1 % MarsBaR batch script to show off MarsBaR batching
   2 %  See http://marsbar.sourceforge.net
   3 %Adapted by J Grahn
   4 
   5 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   6 %Need to be IN directory where con images are.
   7 %%%%%%%%%%%%%%%%%%%%%%%%%%%
   8 
   9  root_dir = '/imaging/jessica/Beat/RFX/';
  10 %sesses = {'sess1','sess2' 'sess3'};
  11 con_dir = 'cons/' %where contrast images are, subdirectory of root directory
  12 con_dirname = 'AudVis' %this is prefixed to the text files that contain the extracted data
  13 % Directory to store (and load) ROIs
  14 roi_dir = fullfile(root_dir, 'ROIs'); %where rois are, subdirectory of root directory
  15 %  roi_dir = '/imaging/jessica/anatomy toolboxes/rois'; 
  16 % MarsBaR version check
  17 if isempty(which('marsbar'))
  18   error('Need MarsBaR on the path');
  19 end
  20 v = str2num(marsbar('ver'));
  21 if v < 0.35
  22   error('Batch script only works for MarsBaR >= 0.35');
  23 end
  24 marsbar('on');  % needed to set paths etc
  25 
  26 % SPM version check. We need this to guess which model directory to use and
  27 % to get the SPM configured design name. 
  28 spm_ver = spm('ver');
  29 sdirname = [spm_ver '_ana'];
  30 if strcmp(spm_ver, 'SPM99') 
  31   conf_design_name = 'SPMcfg.mat';
  32 else
  33   spm_defaults;
  34   conf_design_name = 'SPM.mat';
  35 end
  36 
  37 % Set up the SPM defaults, just in case
  38 spm('defaults', 'fmri');
  39 
  40 % We will do estimation for all ROIs in this directory: remove prefix as
  41 % necessary to get right filter to load the files
  42 roinames = dir(fullfile(roi_dir, 'roi*_roi.mat'))
  43 
  44 P = dir(fullfile(root_dir,con_dir,'*.img'));       % get images from contrast directory where they are stored
  45 V = spm_vol(P);
  46 D = strvcat(V(:).name); %load images into format for Marsbar
  47 
  48  for roi_no = 1:length(roinames)
  49     roi_array{roi_no} = maroi(fullfile(roi_dir, roinames(roi_no).name));
  50 
  51     % Extract data
  52   Y = get_marsy(roi_array{roi_no}, D, 'mean');%get the values
  53 %mars_arm('save', 'roi_data', 'test.mat');
  54 [datamean datavar o] = summary_data(Y, 'mean'); %assign the mean extractions for each ROI and each image to variable called datamean
  55 regionname{roi_no}  = char(region_name(Y)); %note the regionname
  56 if roi_no ==1
  57     data = datamean;
  58     regionnames = char(regionname{roi_no});
  59 else
  60     data = [data datamean];
  61     regionnames = strvcat([regionnames ' ' char(regionname{roi_no})]);
  62 end
  63 %data{roi_no} = datamean;
  64 
  65 %[Y Yvar o] = summary_data(o, 'median');
  66 %      % MarsBaR estimation
  67 %      E = estimate(D, Y);
  68 %      
  69 %      % Add contrast, return model, and contrast index
  70 %      [E Ic] = add_contrasts(E, 'stim_hrf', 'T', [1 0 0]);
  71 %      
  72 %      % Get, store statistics
  73 %      stat_struct(ss) = compute_contrasts(E, Ic);
  74 %      
  75 %      % And fitted time courses
  76 %      [this_tc dt] = event_fitted(E, event_spec, event_duration);
  77 %  
  78 %      % Make fitted time course into ~% signal change
  79 %      tc(:, ss) = this_tc / block_means(E) * 100;
  80  end
  81 %assign concatenated data to file and save data, regionnames, and image
  82 %file list to 3 separate files.
  83 
  84 fname = [con_dirname 'extracteddata.txt'] %this file contains as many columns as ROIS extracted, and as many rows as you have con images
  85 save(fname, 'data', '-ascii');
  86 
  87 fname2 = [con_dirname 'imgnames.txt']; %the list of the con images extracted from
  88 fid = fopen(fname2, 'w');
  89 fprintf(fid,'%s\n', P.name);
  90 fclose(fid);
  91 
  92 fname3 = [con_dirname 'regions.txt']; %the list of the rois extracted 
  93 fid = fopen(fname3, 'w');
  94 fprintf(fid, regionnames);
  95 fclose(fid);