% % nov 25,2003 jimmy: response_fn should use common_coords to detect brain % voxel (common_coords in this file), and use org. datamat coords to % get the voxel location in that datamat (st_coords in this file). % %------------------------------------------------------------------------ function fig = bfm_plot_rf(action,varargin) % % bfm_plot_rf(action,action_arg1,...) % Application Data % % STDatamat % SelectedCondition % ObjPositin % PlottedDatamat % AxesBoundary % if ~exist('action','var') | isempty(action) % no action argument return; end; fig = []; if strcmp(action,'STARTUP') PLSresultFile = varargin{1}; init(PLSresultFile); gen_condition_chk_box(1); SetObjPosition; return; elseif strcmp(action,'LINK') % call from other figure PLSresultFile = varargin{1}; fig = init(PLSresultFile); gen_condition_chk_box(1); SetObjPosition; figure(gcbf); return; end; % clear the message line, % % h = findobj(gcf,'Tag','MessageLine'); % set(h,'String',''); if strcmp(action,'LoadSTDatamat') selected_datamat = get(findobj(gcbf,'Tag','STDatamatPopup'),'Value'); gen_condition_chk_box(selected_datamat); if ~getappdata(gcbf,'actualHRF') %getappdata(gcbf,'isbehav') plot_datamatcorrs; else plot_response_fn; end elseif strcmp(action,'change_group') change_group; elseif strcmp(action,'NewCoord') new_coord = varargin{1}; new_xyz = varargin{2}; setappdata(gcf,'Coord',new_coord); setappdata(gcf,'XYZ',new_xyz); if ~getappdata(gcbf,'actualHRF') %getappdata(gcbf,'isbehav') plot_datamatcorrs; else plot_response_fn; end elseif strcmp(action,'PlotBnPress') coord = getappdata(gcf,'Coord'); plot_response_fn; elseif strcmp(action,'SliderMotion') condition_update; elseif strcmp(action,'ResizeFigure') resize_fig; elseif strcmp(action,'DeleteFigure') delete_fig; elseif strcmp(action,'MENU_ExportData') save_response_fn; elseif strcmp(action,'MENU_ExportBehavData') save_response_fn2; elseif strcmp(action,'MENU_ExportDataBehav') save_response_behav; end; return; %-------------------------------------------------------------------------- % function fig = init(PLSresultFile) CallBackFig = gcbf; cond_selection = getappdata(gcf,'cond_selection'); save_setting_status = 'on'; bfm_plot_rf_pos = []; try load('pls_profile'); catch end if ~isempty(bfm_plot_rf_pos) & strcmp(save_setting_status,'on') pos = bfm_plot_rf_pos; else w = 0.8; h = 0.7; x = (1-w)/2; y = (1-h)/2; pos = [x y w h]; end hh = figure('Units','normal', ... 'Name','Voxel Intensity Plot', ... 'NumberTitle','off', ... 'Color', [0.8 0.8 0.8], ... 'DoubleBuffer','on', ... 'DeleteFcn', 'bfm_plot_rf(''DeleteFigure'');', ... 'Position',pos, ... 'Tag','PlotRFFig'); % 'Menubar', 'none', ... % 'Name','Response Function Plot', ... % display 'Datamat: ' % x = 0.05; y = 0.9; w = 0.15; h = 0.06; pos = [x y w h]; fnt = 0.4; h0 = uicontrol('Parent',hh, ... 'Units','normal', ... 'FontUnits', 'normal', ... 'FontSize', fnt, ... 'BackgroundColor', [0.8 0.8 0.8], ... 'Style', 'text', ... 'Position', pos, ... 'HorizontalAlignment', 'left',... 'String', 'Datamat:', ... 'Tag', 'STDatamatLabel'); % create Datamat popup menu % y = 0.84; w = 0.22; pos = [x y w h]; cb_fn = [ 'bfm_plot_rf(''change_group'');']; popup_h = uicontrol('Parent',hh, ... 'units','normal', ... 'FontUnits', 'normal', ... 'FontSize', fnt, ... 'Style', 'popupmenu', ... 'Position', pos, ... 'HorizontalAlignment', 'left',... 'String', ' ', ... 'Value', 1, ... 'Tag', 'STDatamatPopup', ... 'Callback',cb_fn); y = 0.18; h = 0.62; pos = [x y w h]; h0 = uicontrol('Parent',hh, ... 'Units','normal', ... 'BackgroundColor', [0.8 0.8 0.8], ... 'Style', 'frame', ... 'Position', pos, ... 'HorizontalAlignment', 'left',... 'Tag', 'CondFrame'); x = 0.09; y = 0.76; w = 0.14; h = 0.06; pos = [x y w h]; h0 = uicontrol('Parent',hh, ... 'Units','normal', ... 'FontUnits', 'normal', ... 'FontSize', fnt, ... 'BackgroundColor', [0.8 0.8 0.8], ... 'Style', 'text', ... 'Position', pos, ... 'HorizontalAlignment', 'center',... 'String', 'Conditions', ... 'Tag', 'ConditionLabel'); x = 0.05; y = 0.08; w = 0.1; pos = [x y w h]; h0 = uicontrol('Parent',hh, ... 'Units','normal', ... 'FontUnits', 'normal', ... 'FontSize', fnt, ... 'Style', 'push', ... 'Position', pos, ... 'String', 'Plot', ... 'Enable', 'off', ... 'visible', 'off', ... 'Tag', 'PlotButton', ... 'CallBack', 'bfm_plot_rf(''PlotBnPress'');'); x = 0.1; y = 0.08; w = 0.12; pos = [x y w h]; h0 = uicontrol('Parent',hh, ... 'Units','normal', ... 'FontUnits', 'normal', ... 'FontSize', fnt, ... 'Style', 'push', ... 'Position', pos, ... 'String', 'Close', ... 'CallBack', 'close(gcf)', ... 'Tag', 'CloseButton'); x = 0.01; y = 0; w = 1; h = 0.05; pos = [x y w h]; h0 = uicontrol('Parent',hh, ... % Message Line 'Style','text', ... 'Units','normal', ... 'FontUnits', 'normal', ... 'FontSize', fnt, ... 'BackgroundColor',[0.8 0.8 0.8], ... 'ForegroundColor',[0.8 0.0 0.0], ... 'HorizontalAlignment','left', ... 'Position',pos, ... 'String','', ... 'Tag','MessageLine'); h_plot = uimenu('Parent',hh, ... 'Label','&Plot', ... 'Enable','on',... 'visible', 'off', ... 'Tag','PlotMenu'); h0 = uimenu('Parent',h_plot, ... 'Label','Plot individual datamat', ... 'Tag','PlotIndividualData', ... 'Callback','bfm_plot_rf(''MENU_PlotIndividualData'');'); h0 = uimenu('Parent',h_plot, ... 'Label','Plot group data', ... 'Tag','PlotGroupData', ... 'visible', 'off', ... 'Callback','bfm_plot_rf(''MENU_PlotGroupData'');'); h0 = uimenu('Parent',h_plot, ... 'Label','Plot all data', ... 'Tag','PlotAllData', ... 'Callback','bfm_plot_rf(''MENU_PlotAllData'');'); h_option = uimenu('Parent',hh, ... 'Label','&Data', ... 'Tag','DataMenu', ... 'Enable','on',... 'Visible','off'); h0 = uimenu('Parent',h_option, ... 'Label','Export data', ... 'Tag','ExportData', ... 'Callback','bfm_plot_rf(''MENU_ExportData'');'); h0 = uimenu('Parent',h_option, ... 'Label','Export data for behav analysis', ... 'Tag','ExportBehavData', ... 'Callback','bfm_plot_rf(''MENU_ExportBehavData'');'); h_option = uimenu('Parent',hh, ... 'Label','&Data', ... 'Tag','DataMenuBehav', ... 'Enable','on',... 'Visible','off'); h0 = uimenu('Parent',h_option, ... 'Label','Export data', ... 'Tag','ExportDataBehav', ... 'Callback','bfm_plot_rf(''MENU_ExportDataBehav'');'); % set up object location records % x = 0.05; y = 0.9; w = 0.15; h = 0.06; obj(1).name = 'STDatamatLabel'; obj(1).pos = [x 1-y w h]; y = 0.84; w = 0.22; obj(2).name = 'STDatamatPopup'; obj(2).pos = [x 1-y w h]; x = 0.09; y = 0.76; w = 0.14; h = 0.06; obj(3).name = 'ConditionLabel'; obj(3).pos = [x 1-y w h]; y = 0.7; obj(4).name = 'Condition1'; obj(4).pos = [x 1-y w h]; setappdata(hh,'ObjPosition',obj); setappdata(hh,'CallBackFig',CallBackFig'); setappdata(CallBackFig,'VoxelIntensityFig',hh); setappdata(hh,'VoxelIntensityFig',hh); setappdata(hh,'cond_selection',cond_selection); % construct the popup label list % % get_st_datamat_filename(PLSresultFile); % make_datamat_popup(1); if (nargout >= 1), fig = hh; end; setappdata(gcf, 'sa', getappdata(gcbf, 'sa')); setappdata(gcf, 'isbehav', getappdata(gcbf,'isbehav')); setappdata(gcf, 'actualHRF', getappdata(gcbf,'actualHRF')); if ~getappdata(gcbf,'actualHRF') %getappdata(gcbf,'isbehav') set(gcf, 'name', 'Datamat Correlations'); load_datamatcorrs(PLSresultFile); else load_voxel_intensity(PLSresultFile); end return; %-------------------------------------------------------------------------- % function gen_condition_chk_box(selected_idx) num_cond = getappdata(gcf,'num_cond'); cname = getappdata(gcf,'cond_name'); % display 'Conditions: ' % h0 = findobj(gcf,'Tag','ConditionLabel'); if ~isempty(h0) % no condition has been defined yet cond_h = get(h0,'UserData'); for i=1:length(cond_h); delete(cond_h(i)); % remove the old conditions end; end; % create check box for the conditions % h_list = []; for i=1:num_cond, % create the condition check box % h1 = uicontrol('Parent',gcf, ... 'Units','normal', ... 'BackgroundColor', [0.8 0.8 0.8], ... 'Value', 1, ... 'Style', 'text', ... 'String', sprintf(' (%d) %s', i,cname{i}), ... 'HorizontalAlignment', 'left',... 'SelectionHighlight', 'off',... 'FontSize', 10, ... 'Tag', sprintf('Condition%d',i)); % 'Style', 'check', ... % 'Callback',cbf); h_list = [h_list h1]; end; set(h0,'UserData',h_list); % set up the scroll bar for the conditions % h1 = uicontrol('Parent',gcf, ... 'Style', 'slider', ... 'Units','normal', ... 'Tag', 'CondSlider', ... 'Callback','bfm_plot_rf(''SliderMotion'');'); SetObjPosition('ConditionChkBoxes'); setappdata(gcf,'SelectedCondition',ones(1,num_cond)); return; %-------------------------------------------------------------------------- % function h = delete_fig() link_figure = getappdata(gcbf,'LinkFigureInfo'); try rmappdata(link_figure.hdl,link_figure.name); end; try load('pls_profile'); pls_profile = which('pls_profile.mat'); bfm_plot_rf_pos = get(gcbf,'position'); save(pls_profile, '-append', 'bfm_plot_rf_pos'); catch end return; % delete_fig %-------------------------------------------------------------------------- % function obj_pos = GetObjPosition(ObjName) obj = getappdata(gcf,'ObjPosition'); i = 1; while i <= length(obj); if strcmp(ObjName,obj(i).name) obj_pos = obj(i).pos; return; end; i = i+1; end; return; % get_obj_pos %-------------------------------------------------------------------------- % function SetObjPosition(ObjName) hh = getappdata(gcf,'VoxelIntensityFig'); obj = getappdata(hh,'ObjPosition'); % set the positions for all objects % if ~exist('ObjName','var') | isempty(ObjName) ObjName = 'STDatamat'; end; if strcmp(ObjName,'STDatamat') | strcmp(ObjName,'ALL'), for i=1:length(obj), obj_pos = obj(i).pos; obj_pos(2) = 1 - obj_pos(2); set(findobj(hh,'Tag',obj(i).name),'Position',obj_pos); end; end; % set positions for the condition check box % if strcmp(ObjName,'ConditionChkBoxes') | strcmp(ObjName,'ALL'), % find the position of the PLOT Button plot_pos = get(findobj(hh,'Tag', 'PlotButton'),'Position'); lowest_v_pos = plot_pos(2) + plot_pos(4) * 1.5; chk_box_hlist = get(findobj(hh,'Tag','ConditionLabel'),'UserData'); num_cond = length(chk_box_hlist); cond1_pos = GetObjPosition('Condition1'); cond1_pos(2) = 1 - cond1_pos(2); cond_h = 0.06; rows = floor((cond1_pos(2) - lowest_v_pos) / cond_h); pages = ceil(num_cond / rows); v_pos = cond1_pos(2)-mod([1:num_cond]-1,rows)*cond_h; for i=1:num_cond, obj_pos = [cond1_pos(1) v_pos(i) cond1_pos(3) cond1_pos(4)]; if (i <= rows), visibility = 'on'; else visibility = 'off'; end; set(chk_box_hlist(i),'Position',obj_pos,'Visible',visibility); end; % set the slider position % h = findobj(hh,'Tag', 'CondSlider'); if (pages <= 1) set(h,'Visible','off'); else s_pos = [cond1_pos(1)+cond1_pos(3)+0.01 v_pos(rows) 0.02 cond_h*rows]; set(h,'Min',1,'Max',pages, ... 'Position',s_pos, ... 'Value',pages, ... 'Sliderstep',[1/(pages-1)-0.00001 1/(pages-1)] ); set(h,'Visible','on'); set(h,'UserData',rows); end; end; return; % get_obj_pos %-------------------------------------------------------------------------- function make_datamat_popup(data_option) % data_option = 1 - plot individual ST datamat % data_option = 2 - plot group data % data_option = 3 - plot all data popup_h = findobj(gcf,'Tag','STDatamatPopup'); curr_option = get(popup_h,'Userdata'); if ~isempty(curr_option) & (curr_option == data_option) return; % no change, do nothing end; st_filenames = getappdata(gcf,'STFiles') switch (data_option) case {2} % plot individual data num_st_datamat = length(st_filenames); popup_list = cell(1,num_st_datamat); for i=1:num_st_datamat, % get rid of ".mat" extension if there is any if strcmp(st_filenames{i}.name(end-3:end),'.mat')==1 popup_list{i} = sprintf('[%d] %s', ... st_filenames{i}.group, st_filenames{i}.name(1:end-4)); else popup_list{i} = sprintf('[%d] %s', ... st_filenames{i}.group, st_filenames{i}.name); end; end; alignment = 'left'; case {1} % plot group data num_group = st_filenames{end}.group; popup_list = cell(1,num_group); for i=1:num_group, popup_list{i} = sprintf('[ Group #%d ]',i); end; alignment = 'left'; case {3} % plot all data popup_list{1} = '< All Data >'; alignment = 'center'; end; set(popup_h,'String',popup_list,'Userdata',data_option, ... 'HorizontalAlignment', alignment,'Value',1); msg = 'Click a voxel to see the plot'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; % make_datamat_popup %-------------------------------------------------------------------------- function condition_update(sessionFileList,with_path) % h = findobj(gcf,'Tag', 'CondSlider'); rows = get(h,'UserData'); max_page = get(h,'Max'); slider_value = round(get(h,'Value')); page = max_page - slider_value +1; set(h,'Value',slider_value); chk_box_hlist = get(findobj(gcf,'Tag','ConditionLabel'),'UserData'); num_cond = length(chk_box_hlist); visible_list = zeros(1,num_cond); visible_list((page-1)*rows+1:page*rows) = 1; for i=1:num_cond, if(visible_list(i) == 0) set(chk_box_hlist(i),'Visible','off'); else set(chk_box_hlist(i),'Visible','on'); end; end; return; % %-------------------------------------------------------------------------- function get_st_datamat_filename(DatamatFileList) % % INPUT: % sessionFileList - vector of cell structure, each element contains % the full path of a session file. % num_groups = length(DatamatFileList); for i=1:num_groups, fn = DatamatFileList{i}; load( fn, 'session_info', 'selected_conditions' ); [pname, fname] = fileparts(fn); st_filename{i}.name = fname; st_filename{i}.fullname = fn; st_filename{i}.group = i; st_filename{i}.profile = session_info; st_filename{i}.selected_conditions = selected_conditions; end; setappdata(gcf,'STFiles',st_filename); return; % get_st_datamat_filename %-------------------------------------------------------------------------- % function [raw_datamat,coords,num_subj,subj_name,behavname] = ... load_plotted_datamat old_pointer = get(gcf,'Pointer'); set(gcf,'Pointer','watch'); selected_files = get_selected_filename; if (length(selected_files) == 1) warning off; load(selected_files{1},'raw_datamat','coords','session_info', ... 'behavdata','behavname'); warning on; if ~exist('behavname','var') behavname = {}; if exist('behavdata','var') for i=1:size(behavdata, 2) behavname = [behavname, {['behav', num2str(i)]}]; end end end num_subj = session_info.num_subjects; subj_name = session_info.subj_name; else % merge files together % [st_datamat,st_coords,st_win_size,st_evt_list] = ... % merge_st_datamat(selected_files); [tmp,datmat,coords,dims,num_cond_lst,num_subj_lst,... voxel_size,origin] = pet_get_common(selected_files); end; set(gcf,'Pointer',old_pointer); return; % load_plotted_datamat %-------------------------------------------------------------------------- % function [selected_files] = get_selected_filename(select_all_flg), st_filename = getappdata(gcf,'STFiles'); if exist('select_all_flg','var') & (select_all_flg == 1) data_option = 3; else h = findobj(gcf,'Tag','STDatamatPopup'); selected_idx = get(h,'Value'); data_option = get(h,'Userdata'); end; switch (data_option) case {1}, % individual file selected_files{1} = st_filename{selected_idx}.fullname; case {3}, % all data for i=1:length(st_filename), selected_files{i} = st_filename{i}.fullname; end; end; return; % get selected filenames %-------------------------------------------------------------------------- % function [grp_st_datamat,coords,win_size,evt_list] = ... merge_st_datamat(selected_files), num_files = length(selected_files); % compute the common coords first and the total number of events % load(selected_files{1},'st_dims','st_win_size'); total_num_evt = 0; m = zeros(st_dims); for i=1:num_files, load(selected_files{i},'st_coords','st_evt_list'); total_num_evt = total_num_evt + length(st_evt_list); m(st_coords) = m(st_coords) + 1; end; coords = find(m == num_files); % ready to merge the st_datamat together now ... % win_size = st_win_size; num_voxels = length(coords); num_cols = win_size * num_voxels; grp_st_datamat = zeros(total_num_evt,num_cols); evt_list = []; first_row = 1; for i=1:num_files, load(selected_files{i}); coord_idx = find(m(st_coords) == num_files); nr = length(st_evt_list); nc = length(st_coords); last_row = nr + first_row - 1; tmp_datamat = reshape(st_datamat,[nr,win_size,nc]); tmp_datamat = reshape(tmp_datamat(:,:,coord_idx),[nr,num_cols]); grp_st_datamat(first_row:last_row,:) = tmp_datamat; evt_list = [evt_list st_evt_list]; first_row = last_row + 1; clear st_datamat tmp_datamat; end; return; % merge_st_datamat %-------------------------------------------------------------------------- % function plot_response_fn() % extract the currect ploting data % cur_coord = getappdata(gcf,'Coord'); if isempty(cur_coord) msg = 'ERROR: No point has been seleted to plot.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; % find out the coord_idx % st_coords = getappdata(gcf,'STCoords'); common_coords = getappdata(gcf,'common_coords'); coord_idx = find(common_coords == cur_coord); if isempty(coord_idx) msg = 'ERROR: The selected point is outside the brain region.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; coord_idx = find(st_coords == cur_coord); st_datamat = getappdata(gcf,'STDatamat'); st_data = st_datamat; selected_condition = getappdata(gcf,'SelectedCondition'); % generate the plots % cond_idx = find(selected_condition == 1); axes_margin = [.37 .05 .15 .1]; setappdata(gcf,'ST_data',st_data); setappdata(gcf,'PlotCondIdx',cond_idx); if isempty(getappdata(gcf,'CombinePlots')) setappdata(gcf,'CombinePlots',0); end; if isempty(getappdata(gcf,'ShowAverage')) setappdata(gcf,'ShowAverage',0); end; % set up axes, and the values of 'AxesMargin', 'AxesHlds' and 'AxesPos' % setappdata(gcf,'AxesMargin',axes_margin); set_cond_axes(1,1,axes_margin); % set up axes % the following code is to get an intensity array for the voxel and plot it % num_subj = getappdata(gcf,'num_subj'); subj_name = getappdata(gcf,'subj_name'); subjects = [subj_name, {'mean'}]; for k = cond_idx % cond for n = 1:num_subj % subj j = n+(k-1)*num_subj; % row number in datamat intensity(k,n) = st_data(j, coord_idx); intensity_hdl(k,n) = 0; % initialization end intensity_avg_hdl(k) = 0; end intensity_avg = mean(intensity,2); color_code =[ 'bo';'rx';'g+';'m*';'bs';'rd';'g^';'m<';'bp';'r>'; ... 'gh';'mv';'ro';'gx';'m+';'b*';'rs';'gd';'m^';'b<']; % need more color % if num_subj+1 > size(color_code,1) tmp = []; for i=1:ceil((num_subj+1)/size(color_code,1)) tmp = [tmp; color_code]; end color_code = tmp; end cla; grid off; hold on; for k = cond_idx for n = 1:num_subj intensity_hdl(k,n) = plot(k,intensity(k,n), ... color_code(n,:)); end intensity_avg_hdl(k) = bar(k,intensity_avg(k)); set(intensity_avg_hdl(k),'facecolor','none') % set(intensity_avg_hdl(k), 'linewidth', 2); end % normalize with intensity(:), not st_data(:) % min_y = min(intensity(:)); max_y = max(intensity(:)); margin_y = abs((max_y - min_y) / 100); axis([0 length(cond_idx)+1 min_y-margin_y max_y+margin_y]); set(gca, 'xtick', cond_idx); xlabel('Conditions'); ylabel('Intensities'); xyz = getappdata(gcf,'XYZ'); title(['Intensity for subjects and mean at voxel: [',num2str(xyz),']']); hold off; l_hdl = []; if ~isempty(subjects), intensity_legend = [intensity_hdl(1,:), intensity_avg_hdl(1)]; % remove the old legend to avoid the bug in the MATLAB5 old_legend = getappdata(gcf,'LegendHdl'); if ~isempty(old_legend), try delete(old_legend{1}); catch end; end; % create a new legend, and save the handles [l_hdl, o_hdl] = legend(intensity_legend, subjects, 0); set(l_hdl,'color',[0.9 1 0.9]); setappdata(gcf,'LegendHdl',[{l_hdl} {o_hdl}]); else setappdata(gcf,'LegendHdl',[]); end; set(findobj(gcf,'Tag','DataMenu'),'visible','on'); return; %-------------------------------------------------------------------------- % function save_response_fn() st_coords = getappdata(gcf,'STCoords'); common_coords = getappdata(gcf,'common_coords'); xyz = getappdata(gcf,'XYZ'); % extract the currect ploting data % cur_coord = getappdata(gcf,'Coord'); if isempty(cur_coord) msg = 'ERROR: No point has been seleted to plot.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; coord_idx = find(common_coords == cur_coord); if isempty(coord_idx) msg = 'ERROR: The selected point is outside the brain region.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; coord_idx = find(st_coords == cur_coord); % get selected file names % st_files = getappdata(gcf,'DatamatFile'); h = findobj(gcf,'Tag','STDatamatPopup'); selected_idx = get(h,'Value'); selected_files = st_files{selected_idx}; num_cond = getappdata(gcf,'num_cond'); num_subj_lst = getappdata(gcf,'num_subj_lst'); num_subj = num_subj_lst(selected_idx); mask = 1:num_subj*num_cond; mask = reshape(mask, [num_subj, num_cond]); % extract the data of the selected voxel % st_data = getappdata(gcf,'STDatamat'); data = st_data(:,coord_idx); % save behavdata % for i = 1:size(mask,1) behavdata.subject{i} = [data(mask(i,:))]'; end; [filename, pathname] = ... uiputfile('*_BfMRI_rf_plot.mat','Save the Response Functions',350,150); if ischar(filename) & isempty(findstr(lower(filename),'_bfmri_rf_plot')) filename = [filename, '_BfMRI_rf_plot.mat']; end if isequal(filename,0) return; end; rf_plot_file = fullfile(pathname,filename); xyz_str = 'xyz'; sa = getappdata(gcf, 'sa'); if ~isempty(sa) & sa == 1 yzx = xyz; xyz_str = 'yzx'; elseif ~isempty(sa) & sa == 0 xzy = xyz; xyz_str = 'xzy'; end try save (rf_plot_file, 'selected_files', 'data', xyz_str ); catch msg = sprintf('Cannot save the response function data to %s',rf_plot_file); set(findobj(gcf,'Tag','MessageLine'),'String',['ERROR: ', msg]); status = 0; return; end; return; % save_response_fn %-------------------------------------------------------------------------- % function save_response_fn2() st_coords = getappdata(gcf,'STCoords'); common_coords = getappdata(gcf,'common_coords'); xyz = getappdata(gcf,'XYZ'); % extract the currect ploting data % cur_coord = getappdata(gcf,'Coord'); if isempty(cur_coord) msg = 'ERROR: No point has been seleted to plot.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; coord_idx = find(common_coords == cur_coord); if isempty(coord_idx) msg = 'ERROR: The selected point is outside the brain region.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; coord_idx = find(st_coords == cur_coord); % get selected file names % st_files = getappdata(gcf,'DatamatFile'); h = findobj(gcf,'Tag','STDatamatPopup'); selected_idx = get(h,'Value'); selected_files = st_files{selected_idx}; num_cond = getappdata(gcf,'num_cond'); num_subj_lst = getappdata(gcf,'num_subj_lst'); num_subj = num_subj_lst(selected_idx); mask = 1:num_subj*num_cond; mask = reshape(mask, [num_subj, num_cond]); % extract the data of the selected voxel % st_data = getappdata(gcf,'STDatamat'); data = st_data(:,coord_idx); % save behavdata % for i = 1:size(mask,1) behavdata.subject{i} = [data(mask(i,:))]'; end; pattern = ... ['*_BfMRI_grp',num2str(selected_idx),'_subj1_behavdata1.txt']; [filename, pathname] = uiputfile(pattern,'Save Behav Data',350,150); if isequal(filename,0) return; end; for i = 1:size(mask,1) rf_plot_file = fullfile(pathname, ... sprintf('%s_BfMRI_grp%d_subj%d_behavdata1.txt',filename,selected_idx,i)); behavdata = data(mask(i,:)); save (rf_plot_file, '-ascii', 'behavdata'); end return; % save_response_fn2 %-------------------------------------------------------------------------- % function save_response_behav() xyz = getappdata(gcf,'XYZ'); % extract the currect ploting data % cur_coord = getappdata(gcf,'Coord'); if isempty(cur_coord) msg = 'ERROR: No point has been seleted to plot.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; % find out the coord_idx % st_coords = getappdata(gcf,'STCoords'); common_coords = getappdata(gcf,'common_coords'); coord_idx = find(common_coords == cur_coord); if isempty(coord_idx) msg = 'ERROR: The selected point is outside the brain region.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; coord_idx = find(st_coords == cur_coord); st_data = getappdata(gcf,'datamatcorrs'); data = st_data(:,coord_idx); [filename, pathname] = ... uiputfile('*_BfMRI_datamatcorr_plot.mat','Save the Response Functions',350,150); if ischar(filename) & isempty(findstr(lower(filename),'_bfmri_datamatcorr_plot')) filename = [filename, '_BfMRI_datamatcorr_plot.mat']; end if isequal(filename,0) return; end; rf_plot_file = fullfile(pathname,filename); try save (rf_plot_file, 'data', 'xyz' ); catch msg = sprintf('Cannot save the response function data to %s',rf_plot_file); set(findobj(gcf,'Tag','MessageLine'),'String',['ERROR: ', msg]); status = 0; return; end; return; % save_response_behav %-------------------------------------------------------------------------- % function set_cond_axes(num_rows,num_cols,axes_margin) % % Define the axes for the response functions of different conditions % % axes_margin: [left right bottom top], which specified in terms of % normal unit respect to the figure; % show_avg = getappdata(gcf,'ShowAverage'); if (show_avg == 1), num_cols = num_cols + 1; end; % clear up the old handles % old_hdls = getappdata(gcf,'AxesHdls'); if ~isempty(old_hdls) for i=1:length(old_hdls(:)) if ishandle(old_hdls{i}), delete(old_hdls{i}); end end; end; old_hdls = getappdata(gcf,'AxesCombineHdls'); if ~isempty(old_hdls) for i=1:length(old_hdls(:)) if ishandle(old_hdls{i}), delete(old_hdls{i}); end end; end; f_pos = get(gcf,'Position'); axes_boundary(1) = axes_margin(1); axes_boundary(2) = 1 - axes_margin(2); axes_boundary(3) = axes_margin(3); axes_boundary(4) = 1 - axes_margin(4); % plot data in each axis % ax_hdls = cell(num_rows,num_cols); ax_pos = cell(num_rows,num_cols); ax_combine_hdls = cell(num_rows,1); ax_combine_pos = cell(num_rows,1); plot_width = (axes_boundary(2) - axes_boundary(1)) / num_cols; plot_height = (axes_boundary(4) - axes_boundary(3)) / num_rows; axes_min_x = axes_boundary(1); axes_min_y = axes_boundary(3); for row=1:num_rows, axes_y = axes_min_y + plot_height*(num_rows-row); % for separate plots within each condition % for col=1:num_cols, % determine the position of the figure % axes_x = axes_min_x + plot_width*(col-1); if (col == num_cols & show_avg == 1) axes_pos = [axes_x+0.02 axes_y plot_width-0.01 plot_height-0.03]; else axes_pos = [axes_x axes_y plot_width-0.01 plot_height-0.03]; end; ax = axes('units','normal','Position',axes_pos); set(ax,'units',get(gcf,'defaultaxesunits')); set(ax,'visible','off'); ax_hdls{row,col} = ax; ax_pos{row,col} = axes_pos; end, % for combine plots within each condition % combine_axes_x = axes_min_x; combine_axes_y = axes_y; if (show_avg == 1) combine_axes_w = plot_width*(num_cols-1)-0.01; else combine_axes_w = plot_width*num_cols-0.01; end; combine_axes_h = plot_height-0.03; axes_pos = [combine_axes_x combine_axes_y combine_axes_w combine_axes_h]; ax = axes('units','normal','Position',axes_pos, ... 'box', 'on', ... 'tickdir', 'out', ... 'ticklength', [0.005 0.005]); set(ax,'units',get(gcf,'defaultaxesunits')); % set(ax,'visible','off'); ax_combine_hdls{row} = ax; ax_combine_pos{row} = axes_pos; end; setappdata(gcf,'AxesHdls',ax_hdls); setappdata(gcf,'AxesPos',ax_pos); setappdata(gcf,'AxesCombineHdls',ax_combine_hdls); setappdata(gcf,'AxesCombinePos',ax_combine_pos); return; % set_cond_axes %-------------------------------------------------------------------------- % function plot_datamatcorrs % extract the currect ploting data % cur_coord = getappdata(gcf,'Coord'); if isempty(cur_coord) msg = 'ERROR: No point has been seleted to plot.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; % find out the coord_idx % st_coords = getappdata(gcf,'STCoords'); common_coords = getappdata(gcf,'common_coords'); coord_idx = find(common_coords == cur_coord); if isempty(coord_idx) msg = 'ERROR: The selected point is outside the brain region.'; set(findobj(gcf,'Tag','MessageLine'),'String',msg); return; end; coord_idx = find(st_coords == cur_coord); num_cond = getappdata(gcf,'num_cond'); st_data = getappdata(gcf,'datamatcorrs'); num_behav = getappdata(gcf,'num_behav'); % generate the plots % cond_idx = [1:num_cond]; axes_margin = [.37 .05 .15 .1]; setappdata(gcf,'ST_data',st_data); setappdata(gcf,'PlotCondIdx',cond_idx); if isempty(getappdata(gcf,'CombinePlots')) setappdata(gcf,'CombinePlots',0); end; if isempty(getappdata(gcf,'ShowAverage')) setappdata(gcf,'ShowAverage',0); end; % set up axes, and the values of 'AxesMargin', 'AxesHlds' and 'AxesPos' % setappdata(gcf,'AxesMargin',axes_margin); set_cond_axes(1,1,axes_margin); % set up axes behavname = getappdata(gcf,'behavname'); for k = cond_idx % cond for n = 1:num_behav % behav j = n+(k-1)*num_behav; % row number in datamat intensity(j) = st_data(j, coord_idx); end end mask = []; for i=1:num_behav for j=1:num_cond mask = [mask (j-1)*num_behav+i]; end end cla;grid on;box on;hold on; load('rri_color_code'); for i=1:num_behav for j=1:num_cond k = (i-1)*num_cond + j; bar_hdl = bar(k, intensity(mask(k))); set(bar_hdl,'facecolor',color_code(j,:)); end end min_x = 0.5; max_x = num_cond * num_behav + 0.5; min_y =-1; max_y = 1; margin_x = abs((max_x - min_x) / 20); margin_y = abs((max_y - min_y) / 20); axis([min_x-margin_x,max_x+margin_x,min_y-margin_y,max_y+margin_y]); set(gca,'xtick',[1:num_cond:num_cond*num_behav]); cond_name = getappdata(gcf,'cond_name'); set(gca,'xticklabel',behavname); ylabel('Correlation'); xyz = getappdata(gcf,'XYZ'); title(['Datamat correlations at voxel: [',num2str(xyz),']']); hold off; l_hdl = []; if ~isempty(cond_name), % remove the old legend to avoid the bug in the MATLAB5 old_legend = getappdata(gcf,'LegendHdl'); if ~isempty(old_legend), try delete(old_legend{1}); catch end; end; % create a new legend, and save the handles [l_hdl, o_hdl] = legend(cond_name, 0); set(l_hdl,'color',[0.9 1 0.9]); setappdata(gcf,'LegendHdl',[{l_hdl} {o_hdl}]); else setappdata(gcf,'LegendHdl',[]); end; set(findobj(gcf,'Tag','DataMenuBehav'),'visible','on'); return; % plot_datamatcorrs %-------------------------------------------------------------------------- % function load_datamatcorrs(PLSresultFile) old_pointer = get(gcf,'Pointer'); set(gcf,'Pointer','watch'); warning off; load(PLSresultFile, 'datamatcorrs_lst', 'num_subj_lst', 'behavname', ... 'num_conditions', 'st_coords', 'cond_name', 'subj_name'); warning on; common_coords = st_coords; if ~exist('datamatcorrs_lst', 'var') uiwait(msgbox('Need use new version to run PLS analysis again in order to get the correlation file')); return; end % apply origin_pattern here % mainfig = getappdata(gcf,'CallBackFig'); origin_pattern = getappdata(mainfig,'origin_pattern'); if ~isempty(origin_pattern) dims = getappdata(mainfig,'STDims'); new_coord = zeros(dims); new_coord(st_coords) = 1; new_coord = find(new_coord(origin_pattern)); for i=1:length(datamatcorrs_lst) datamat = datamatcorrs_lst{i}; datamat = rri_xy_orient_data(datamat',st_coords,new_coord,... dims,origin_pattern); datamatcorrs_lst{i} = datamat'; end st_coords = new_coord; common_coords = new_coord; end setappdata(gcf,'datamatcorrs_lst',datamatcorrs_lst); setappdata(gcf,'STCoords',st_coords); setappdata(gcf,'common_coords',common_coords); setappdata(gcf,'num_subj_lst',num_subj_lst); setappdata(gcf,'num_cond',num_conditions); setappdata(gcf,'behavname',behavname); setappdata(gcf,'subj_name',subj_name); setappdata(gcf,'cond_name',cond_name); setappdata(gcf,'num_behav',length(behavname)); setappdata(gcf,'datamatcorrs', datamatcorrs_lst{1}); setappdata(gcf,'num_behav_subj',num_subj_lst(1)); num_group = length(num_subj_lst); popup_list = cell(1,num_group); for i=1:num_group popup_list{i} = sprintf('[ Group #%d ]',i); end; popup_h = findobj(gcf,'Tag','STDatamatPopup'); set(popup_h,'String',popup_list, ... 'HorizontalAlignment', 'left','Value',1); set(gcf,'Pointer',old_pointer); return; %-------------------------------------------------------------------------- % function change_group popup_h = findobj(gcf,'Tag','STDatamatPopup'); grp_idx = get(popup_h,'value'); if ~getappdata(gcf,'actualHRF') %getappdata(gcf,'isbehav') datamatcorrs_lst = getappdata(gcf,'datamatcorrs_lst'); num_subj_lst = getappdata(gcf,'num_subj_lst'); setappdata(gcf,'datamatcorrs', datamatcorrs_lst{grp_idx}); setappdata(gcf,'num_behav_subj',num_subj_lst(grp_idx)); plot_datamatcorrs; else datamat_lst = getappdata(gcf,'datamat_lst'); subj_name_lst = getappdata(gcf,'subj_name_lst'); num_subj_lst = getappdata(gcf,'num_subj_lst'); setappdata(gcf,'STDatamat', datamat_lst{grp_idx}); setappdata(gcf,'subj_name', subj_name_lst{grp_idx}); setappdata(gcf,'num_subj', num_subj_lst(grp_idx)); plot_response_fn; end return; %-------------------------------------------------------------------------- % function load_voxel_intensity(PLSresultFile) cond_selection = getappdata(gcf,'cond_selection'); old_pointer = get(gcf,'Pointer'); set(gcf,'Pointer','watch'); warning off; % load(PLSresultFile, 'datamatcorrs_lst', 'num_subj_lst', 'behavname', ... % 'num_conditions', 'st_coords', 'cond_name', 'subj_name'); load(PLSresultFile, 'SessionProfiles', 'subj_group', 'num_conditions', ... 'st_coords', 'cond_name'); warning on; rri_changepath('bfmriresult'); common_coords = st_coords; if ~exist('subj_group', 'var') uiwait(msgbox('Need use new version to run PLS analysis again in order to get the correlation file')); return; end num_group = length(SessionProfiles); DatamatFile = cell(size(SessionProfiles)); datamat_lst = {}; subj_name_lst = {}; num_subj_lst = []; for i = 1:num_group grp_datamat = []; subj_name = {}; num_subj = length(SessionProfiles{i}); % session group (actually subj.) for n = 1:num_subj load(SessionProfiles{i}{n}); rri_changepath('bfmrisession'); num_conditions = session_info.num_conditions; % if findstr('BfMRIsession.mat', SessionProfiles{i}{n}) % DatamatFile{i}{n} = sprintf('%s_BfMRIdatamat.mat', session_info.datamat_prefix); % else % DatamatFile{i}{n} = sprintf('%s_fMRIdatamat.mat', session_info.datamat_prefix); % end if isempty(cond_selection) cond_selection = ones(1, num_conditions); else num_conditions = sum(cond_selection); end % DatamatFile{i}{n} = strrep(SessionProfiles{i}{n}, 'session', 'datamat'); DatamatFile{i}{n} = fullfile(session_info.pls_data_path, ... [session_info.datamat_prefix, '_BfMRIdatamat.mat']); load(DatamatFile{i}{n}); [tmp, idx] = intersect(st_coords, common_coords); st_datamat = st_datamat(:,idx); % task_idx = cell(1, num_conditions); mean_datamat = zeros(num_conditions, size(st_datamat,2)); % compute the mean data of each condition for this session group % cnt = 1; for k = find(cond_selection) mean_datamat(cnt,:) = mean(st_datamat(find(st_evt_list == k),:), 1); cnt = cnt + 1; end grp_datamat = [grp_datamat; mean_datamat]; subj_name = [subj_name, {['Subj', num2str(n)]}]; end % convert to 'subj in cond' form % mask = [1 : (num_conditions * num_subj)]; mask = reshape(mask, [num_conditions, num_subj]); mask = mask'; mask = mask(:); num_subj_lst = [num_subj_lst num_subj]; coords = st_coords(idx); % apply origin_pattern here % mainfig = getappdata(gcf,'CallBackFig'); origin_pattern = getappdata(mainfig,'origin_pattern'); if ~isempty(origin_pattern) dims = getappdata(mainfig,'STDims'); new_coord = zeros(dims); new_coord(coords) = 1; new_coord = find(new_coord(origin_pattern)); grp_datamat = ... rri_xy_orient_data(grp_datamat',coords,new_coord, ... dims,origin_pattern); grp_datamat = grp_datamat'; end datamat_lst{i} = grp_datamat(mask, :); subj_name_lst{i} = subj_name; end if ~isempty(origin_pattern) st_coords = change_coords(st_coords, dims, origin_pattern); common_coords = change_coords(common_coords, dims, origin_pattern); end setappdata(gcf,'DatamatFile',DatamatFile); setappdata(gcf,'datamat_lst',datamat_lst); setappdata(gcf,'STCoords',st_coords); setappdata(gcf,'num_subj_lst',num_subj_lst); setappdata(gcf,'subj_name_lst',subj_name_lst); setappdata(gcf,'num_cond',num_conditions); setappdata(gcf,'cond_name',cond_name); setappdata(gcf,'STDatamat', datamat_lst{1}); setappdata(gcf,'subj_name',subj_name_lst{1}); setappdata(gcf,'num_subj',num_subj_lst(1)); setappdata(gcf,'common_coords',common_coords); popup_list = cell(1,num_group); for i=1:num_group popup_list{i} = sprintf('[ Group #%d ]',i); end; popup_h = findobj(gcf,'Tag','STDatamatPopup'); set(popup_h,'String',popup_list, ... 'HorizontalAlignment', 'left','Value',1); set(gcf,'Pointer',old_pointer); return; %-------------------------------------------------------------------------- % function new_coords = change_coords(old_coords, dims, pattern) img = zeros(dims); img(old_coords) = 1; img = img(pattern); new_coords = find(img); return;