ge_series2avw - converts a GE series to Analyze
avw = ge_series2avw(examPath,seriesPath)
Converts a series of GE slices into an Analyze
avw struct (see avw_read), which can be output
as an Analyze .hdr/.img pair using avw_write.
examPath - string path to an exam directory,
which contains series directories
below it
seriesPath - the series to convert
(integer or string argument)
examPath is the name of the directory containing
the series subdirectories (e.g., series 1), which
contain the series image files (*.MR or I.*).
This function calls ge_series_read.
The function will attempt to reorient the GE
3D volume into radiological orientation
(axial LAS, which is the default Analyze
orientation). The resulting data should
be SPM compatible when output with avw_write.
This function is in alpha development (as of 03/2003)
although a prior version has been tested with
Ax,Sag,Cor slices (with slice direction going both
ways). It was also tested for oblique axial, but
not on double obliques or anything more complicated.
The function does not provide information for an
SPM compatible .mat file.
see also ge_series_read,
avw_view, avw_read, avw_write0001 function [ avw ] = ge_series2avw(examPath,seriesPath) 0002 0003 % ge_series2avw - converts a GE series to Analyze 0004 % 0005 % avw = ge_series2avw(examPath,seriesPath) 0006 % 0007 % Converts a series of GE slices into an Analyze 0008 % avw struct (see avw_read), which can be output 0009 % as an Analyze .hdr/.img pair using avw_write. 0010 % 0011 % examPath - string path to an exam directory, 0012 % which contains series directories 0013 % below it 0014 % seriesPath - the series to convert 0015 % (integer or string argument) 0016 % 0017 % examPath is the name of the directory containing 0018 % the series subdirectories (e.g., series 1), which 0019 % contain the series image files (*.MR or I.*). 0020 % This function calls ge_series_read. 0021 % 0022 % The function will attempt to reorient the GE 0023 % 3D volume into radiological orientation 0024 % (axial LAS, which is the default Analyze 0025 % orientation). The resulting data should 0026 % be SPM compatible when output with avw_write. 0027 % 0028 % This function is in alpha development (as of 03/2003) 0029 % although a prior version has been tested with 0030 % Ax,Sag,Cor slices (with slice direction going both 0031 % ways). It was also tested for oblique axial, but 0032 % not on double obliques or anything more complicated. 0033 % The function does not provide information for an 0034 % SPM compatible .mat file. 0035 % 0036 % see also ge_series_read, 0037 % avw_view, avw_read, avw_write 0038 % 0039 0040 0041 % $Revision: 1.1 $ $Date: 2004/11/12 01:32:35 $ 0042 0043 % Souheil J. Inati <souheil.inati@nyu.edu> at 03/2003 0044 % Dartmouth College, May 2000 0045 % 0046 % Darren.Weber@flinders.edu.au, March 2003 0047 % - Substantially redesigned file handling and function 0048 % call structures for integration with mri_toolbox at 0049 % http://eeg.sf.net 0050 % - Requested permission to distribute code under GPL licence 0051 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0052 0053 if (nargin < 2), 0054 doc ge_series2avw; 0055 error('...not enough input arguments.') 0056 return 0057 end 0058 0059 0060 0061 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0062 % Read in the GE series header and image volume 0063 [ge, lastfile] = ge_series_read(examPath, seriesPath); 0064 0065 % could try to use lastfile to create avw.fileprefix, but 0066 % it is too variable to be reliable 0067 % avw.fileprefix = lastfile 0068 0069 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0070 % Convert the GE series to an Analyze volume 0071 0072 % Generate the Analyze header 0073 avw = ge_hdr2avw(ge); 0074 0075 version = '[$Revision: 1.1 $]'; 0076 fprintf('\nGE_SERIES2AVW [v%s]\n',version(12:16)); tic; 0077 0078 % Check if ADW scan (not sure this is useful, DLW 03/2003) 0079 %if ge.hdr.image.user9 == 0, adwcount = 1; 0080 %else, adwcount = ge.hdr.image.user9; 0081 %end 0082 0083 0084 % Reorient the GE data into radiological orientation during assignment 0085 % of ge.img into avw.img (leave ge.img in original orientation) 0086 avw = ge_reorient(ge, avw); % see below 0087 0088 % Write the Analyze files (not doing this) 0089 %avw_write(avw,outName); 0090 0091 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0092 % This is the original write code, now replace with above (DLW)... 0093 0094 %outFile = strcat(outName,'.hdr'); 0095 %status = ge_writeSPMHeader(outFile,header); 0096 %outFile = [outName sprintf('.img')]; 0097 %[fid,message] = fopen(outFile,'w'); 0098 %if (fid == -1), 0099 % fprintf('Cannot Open %s for writing.\n',outFile); 0100 % error(message); 0101 %end 0102 %fwrite(fid,reshape(imageVol,1,prod(size(imageVol))),'int16'); 0103 %status = fclose(fid); 0104 0105 t=toc; fprintf('...done (%5.2f sec).\n',t); 0106 0107 return 0108 0109 0110 0111 0112 0113 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0114 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 0115 0116 function [avw] = ge_reorient(ge, avw) 0117 0118 %ge_reorient - Assigns Analyze header dimensions and volume based on GE orientation 0119 % 0120 % avw = ge_reorient(ge, avw) 0121 % 0122 % reorients the GE 3D volume to be radiological 0123 % orientation (axial LAS, which is SPM compatible) 0124 % based on the GE acquition orientation 0125 % 0126 % This has been tested with Ax,Sag,Cor with slices going 0127 % both ways. Also for Oblique axial. Don't count on double 0128 % obliques or anything really fancy. 0129 % 0130 0131 0132 % Have looked over this orientation code carefully (DLW, 03/2003) 0133 % The above comments are from a previous version, note it 0134 % should be LAS, not RAS !!!! I have found some inconsistencies 0135 % in the code (03/2003) and fixed it as best I can for now. Further 0136 % testing with various volumes is required. 0137 0138 0139 series_description = deblank(char(ge.hdr.series.se_desc)'); % unreliable! 0140 0141 fprintf('...checking GE series data orientation.\n'); 0142 0143 % Determine the GE orientation 0144 % orient is 1=axial, 2=sagittal, 3=coronal 0145 % with opposite sign if backwards slice order 0146 ras_start = char(ge.hdr.series.start_ras); 0147 ras_end = char(ge.hdr.series.end_ras); 0148 if strcmp(ras_start,'I') & strcmp(ras_end,'S'), 0149 fprintf('...slices are axial from inferior to superior.\n'); 0150 orient = 1; 0151 elseif strcmp(ras_start,'S') & strcmp(ras_end,'I'), 0152 fprintf('...slices are axial from superior to inferior.\n'); 0153 orient = -1; 0154 elseif strcmp(ras_start,'R') & strcmp(ras_end,'L'), 0155 fprintf('...slices are sagittal from right to left.\n'); 0156 orient = 2; 0157 elseif strcmp(ras_start,'L') & strcmp(ras_end,'R'), 0158 fprintf('...slices are sagittal from left to right.\n'); 0159 orient = -2; 0160 elseif strcmp(ras_start,'P') & strcmp(ras_end,'A'), 0161 fprintf('...slices are coronal from posterior to anterior.\n'); 0162 orient = 3; 0163 elseif strcmp(ras_start,'A') & strcmp(ras_end,'P'), 0164 fprintf('...slices are coronal from anterior to posterior.\n'); 0165 orient = -3; 0166 else, 0167 warning('GE orientation unknown!'); 0168 orient = 0; 0169 end 0170 0171 % Get the GE dimensions 0172 nX = ge.hdr.image.imatrix_X; 0173 nY = ge.hdr.image.imatrix_Y; 0174 nZ = ge.hdr.image.slquant; % slice quantity (Nslices) 0175 pX = ge.hdr.image.pixsize_X; 0176 pY = ge.hdr.image.pixsize_Y; 0177 pZ = ge.hdr.image.slthick + ge.hdr.image.scanspacing; 0178 0179 [vX vY vZ] = size(ge.img); 0180 0181 % Reshape into axial radiological orientation (SPM compatible) 0182 % The default Analyze orientation is +X left, +Y anterior, +Z superior (LAS) 0183 0184 switch orient, 0185 0186 case 0, % Unknown Orientation 0187 0188 warning('avw.img = ge.img without reorientation!\n'); 0189 avw.img = ge.img; 0190 0191 case {1, -1}, % Axial 0192 avw.hdr.dime.dim(2:4) = [ nX nY nZ ]; 0193 avw.hdr.dime.pixdim(2:4) = [ pX pY pZ ]; 0194 0195 avw.img = ge.img; 0196 if orient == 1, % Axial (I to S) 0197 % checked this (03/2003), not sure of L/R orient 0198 avw.img = flipdim(avw.img,2); % flip to P to A 0199 elseif orient == -1, % Axial (S to I) 0200 % have not checked this (03/2003) 0201 avw.img = flipdim(avw.img,2); % flip to P to A 0202 avw.img = flipdim(avw.img,3); % flip to I to S 0203 end 0204 0205 case {2, -2}, % Sagittal 0206 0207 avw.hdr.dime.dim(2:4) = [ nZ nX nY ]; 0208 avw.hdr.dime.pixdim(2:4) = [ pZ pX pY ]; 0209 0210 avw.img = permute(ge.img,[3 1 2]); 0211 if orient == 2, % Sagittal (R to L) 0212 % have not checked this (03/2003) 0213 avw.img = flipdim(avw.img,2); % flip to P to A? 0214 avw.img = flipdim(avw.img,3); % flip to I to S? 0215 elseif orient == -2, % Sagittal (L to R) 0216 % checked this (03/2003) 0217 avw.img = flipdim(avw.img,1); % flip to R to L 0218 avw.img = flipdim(avw.img,2); % flip to P to A 0219 avw.img = flipdim(avw.img,3); % flip to I to S 0220 end 0221 0222 case {3, -3}, % Coronal 0223 0224 avw.hdr.dime.dim(2:4) = [ nX nZ nY ]; 0225 avw.hdr.dime.pixdim(2:4) = [ pX pZ pY ]; 0226 0227 avw.img = permute(ge.img,[1 3 2]); 0228 if orient == 3, % Coronal (P to A) 0229 % have not checked this (03/2003), not sure of L/R orient 0230 avw.img = flipdim(avw.img,3); % flip to I to S? 0231 elseif orient == -3, % Coronal (A to P) 0232 % have not checked this (03/2003), not sure of L/R orient 0233 avw.img = flipdim(avw.img,2); % flip to P to A? 0234 avw.img = flipdim(avw.img,3); % flip to I to S? 0235 end 0236 0237 end 0238 0239 % Set the origin to the center of the volume (not sure this is valid, DLW) 0240 %avw.hdr.dime.originator = [floor(avw.hdr.dime.dim(2)/2) ... 0241 % floor(avw.hdr.dime.dim(3)/2) ... 0242 % floor(avw.hdr.dime.dim(4)/2) 0 0]; 0243 0244 avw.hdr.dime.glmax = max(max(max(avw.img))); 0245 avw.hdr.hist.orient = '0'; 0246 0247 return