Home > fmri > utils > GE2SPM > GE_convertADW.m

GE_convertADW

PURPOSE ^

SYNOPSIS ^

function status = GE_convertADW(inDir,outStem,starttime,nvols)

DESCRIPTION ^

 status = GE_convertADW(inDir,outStem,starttime,nvols)

GE_convertADW

 Converts a series of GE slices acquired on the Advanced
 Development Workstation into Analyze format for SPM.
 inDir is the name of the first directory containing the
      series, e.g. 003
 outStem is the stem used for naming the Analyze files
 starttime is the time point number to start
 nvols is the number of volumes (time points) to convert

 status = 1, error
 status = 0, all is well

 eg GE_convert('DATA/00023/003','converted',5,27)
 Will convert 27 time points starting at the 5th time point
 named converted_i0001.img, converted_i0002.img, ...,
 converted_i0027.img and their associated header files.

 Assumes the data is stored as 003/I.001 through 003/I.999 and
 then 023/I.001 through 023/I.999, etc.
 Remember to skip the template images ie 1 time point for the
 first run.  You don't need to do this for subsequent runs.

 Souheil J. Inati  
 Dartmouth College
 May 2000
 souheil.inati@dartmouth.edu

 Modification history:

 02/19/01 PJ Checks to see that volumes contain data, and quits the conversion
 if they don't

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function status = GE_convertADW(inDir,outStem,starttime,nvols)
0002 %
0003 % status = GE_convertADW(inDir,outStem,starttime,nvols)
0004 %
0005 %GE_convertADW
0006 %
0007 % Converts a series of GE slices acquired on the Advanced
0008 % Development Workstation into Analyze format for SPM.
0009 % inDir is the name of the first directory containing the
0010 %      series, e.g. 003
0011 % outStem is the stem used for naming the Analyze files
0012 % starttime is the time point number to start
0013 % nvols is the number of volumes (time points) to convert
0014 %
0015 % status = 1, error
0016 % status = 0, all is well
0017 %
0018 % eg GE_convert('DATA/00023/003','converted',5,27)
0019 % Will convert 27 time points starting at the 5th time point
0020 % named converted_i0001.img, converted_i0002.img, ...,
0021 % converted_i0027.img and their associated header files.
0022 %
0023 % Assumes the data is stored as 003/I.001 through 003/I.999 and
0024 % then 023/I.001 through 023/I.999, etc.
0025 % Remember to skip the template images ie 1 time point for the
0026 % first run.  You don't need to do this for subsequent runs.
0027 %
0028 % Souheil J. Inati
0029 % Dartmouth College
0030 % May 2000
0031 % souheil.inati@dartmouth.edu
0032 %
0033 % Modification history:
0034 %
0035 % 02/19/01 PJ Checks to see that volumes contain data, and quits the conversion
0036 % if they don't
0037 
0038 status = 0;
0039 
0040 if (nargin < 4)
0041         error('Not enough input arguments.')
0042     status = 1;
0043         return
0044 end
0045 
0046 % Create the name of the first file in inDir
0047 firstfile = fullfile(inDir,'I.001');
0048 
0049 % Generate the Analyze header and other info from the first file
0050 [header, orient, im_offset, adwcount] = GE_createSPMHeader(firstfile);
0051 volSize =  [header.dim(2) header.dim(3) header.dim(4)];
0052 % Reorient the header to SPM orientation
0053 header = GE_reorientHeader(header, orient); 
0054 
0055 % Loop over the volumes until there is no more looping to be done.
0056 for i = 1:nvols
0057   passnum = starttime + i - 1;
0058 
0059   % Create analyze file name
0060 %  vol_str = sprintf('000%d',i);
0061 %  vol_str = vol_str(length(vol_str)-3:length(vol_str));
0062   outName = [outStem sprintf('_i%04d',i)];
0063 
0064   % Read in the volume
0065   [imageVol, lastfile] = GE_readVolume(inDir, passnum, volSize, ...
0066                        header.bitpix, im_offset);
0067 
0068   % Check to see that there is data in imageVol
0069   if isempty(imageVol)
0070     status = 1;
0071     break
0072   end
0073                    
0074   % Reorient the volume to SPM orientation
0075   imageVol = GE_reorientImage(imageVol, orient);
0076 
0077   % Write the SPM header file
0078   outFile = strcat(outName,'.hdr');
0079   status = GE_writeSPMHeader(outFile,header);
0080 
0081   % Write out the Analyze File
0082   outFile = [outName sprintf('.img')];
0083   [fid,message] = fopen(outFile,'w');
0084   if (fid == -1)
0085     fprintf('Cannot Open %s for writing.\n',outFile);
0086     status = 1;
0087     error(message);
0088   end
0089 
0090   fwrite(fid,reshape(imageVol,1,prod(size(imageVol))),'int16');
0091   status = fclose(fid);
0092 
0093   % Done with vol
0094   if (status == 0)
0095     fprintf('Wrote %s\n',outName);
0096   else
0097     error('Error converting %s\n', outName);
0098   end
0099 
0100 end
0101 
0102 % Done
0103 fprintf('\nConversion Finished. \n');
0104 
0105 return

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