1 % Command-line based SPM results display for AA results.
   2 % showAAResults(aadir,subjectn,contrast,correction,threshold)
   3 % Where
   4 % aadir - directory where aap_parameters.mat may be found
   5 % subjectn - I for subject in aap
   6 % contrast - I for contrast in subject's SPM.mat
   7 % correction - 'none','FWE','FDR'
   8 % threshold - p/t value
   9 % All arguments are optional. Try leaving one out (or make it [])
  10 % and see what happens. In particular, leaving out subjectn or
  11 % contrastn brings up reference lists of indices for these.
  12 % 16/1/2011 J Carlin
  13 % 18/2/2011 Updated for SPM8 compatibility
  14 
  15 function showAAResults(aadir,subjectn,contrastn,correction,threshold)
  16 
  17 % If you tell us no dir, assume we're already there
  18 if ~exist('aadir','var') || isempty(aadir)
  19     fprintf('No aadir defined - assume it''s pwd\n')
  20     aadir = pwd;
  21 end
  22 
  23 load(fullfile(aadir,'aap_parameters.mat'))
  24 
  25 
  26 % --- PARAMETER TO CHANGE --- %
  27 %addpath /Users/johan/code/UtilityScripts/BatchPrintSPMs %Change to where this is saved
  28 
  29 subjroot = aadir;
  30 ana_dir = aap.directory_conventions.stats_singlesubj;
  31 
  32 def = '';
  33 if ~exist('correction','var') || isempty(correction)
  34     correction = 'none';
  35     def = 'default ';
  36 end
  37 fprintf('Using %scorrection: %s', def,correction);
  38 
  39 def = '';
  40 if ~exist('threshold','var') || isempty(threshold)
  41     threshold = 0.001;
  42     def = 'default ';
  43 end
  44 fprintf(', %sp<%.03f\n', def, threshold)
  45 
  46 % TODO - second level analysis
  47 
  48 % Get subject paths
  49 for s = 1:length(aap.acq_details.subjects)
  50     subjpaths{s} = aas_getsubjpath(aap,s);
  51 end
  52 
  53 % Test if we need to return a list.
  54 simpletest = @(x) ~exist(x) || isempty(eval(x)) || strcmp(eval(x),'list');
  55 
  56 % Return a list of subjects, with indices
  57 if simpletest('subjectn')
  58     subjlist = [num2str((1:length(subjpaths))','%03d') repmat(' ',length(subjpaths),1) char(subjpaths)];
  59     fprintf('Must define a subject (by its index):\n')
  60     display(subjlist)
  61     return
  62 end
  63 
  64 % Get contrasts for this subject
  65 spmpath = fullfile(subjpaths{subjectn},ana_dir,'SPM.mat');
  66 
  67 if simpletest('contrastn')
  68 	load(spmpath);
  69 	contrastnames = {SPM.xCon.name};
  70     contrastlist = [num2str((1:length(contrastnames))','%03d') repmat(' ',length(contrastnames),1) char(contrastnames)];
  71     fprintf('Must define a contrast (by its index):\n')
  72     display(contrastlist)
  73     return
  74 end
  75 
  76 % Now using SPM8 batch functionality
  77 matlabbatch{1}.spm.stats.results.spmmat = cellstr(spmpath);
  78 matlabbatch{1}.spm.stats.results.conspec.titlestr = '';
  79 matlabbatch{1}.spm.stats.results.conspec.contrasts = contrastn;
  80 matlabbatch{1}.spm.stats.results.conspec.threshdesc = correction;
  81 matlabbatch{1}.spm.stats.results.conspec.thresh = threshold;
  82 matlabbatch{1}.spm.stats.results.conspec.extent = 0;
  83 matlabbatch{1}.spm.stats.results.conspec.mask = struct('contrasts', {}, ...
  84 	'thresh', {}, 'mtype', {});
  85 matlabbatch{1}.spm.stats.results.units = 1;
  86 matlabbatch{1}.spm.stats.results.print = false;
  87 
  88 spm('defaults','FMRI');
  89 spm_jobman('serial',matlabbatch);
  90 return