get_GE_timestamps

 run_id_vect = get_GE_timestamps(inDir);

 Retrieves a vector of run ID numbers for all EPI images contained in the
 series that resides in inDir

0001 function run_info = get_GE_timestamps(sinfo,dataroot,nslice_per_vol)
0002 % run_id_vect = get_GE_timestamps(inDir);
0003 %
0004 % Retrieves a vector of run ID numbers for all EPI images contained in the
0005 % series that resides in inDir
0006 %
0007 
0008 % 09/27/03 PJ Added checking for presence of root directory
0009 % 09/02/04 PJ Brought into compliance with cat syntax
0010 
0011 nsub = length(sinfo);
0012 
0013 if nargin < 2
0014   dataroot = './';
0015 end
0016 
0017 if nargin < 3
0018   error(['Please specify the number of expected slices per volume and try' ...
0019     ' again.'])
0020 end
0021 
0022 for isub = 1:nsub
0023   s = sinfo(isub);
0024   subj_root = s.id;
0025 
0026   total_epi_series = 0;
0027   for iexam = 1:s.nexams
0028     exam_root = sprintf('%05d', s.exam_nums(iexam));
0029     datapath = fullfile(dataroot, subj_root, exam_root);
0030 
0031     series=s.series_mappings{iexam};
0032     epi_idx = strmatch('epi', char(series{:,2}));
0033     
0034     nser=length(epi_idx);
0035     if ~nser
0036       fprintf('Found no EPI series. Subject %s. Exam %d\n', s.id, iexam);
0037     else
0038       for iser = 1:nser
0039     total_epi_series = total_epi_series + 1;
0040     
0041     % Get series ID number
0042     inDir = fullfile(datapath, series{epi_idx(iser),1});
0043     ser_idstr = inDir(end);
0044     ser_idnum = str2num(ser_idstr);
0045 
0046     % Strip tailing directory
0047     GE_data_root = inDir(1:max(findstr('/',inDir))-1);
0048     
0049     % Make sure the root directory exists
0050     if ~exist(GE_data_root)
0051       fprintf('Directory (%s) does not exist\n', GE_data_root);
0052       break
0053     end
0054 
0055     % List directories and extract those corresponding to the desired series
0056     d = dir(GE_data_root);
0057 
0058     dir_idx = find(cat(1,d.isdir));
0059     ndir = length(dir_idx);
0060 
0061     dirmat = char(d.name);
0062 
0063     good_idx = find((dirmat(:,3) == ser_idstr) & isspace(dirmat(:,4)));
0064 
0065     ser_dirnames = char(d(good_idx).name);
0066 
0067     ndir = size(ser_dirnames,1);
0068 
0069     nimg = 0;
0070     im_user17 = [];
0071     for idir = 1:ndir
0072       curdir = fullfile(GE_data_root, ser_dirnames(idir,:));
0073       subd = dir(curdir);
0074       
0075       dirmat = char(subd.name);
0076       good_idx = strmatch('I.', dirmat);
0077       nfiles = length(good_idx);
0078       
0079       disp(sprintf('Found %d image files in directory %s', nfiles, curdir))
0080       
0081       flist = char(subd(good_idx).name);
0082 
0083       % Loop through and read relevant field from each file.  Reading the entire
0084       % header is really slow, so unless there is an explicit need to do this, don't.
0085       for ifile = 1:nfiles
0086         nimg = nimg+1;
0087         imageFile = fullfile(curdir, flist(ifile,:));
0088         
0089         fid = fopen(imageFile,'r','b');
0090         fseek(fid,4936,'bof');
0091         im_user17(nimg) =  fread(fid,1,'float32');
0092         fclose(fid);
0093       end % for ifile=
0094     end % for idir=
0095     run_info.id_vect{isub,total_epi_series} = im_user17;
0096     run_ids = unique(im_user17);
0097     nrun = length(run_ids);
0098     for irun = 1:nrun
0099       run_info.nvol{isub,total_epi_series}(irun) = sum(im_user17 == ...
0100           run_ids(irun))/nslice_per_vol;
0101     end
0102       end % for iser=
0103     end
0104   end % for iexam=
0105 end % for isub=