%FMRI_GET_DATAMAT will create the Event Related or Blocked fMRI datamat
%
%	Usage: fmri_get_datamat(sessionFile, run_idx, brain_mask, ...
%		sd_thresh, ignore_slices, normalize_volume_mean, ...
%		num_skipped_scans, win_size, merge_across_runs_flg, ...
%		behavdata, behavname)
%
%   Input: 
%       sessionFile:  the name of file that contains the session information.
%       brain_mask:  a matrix, with same size as the IMG files, defines the
%                   brain region.  Any element larger than 0 is treated as
%                   part of the brain region.
%       coord_thresh: threshold to generate compute the brain region 
%                    [default: 0.15];
%       ignored_slices: a vector specifies the number of slices which should
%       (optional) be skipped to generate the datamat. [default: []]
%       num_skipped_scans:  (optional) [default: num_skipped_scans = 0]
%       win_size:  (optional) [default: win_size = 8]
%                 number of scans for the temporal windows.
%       run_idx:   (optional) [default: run_idx contains all the runs]
%		  The indices of runs that will be used to generate st_datamat.
%       merge_across_runs_flg:  1 - merge the same condition across all runs
%       (optional)                  to become one row of the ST datamat
%                              0 - merge the same condition only within a run
%                  	       [default: merge_across_runs_flg = 1]
%
%	See also FMRI_GEN_DATAMAT, FMRI_GEN_ST_DATAMAT

%
%	the following paramater is removed:
%
%       sd_thresh: maximum standard deviation (s.d.) for the brain voxels. Any
%       (optional) voxels with s.d. greater than this value will be removed to
%                 avoid the inclusion of venous and sinus. [default: 2];
%

%	called by FMRI_CREATE_DATAMAT_UI
%
%   Modified on 12-May-2003 by Jimmy Shen
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

function fmri_get_datamat(sessionFile, run_idx, varargin)

   progress_hdl = rri_progress_ui('initialize');
   brain_mask_file = '';
   brain_mask = [];
   coord_thresh = [];
   sd_thresh = 2;
   ignore_slices = [];
   normalize_volume_mean = 0;
   num_skipped_scans = 0;
   win_size = 8;

   mask_dims = [];

   if (nargin == 2),
      use_brain_mask = 0;
   elseif (nargin >= 2),
      if  (ischar(varargin{1})) ,	% use predefined brain region
          use_brain_mask = 1;
          brain_mask_file = varargin{1};
          brain_mask = rri_load_img(brain_mask_file);	% use brain mask file
          mask_dims = size(brain_mask);
      else
          use_brain_mask = 0;		% compute brain region from the data
          coord_thresh = varargin{1};
      end;
   
      if (nargin >= 4)
         sd_thresh = varargin{2};
      end;
   
      if (nargin >= 5)
         ignore_slices = varargin{3};
      end;

      if (nargin >= 6)
         normalize_volume_mean = varargin{4};
      end;

      if (nargin >= 7)
         num_skipped_scans = varargin{5};
      end;

      if (nargin >= 8)
         win_size = varargin{6};
      end;

      if (nargin >= 9)
         merge_across_runs_flg = varargin{7};
      end;

      if (nargin >= 10)
         behavdata = varargin{8};
      end;

      if (nargin >= 11)
         behavname = varargin{9};
      end;

      if (nargin >= 12)
         session_win_hdl = varargin{10};
      end;

      if (nargin >= 13)
         normalize_signal_mean = varargin{11};
      end;

      if (nargin >= 14)
         ConsiderAllVoxels = varargin{12};
      end;

      if (nargin >= 15)
         orient = varargin{13};
      end;

   end

   create_datamat_info.brain_mask_file = brain_mask_file;
   create_datamat_info.brain_coord_thresh = coord_thresh;
   create_datamat_info.num_skipped_scans = num_skipped_scans;
   create_datamat_info.run_idx = run_idx;
   create_datamat_info.ignore_slices = ignore_slices;
   create_datamat_info.normalize_volume_mean = normalize_volume_mean;
   create_datamat_info.normalize_with_baseline = normalize_signal_mean;
   create_datamat_info.merge_across_runs = merge_across_runs_flg;

   load(sessionFile);		% load the session information

   pls_data_path = session_info.pls_data_path;
   datamat_prefix = session_info.datamat_prefix;

   %  save temp data into datamat_file
   %
%   fname = sprintf('%s_run.mat',datamat_prefix);
%   datamat_file = fullfile(pls_data_path,fname);

      curr = pwd;
      if isempty(curr)
         curr = filesep;
      end

   if (sessionFile ~= filesep)		

      sessionFile = fullfile(curr,sessionFile);
   end;

   %  get stuff from session_info first
   %
   cond_baseline = session_info.condition_baseline;
   num_conds = session_info.num_conditions;

   % get maximum number of onsets
   %
   max_onsets = 0;

   for i = run_idx
      run_info = session_info.run(i);
      tmp = find_max_onsets(run_info);

      if tmp > max_onsets
         max_onsets = tmp;
      end
   end

   %  get image files path/file name <for read only one image file>
   %
   data_path = run_info.data_path;
   flist = run_info.data_files;

   img_file = fullfile(data_path,flist{1});

   if ~isempty(orient) & ~isempty(orient.orient_pattern)
       dims = orient.dims;
       voxel_size = orient.voxel_size;
       origin = orient.origin;
   else
      [dims,voxel_size,origin] = rri_imginfo(img_file);
   end

   dims = [dims(1) dims(2) 1 dims(3)];

   if (use_brain_mask==1) & ~isequal(dims,mask_dims),
       close(progress_hdl);
       errmsg ='ERROR: Dimensions of the data do not match that of the brain mask!';
       errordlg(errmsg,'Brain Mask Error');
       waitfor(gcf);
       return;
   end;

   %  runs included
   %
   num_runs = session_info.num_runs;
   if ~exist('run_idx','var') | isempty(run_idx),
      run_idx = [1:num_runs];
   else
      num_runs = length(run_idx);
   end;

   %  default is merge_across_runs
   %
   if ~exist('merge_across_runs_flg','var') | isempty(merge_across_runs_flg),
      merge_across_runs_flg = 1;
   end;

   %  skipped scans handling
   %
   if ~exist('num_skipped_scans','var') | isempty(num_skipped_scans)
      num_skipped_scans = 0;
   end;

   %  ignored slices handling
   %
   if ~exist('ignore_slices','var') | isempty(ignore_slices)
      s_idx = [1:dims(4)];			% handle all slices
   else
      idx = zeros(1,dims(4));
      idx(ignore_slices) = 1;
      s_idx = find(s_idx == 0);
   end;

   if (use_brain_mask == 1)			% coords from brain_mask
      coords = find( brain_mask(:) > 0)';
      if ~isempty(ignore_slices)		% skip the slices if any
         m = zeros(dims);		
         m(coords) = 1;
         m(:,:,:,s_idx);
         coords = find(m == 1)';
      end;
   end;

   num_voxels = prod(dims);
   num_cols = num_voxels * win_size;

   if (use_brain_mask == 0)
      coords = zeros(1, num_voxels);		% initial st_coords
   end

   datamat = [];				% st datamat before coords
   st_datamat = [];				% st datamat
   st_evt_list = [];
   st_evt_cnt = [];

   % create step for progress bar
   %
   progress_step = 1 / (num_runs * num_conds * max_onsets);

   for i = run_idx

      run_info = session_info.run(i);

      %  get image files path/file name
      %
      data_path = run_info.data_path;
      flist = run_info.data_files;
      num_files = length(flist);

      for j = 1:num_conds

         num_onsets = length(run_info.evt_onsets{j});

         %  extract the datamat scans that matches the current condition
         %
         row_idx = 0;
         num_onsets = length(run_info.evt_onsets{j});
%         evt_datamat = zeros(num_onsets,num_cols);
         evt_datamat = zeros(1,num_cols);

         rri_progress_ui(progress_hdl, '', ...
            sprintf('Creating datamat for run#%d condition#%d ... ',i,j));

         for k = 1:num_onsets

            start_scan = floor(run_info.evt_onsets{j}(k) - num_skipped_scans) + 1;
            end_scan = start_scan + win_size - 1;

            if isempty(cond_baseline)
               baseline_start = start_scan;
               baseline_end = baseline_start;
            else
               baseline_info = cond_baseline{j};
               baseline_start = start_scan + baseline_info(1);
               baseline_end = baseline_start+baseline_info(2)-1;
            end;

            if (start_scan <= 0) | (num_files < end_scan)	% out of bound
                disp(sprintf('Scans %03d for the condition %d of run%d are not included due to out of bound',floor(run_info.evt_onsets{j}(k)),j,run_idx(i)));
            elseif (baseline_start <= 0)
                disp(sprintf('Scans %03d for the condition %d of run%d are not included due to out of bound baseline',floor(run_info.evt_onsets{j}(k)),j,run_idx(i)));
            else

               %  read in image files
               %
               dataset = zeros(length([start_scan:end_scan]), num_voxels);

               for scan = start_scan:end_scan
                  img_file = [data_path filesep flist{scan}];
                  img = rri_load_img(img_file);

                  if ~isempty(orient) & ~isempty(orient.orient_pattern)
                     img = img(orient.orient_pattern);
                     img = reshape(img,dims);
                  end

                  img = img(:,:,:,s_idx);
                  dataset(scan - start_scan + 1,:) = img(:)';
               end;

               tmp_datamat = dataset;
%               datamat = [datamat; tmp_datamat{j,k}];

               %  find brain voxel coords for each onset, and
               %  accumulated to find common coords for all onsets
               %
               if (use_brain_mask == 0)
                  coords = coords + find_onset_coords(dataset,coord_thresh,ConsiderAllVoxels);
               end

               if (normalize_volume_mean == 1)
                  if (use_brain_mask == 0)
                     mean_dataset = dataset(:,find(coords == 0));
                  else
                     mean_dataset = dataset(:,coords);
                  end

                  mean_dataset = mean(mean_dataset, 2);
                  mean_dataset = mean_dataset(:,ones(1,num_voxels));
                  tmp_datamat = dataset ./ mean_dataset;
               end

               %  read in baseline_signals image files
               %
               dataset = zeros(length([baseline_start:baseline_end]), num_voxels);

               for scan = baseline_start:baseline_end
                  img_file = [data_path filesep flist{scan}];
                  img = rri_load_img(img_file);

                  if ~isempty(orient) & ~isempty(orient.orient_pattern)
                     img = img(orient.orient_pattern);
                     img = reshape(img,dims);
                  end

                  img = img(:,:,:,s_idx);
                  dataset(scan - baseline_start + 1,:) = img(:)';
               end;

               if (normalize_volume_mean == 1)
                  if (use_brain_mask == 0)
                     mean_dataset = dataset(:,find(coords == 0));
                  else
                     mean_dataset = dataset(:,coords);
                  end

                  mean_dataset = mean(mean_dataset, 2);
                  mean_dataset = mean_dataset(:,ones(1,num_voxels));
                  dataset = dataset ./ mean_dataset;
               end

               baseline_signals = mean(dataset,1);
%               datamat = [datamat; baseline_signals{j,k}];

               %  repmat for win_size of rows
               %
               baseline_signals = baseline_signals(ones(1,win_size),:);

               %  if 0, make it less significant, so it can be removed later
               %
		zero_baseline_idx = find(baseline_signals==0);
               baseline_signals(find(baseline_signals==0)) = 99999;

               if normalize_signal_mean
                  tmp_datamat = ...
                     (tmp_datamat - baseline_signals ) * 100 ./ baseline_signals;
               end

		tmp_datamat(zero_baseline_idx) = 0; %99999

               row_idx = row_idx + 1;
%               evt_datamat(row_idx,:) = reshape(tmp_datamat,[1 num_cols]);
               evt_datamat = evt_datamat + reshape(tmp_datamat,[1 num_cols]);

               stp = (i-1)*num_conds*max_onsets + (j-1)*max_onsets + k;
               rri_progress_ui(progress_hdl, '', stp * progress_step)

            end;
         end;				% for num_onsets

         if (merge_across_runs_flg == 0 & row_idx == 0),
            close(progress_hdl);
            errmsg = sprintf('No onsets for condition #%d in the run #%d',j,i);
            errordlg(['ERROR: ' errmsg],'Generating ST Datamat Error');
            waitfor(gcf);
            return;
         end;

         %  Generate the spatial/temporal datamat from evt_datamat
         %  depending on 'across run' or 'within run'
         %
         if (row_idx ~= 0),		% some stimuli for the current condition

            if (merge_across_runs_flg == 0)	% merge data within run only
               st_evt_list = [st_evt_list j];
%               datamat = [datamat; mean(evt_datamat(1:row_idx,:),1)];
               datamat = [datamat; evt_datamat / num_onsets];
            else
               if isempty(st_evt_list) 
                  idx = [];
               else
                  idx = find(st_evt_list == j);
               end;

               if isempty(idx),			% new event
                  st_evt_list = [st_evt_list j];
                  st_evt_cnt = [st_evt_cnt row_idx];
%                  datamat = [datamat; sum(evt_datamat(1:row_idx,:),1)];
                  datamat = [datamat; evt_datamat];
               else
                  st_evt_cnt(idx) = st_evt_cnt(idx) + row_idx;
                  datamat(idx,:) = datamat(idx,:) + ...
			evt_datamat;
%			sum(evt_datamat(1:row_idx,:),1);
               end;
            end;	% if across_run==0
         end;		% for (row_idx~=0)

      end;		% for num_conds

      %  save some memory usage
      %
%      clear('evt_datamat', 'tmp_datamat');
      clear('tmp_datamat');

   end;			% for num_runs (run_idx)

   %    determine the coords of the brain region
   %
   if (use_brain_mask == 0)	% coords from thresh by 'find_onset_coords' 

      coords = find(coords == 0);

   end
% move ahead   else				% coords from brain_mask

   %    apply the coords of the brain region
   %
   for i = 1:size(datamat,1)
      tmp = datamat(i,:);
      tmp = reshape(tmp, [win_size, num_voxels]);

      tmp = tmp(:, coords);
      tmp = reshape(tmp, [1, win_size*length(coords)]);
      st_datamat = [st_datamat; tmp];
   end

   if (merge_across_runs_flg == 1)	% merge across all runs 
      for j=1:length(st_evt_list)
         st_datamat(j,:) = st_datamat(j,:) / st_evt_cnt(j);
      end;
   end;

   [new_evt_list, order_idx] = reorder_evt_list(st_evt_list,num_conds);
   if isempty(new_evt_list),
      close(progress_hdl);
      errmsg = sprintf('ERROR: Some conditions have no trials at all.\n');
      errordlg(errmsg,'Creating ST Datamat Error');
      waitfor(gcf);
      return;
   end;

   st_datamat = st_datamat(order_idx,:);
   st_evt_list = new_evt_list;

   %  everything is done, ready to save the information
   %
   st_dims = dims;
   st_voxel_size = voxel_size;
   st_origin = origin;
%   st_coords = coords_info.common;
   st_coords = coords;
   st_win_size = win_size;

   st_sessionFile = sessionFile;

   if (st_sessionFile ~= filesep),			
      curr = pwd;
      if isempty(curr)
         curr = filesep;
      end

      st_sessionFile = fullfile(curr,st_sessionFile);
   end;

   fname = sprintf('%s_fMRIdatamat.mat',datamat_prefix);
%   st_datafile = fullfile(pls_data_path,fname);
   st_datafile = fullfile(curr,fname);

%   ShowProgress(progress_hdl,(num_runs+2));
   rri_progress_ui(progress_hdl,'',1);
%   ShowProgress(progress_hdl,['Saving ST Datamat into the file: ' fname]);
   rri_progress_ui(progress_hdl,'',['Saving ST Datamat into the file: ' fname]);

   if(exist(st_datafile,'file')==2)  % datamat file with same filename exist
      dlg_title = 'Confirm File Overwrite';
      msg = ['File ',fname,' exist. Are you sure you want to overwrite it?'];
      response = questdlg(msg,dlg_title,'Yes','No','Yes');

      if(strcmp(response,'No'))
%         cd(pls_data_path);

       savfig = [];
       if strcmpi(get(gcf,'windowstyle'),'modal')
          savfig = gcf;
          set(gcf,'windowstyle','normal');
       end

       done1 = 0;
       while ~done1

         putfile_filter = [datamat_prefix,'_fMRIdatamat.mat'];
         [filename, pathname] = uiputfile(putfile_filter,'Save As',350,150);
         if isequal(filename,0)
            close(progress_hdl);
            msg1 = ['ERROR: No file is saved.'];
            %uiwait(msgbox(msg1,'Uncomplete','modal'));
            set(findobj(session_win_hdl,'Tag','MessageLine'),'String',msg1);
            done1=1;
            return;
         else
          if rri_chkfname(filename, 'fMRI', 'datamat')
            done1=1;
            st_datafile = fullfile(pathname, filename);
            session_info.datamat_prefix = strrep(filename,'_fMRIdatamat.mat','');

            try
               save(sessionFile,'session_info');
               setappdata(session_win_hdl,'SessionDatamatPrefix',session_info.datamat_prefix);
               OldSessionInfo = getappdata(session_win_hdl,'OldSessionInfo');
               OldSessionInfo.datamat_prefix = session_info.datamat_prefix;
               setappdata(session_win_hdl,'OldSessionInfo',OldSessionInfo);
            catch
               close(progress_hdl);
               msg1 = ['ERROR: Session file write error, no file is saved'];
               set(findobj(session_win_hdl,'Tag','MessageLine'),'String',msg1);
               return;
            end

            set(findobj(session_win_hdl,'Tag','DatamatPrefixEdit'), ...
		'String', session_info.datamat_prefix);
            msg1 = ['WARNING: Prefix in Session Profile has been renamed to "', ...
			session_info.datamat_prefix, '"'];
            uiwait(msgbox(msg1,'Prefix has been renamed'));
          else
            msg = ['File name must be ended with _fMRIdatamat.mat'];
            uiwait(msgbox(msg,'Wrong filename','modal'));
          end
         end

       end

       if ~isempty(savfig)
          set(savfig,'windowstyle','modal');
       end

      end
   end

   create_ver = plsgui_vernum;

   savfig = [];
   if strcmpi(get(gcf,'windowstyle'),'modal')
      savfig = gcf;
      set(gcf,'windowstyle','normal');
   end

   done = 0;

   while ~done
      try
         save(st_datafile,'st_datamat','st_coords','st_dims','st_voxel_size', ...
                'st_origin','st_evt_list', 'st_win_size','st_sessionFile', ...
		'normalize_volume_mean','behavdata','behavname','create_ver', ...
		'create_datamat_info');
         done = 1;
      catch

       done1=0;
       while ~done1

         putfile_filter = [session_info.datamat_prefix,'_fMRIdatamat.mat'];
         [filename, pathname] = uiputfile(putfile_filter, ...
		'Can not save datamat file, please try again',350,150);

         if isequal(filename,0)
            close(progress_hdl);
            msg1 = ['ERROR: No file is saved.'];
            %uiwait(msgbox(msg1,'Uncomplete','modal'));
            set(findobj(session_win_hdl,'Tag','MessageLine'),'String',msg1);
            done1=1;
            return;
         else
          if rri_chkfname(filename, 'fMRI', 'datamat')
            done1=1;
            st_datafile = fullfile(pathname, filename);
            session_info.datamat_prefix = strrep(filename,'_fMRIdatamat.mat','');

            try
               save(sessionFile,'session_info');
               setappdata(session_win_hdl,'SessionDatamatPrefix',session_info.datamat_prefix);
               OldSessionInfo = getappdata(session_win_hdl,'OldSessionInfo');
               OldSessionInfo.datamat_prefix = session_info.datamat_prefix;
               setappdata(session_win_hdl,'OldSessionInfo',OldSessionInfo);
            catch
               close(progress_hdl);
               msg1 = ['ERROR: Session file write error, no file is saved'];
               set(findobj(session_win_hdl,'Tag','MessageLine'),'String',msg1);
               return;
            end

            set(findobj(session_win_hdl,'Tag','DatamatPrefixEdit'), ...
		'String', session_info.datamat_prefix);
            msg1 = ['WARNING: Prefix in Session Profile has been renamed to "', ...
			session_info.datamat_prefix, '"'];
            uiwait(msgbox(msg1,'Prefix has been renamed'));
          else
            msg = ['File name must be ended with _BfMRIdatamat.mat'];
            uiwait(msgbox(msg,'Wrong filename','modal'));
          end
         end

       end

      end
   end

   if ~isempty(savfig)
      set(savfig,'windowstyle','modal');
   end

   close(progress_hdl);
   set(findobj(session_win_hdl,'Tag','MessageLine'),'String','');
   msg1 = ['WARNING: Do not change file name manually in command window.'];
   uiwait(msgbox(msg1,'File has been saved'));

   return;


   %    determine the coords of the brain region
   %
   if (use_brain_mask == 0)		% compute coords from (temp) datamat
      coords = rri_make_coords(datamat, 1/coord_thresh);
      datamat = datamat(:,coords);

      %  get rid of voxels that have standard deviation "sd_thresh" times larger 
      %  than the grand average standard deviation.
      %
      std_d = std(datamat);
      thresh = mean(std_d) * sd_thresh;
      idx = find(std_d < thresh);
      coords = coords(idx);
   else
      coords = find( brain_mask(:) > 0)';
      if ~isempty(ignore_slices)	% skip the slices if any
         m = zeros(dims);		
         m(coords) = 1;
         m(:,:,:,s_idx);
         coords = find(m == 1)';
      end;
   end;

   %    apply the coords of the brain region
   %
   for j = 1:num_conds
      num_onsets = length(run_info.evt_onsets{j});
      for k = 1:num_onsets
         tmp_datamat{j,k} = tmp_datamat{j,k}(:,coords);
         baseline_signals{j,k} = baseline_signals{j,k}(:,coords);

         if (normalize_volume_mean == 1),
            num_voxels = length(coords);

            mean_tmp_datamat = mean(tmp_datamat{j,k},2);
            tmp_datamat{j,k} = tmp_datamat{j,k} ./ ...
		mean_tmp_datamat(:,ones(1,num_voxels));

            mean_baseline_signals = mean(baseline_signals{j,k},2);
            baseline_signals{j,k} = baseline_signals{j,k} ./ ...
		mean_baseline_signals(:,ones(1,num_voxels));
         end;
      end;
   end;

   ShowProgress(progress_hdl, (num_conds * max_onsets + 1) * progress_step);

   %  save the datamat, which is a matrix contains only the brain voxels.
   %
   ShowProgress(progress_hdl,['Saving datamat into the file: ' fname ]);

   try 
      save(datamat_file,'tmp_datamat','baseline_signals','coords', ...
	'dims','voxel_size','origin','sessionFile','normalize_volume_mean');
   catch
      errmsg = sprintf('ERROR: Cannot save datamat to file: \n   %s.', ...
                       datamat_file);
      errordlg(errmsg,'Save Datamat Error');
      waitfor(gcf);
      return;
   end

   return;						% fmri_get_datamat


%-------------------------------------------------------------------------
%
function detrended_datamat = detrend(datamat);

  num_scans = size(datamat,1);
  linear_term = [1:num_scans]';
  linear_term = linear_term - mean(linear_term);
  quad_term = linear_term .* linear_term;
  
  detrend_terms = [ones(num_scans,1) linear_term quad_term]; 

  beta = detrend_terms \ datamat;
  pred = detrend_terms * beta;

  detrended_datamat = datamat - pred;

  %% add the mean back to the detrended datamat for computing the
  %% percent signal change in later stage.   [by Barry Giesbrecht]
  
  voxel_mean = mean(datamat,1);
  detrended_datamat = detrended_datamat + voxel_mean(ones(1,num_scans),:);

  return;					% detrend


%-------------------------------------------------------------------------
function [new_evt_list,reorder_idx] = reorder_evt_list(evt_list,num_conditions)
%  make sure the row order of the st_datamat is repeat order of
%  conditions, i.e cond#1, cond#2,... cond#1, cond#2, .... etc
%

  num_rep = length(evt_list) / num_conditions;

  [new_evt_list, reorder_idx] = sort(evt_list);
  if ~isequal(reshape(new_evt_list,[num_rep,num_conditions]), ...
             repmat([1:num_conditions],num_rep,1))
     new_evt_list = [];
     reorder_idx = [];
  end;

  return;					% reorder evt_list


%-------------------------------------------------------------------------
function hdl = ShowProgress(progress_hdl,info)

  %  'initialize' - return progress handle if any
  %
  if ischar(progress_hdl) & strcmp(lower(progress_hdl),'initialize'),
     if ~isempty(gcf) & isequal(get(gcf,'Tag'),'ProgressFigure'),
         hdl = gcf;
     else
         hdl = [];
     end;
     return;
  end;


  if ~isempty(progress_hdl)
      if ischar(info)
         rri_progress_status(progress_hdl,'Show_message',info);
      else
         rri_progress_status(progress_hdl,'Update_bar',info);
      end;
      return;
  end;

  if ischar(info),
     disp(info)
  end;

  return;					% ShowProgress


%-------------------------------------------------------------------------
function hdl = ShowProgress2(progress_hdl,info)

  %  'initialize' - return progress handle if any
  %
  if ischar(progress_hdl) & strcmp(lower(progress_hdl),'initialize'),
     if ~isempty(gcf) & isequal(get(gcf,'Tag'),'ProgressFigure'),
         hdl = gcf;
     else
         hdl = [];
     end;
     return;
  end;

  if ~isempty(progress_hdl)
     if ischar(info)
         rri_progress_status(progress_hdl,'Show_message',info);
     else
         rri_progress_status(progress_hdl,'Update_bar',info);
     end;
     return;
  end;

  if ischar(info),
     disp(info)
  end;

  return;					% ShowProgress


%----------------------------------------------------------------------------
%
%  get the maximum number of onsets within a run
%
%----------------------------------------------------------------------------

function max_onsets = find_max_onsets(run_info)

   num_cond = length(run_info.evt_onsets);
   max_onsets = 0;

   for i = 1:num_cond
      if length(run_info.evt_onsets{i}) > max_onsets
         max_onsets = length(run_info.evt_onsets{i});
      end;
   end;

   return;						% find_max_onsets


%----------------------------------------------------------------------------
%
%  find brain voxel coords for each onset, and return onset_coords array
%
%	1:	represents non_brain voxels
%	0:	represents brain voxels
%
%----------------------------------------------------------------------------

function nonbrain_coords = find_onset_coords(dataset,coord_thresh,considerall)

   [num_scans num_voxels] = size(dataset);
   nonbrain_coords = zeros(1,num_voxels);

   for i=1:num_scans,
      scan_threshold = max(dataset(i,:)) * coord_thresh;

      if considerall
         idx = find(dataset(i,:) < scan_threshold);
      else
         idx = find(dataset(i,:) <= scan_threshold);
      end

      nonbrain_coords(idx) = 1; 
   end

   return;