs from inferior (low Z) to superior (high Z) 0677 % 0678 %---------------------------------------------------------------------------- 0679 0680 0681 0682 %---------------------------------------------------------------------------- 0683 % SPM2 NOTES from spm2 webpage: One thing to watch out for is the image 0684 % orientation. The proper Analyze format uses a left-handed co-ordinate 0685 % system, whereas Talairach uses a right-handed one. In SPM99, images were 0686 % flipped at the spatial normalisation stage (from one co-ordinate system 0687 % to the other). In SPM2b, a different approach is used, so that either a 0688 % left- or right-handed co-ordinate system is used throughout. The SPM2b 0689 % program is told about the handedness that the images are stored with by 0690 % the spm_flip_analyze_images.m function and the defaults.analyze.flip 0691 % parameter that is specified in the spm_defaults.m file. These files are 0692 % intended to be customised for each site. If you previously used SPM99 0693 % and your images were flipped during spatial normalisation, then set 0694 % defaults.analyze.flip=1. If no flipping took place, then set 0695 % defaults.analyze.flip=0. Check that when using the Display facility 0696 % (possibly after specifying some rigid-body rotations) that: 0697 % 0698 % The top-left image is coronal with the top (superior) of the head displayed 0699 % at the top and the left shown on the left. This is as if the subject is viewed 0700 % from behind. 0701 % 0702 % The bottom-left image is axial with the front (anterior) of the head at the 0703 % top and the left shown on the left. This is as if the subject is viewed from above. 0704 % 0705 % The top-right image is sagittal with the front (anterior) of the head at the 0706 % left and the top of the head shown at the top. This is as if the subject is 0707 % viewed from the left. 0708 %----------------------------------------------------------------------------