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| function aedes_fmri_gui(DATA,mask) | |
| % fMRI tool GUI | |
| % Check input arguments | |
| if nargin == 0 | |
| error('Too few input arguments.') | |
| elseif nargin == 1 | |
| mask = []; | |
| elseif nargin > 2 | |
| error('Too many input arguments.') | |
| end | |
| % Check data | |
| if isstruct(DATA) && isfield(DATA,'FTDATA') | |
| Dat.data = DATA.FTDATA; | |
| elseif isnumeric(DATA) && ndims(DATA)==4 | |
| Dat.data=DATA; | |
| else | |
| error('Input data has to be a 4D numeric matrix or Aedes data structure!') | |
| end | |
| Dat.nVolumes = size(Dat.data,4); | |
| % Check mask | |
| if islogical(mask) | |
| Dat.mask = mask; | |
| else | |
| Dat.mask = []; | |
| end | |
| % Check mask size | |
| if ~isempty(Dat.mask) | |
| sz_mask = [size(Dat.mask,1),size(Dat.mask,2),size(Dat.mask,3)]; | |
| sz_data = [size(Dat.data,1),size(Dat.data,2),size(Dat.data,3)]; | |
| if ~isequal(sz_mask,sz_data) | |
| warning('Mask size does not match with data volume size. Disabling masking...') | |
| Dat.mask = []; | |
| end | |
| end | |
| % Construct the GUI | |
| H = l_MainGui; | |
| % Build the main GUI ----------------------------------------------------- | |
| function H=l_MainGui() | |
| % Load default font and colors | |
| GD=aedes_gui_defaults; | |
| % Overlay controls figure | |
| fig_h = 500; | |
| fig_w = 500; | |
| fig_location = aedes_dialoglocation([fig_w,fig_h]); | |
| fig_left = fig_location(1); | |
| fig_bottom = fig_location(2); | |
| % Main figure | |
| H.fig = figure('units','pixel',... | |
| 'position',... | |
| [fig_left fig_bottom ... | |
| fig_w fig_h],... | |
| 'Name','Aedes - fMRI Analysis',... | |
| 'numbertitle','off',... | |
| 'tag','aedes_fmri_analysis_tool_fig',... | |
| 'Toolbar','none',... | |
| 'Color',GD.col.mainfig,... | |
| 'Menubar','none',... | |
| 'DockControls','off',... | |
| 'renderer','painters',... | |
| 'resize','off',... | |
| 'CloseRequestFcn',@l_Close,... | |
| 'Handlevisibility','off'); | |
| if ~GD.HG2graphics | |
| set(H.fig, 'DoubleBuffer','on') | |
| end | |
| % % Data uipanel ----------------------------------- | |
| % H.uipanel_data = uipanel('parent',H.fig,... | |
| % 'units','pixel',... | |
| % 'position',[10 fig_h-10-100 fig_w-20 100],... | |
| % 'title','Image data',... | |
| % 'backgroundcolor',GD.col.mainfig); | |
| % Templates uipanel ------------------------------ | |
| % pos = get(H.uipanel_data,'position'); | |
| % H.uipanel_tmpl = uipanel('parent',H.fig,... | |
| % 'units','pixel',... | |
| % 'position',[pos(1) fig_h-20-pos(4)-60 fig_w-20 60],... | |
| % 'title','Analysis parameter templates',... | |
| % 'backgroundcolor',GD.col.mainfig); | |
| H.uipanel_tmpl = uipanel('parent',H.fig,... | |
| 'units','pixel',... | |
| 'position',[10 fig_h-10-60 fig_w-20 60],... | |
| 'title','Analysis parameter templates',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| if ispref('Aedes','fMRIToolTemplates') | |
| tmp = getpref('Aedes','fMRIToolTemplates'); | |
| popup_str = {' ',tmp{:,1}}; | |
| else | |
| popup_str = ' '; | |
| end | |
| H.popup_tmpl = uicontrol('parent',H.uipanel_tmpl,... | |
| 'style','popupmenu','position',[20 10 200 25],... | |
| 'string',popup_str); | |
| pos = get(H.popup_tmpl,'position'); | |
| btn_w = (fig_w-20-20-pos(3)-4*10)/3; | |
| H.loadbtn_tmpl = uicontrol('parent',H.uipanel_tmpl,... | |
| 'style','pushbutton','position',[pos(1)+pos(3)+10 10 btn_w 25],... | |
| 'string','Load',... | |
| 'callback',@l_LoadTemplate); | |
| H.savebtn_tmpl = uicontrol('parent',H.uipanel_tmpl,... | |
| 'style','pushbutton','position',[pos(1)+pos(3)+2*10+btn_w 10 btn_w 25],... | |
| 'string','Save',... | |
| 'callback',@l_SaveTemplate); | |
| H.deletebtn_tmpl = uicontrol('parent',H.uipanel_tmpl,... | |
| 'style','pushbutton','position',[pos(1)+pos(3)+3*10+2*btn_w 10 btn_w 25],... | |
| 'string','Delete',... | |
| 'callback',@l_DeleteTemplate); | |
| % Parameters buttons ------------------------------ | |
| pos = get(H.uipanel_tmpl,'position'); | |
| H.preprocessing_toggle = uicontrol('parent',H.fig,... | |
| 'style','togglebutton','position',[pos(1) pos(2)-20-30 100 30],... | |
| 'string','Preprocessing',... | |
| 'value',1,... | |
| 'callback',@l_ChangeTab); | |
| pos = get(H.preprocessing_toggle,'position'); | |
| H.design_toggle = uicontrol('parent',H.fig,... | |
| 'style','togglebutton','position',[pos(1)+pos(3)+15 pos(2) pos(3:4)],... | |
| 'string','Design',... | |
| 'value',0,... | |
| 'callback',@l_ChangeTab); | |
| pos = get(H.design_toggle,'position'); | |
| H.results_toggle = uicontrol('parent',H.fig,... | |
| 'style','togglebutton','position',[pos(1)+pos(3)+15 pos(2) pos(3:4)],... | |
| 'string','Results',... | |
| 'value',0,... | |
| 'callback',@l_ChangeTab); | |
| % Preprocessing tab ------------------------------- | |
| pos = get(H.preprocessing_toggle,'position'); | |
| H.uipanel_preprocessing = uipanel('parent',H.fig,... | |
| 'units','pixel',... | |
| 'position',[10 10+40 fig_w-20 pos(2)-20-40],... | |
| 'title','Preprocessing',... | |
| 'visible','on',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.uipanel_preprocessing,'position'); | |
| H.TR_tx = uicontrol('parent',H.uipanel_preprocessing,... | |
| 'style','text',... | |
| 'string','Repetition time, TR (sec.):',... | |
| 'position',[20 pos(4)-25-25-10 250 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.TR_tx,'position'); | |
| H.TR_edit = uicontrol('parent',H.uipanel_preprocessing,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 100 25],... | |
| 'backgroundcolor','w'); | |
| H.smooth_checkbox = uicontrol('parent',H.uipanel_preprocessing,... | |
| 'style','checkbox',... | |
| 'string','Spatial smoothing',... | |
| 'value',1,... | |
| 'position',[pos(1) pos(2)-35-5 pos(3:4)],... | |
| 'backgroundcolor',GD.col.mainfig,... | |
| 'callback',@checkbox_callback); | |
| pos = get(H.smooth_checkbox,'position'); | |
| H.smooth_tx = uicontrol('parent',H.uipanel_preprocessing,... | |
| 'style','text',... | |
| 'string','Smoothing kernel FWHM (pixels):',... | |
| 'position',[pos(1)+20 pos(2)-25-5 230 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.smooth_tx,'position'); | |
| H.smooth_edit = uicontrol('parent',H.uipanel_preprocessing,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 100 25],... | |
| 'backgroundcolor','w'); | |
| pos = get(H.smooth_checkbox,'position'); | |
| H.hp_checkbox = uicontrol('parent',H.uipanel_preprocessing,... | |
| 'style','checkbox',... | |
| 'string','Temporal filtering',... | |
| 'value',1,... | |
| 'position',[pos(1) pos(2)-35-25-10 pos(3:4)],... | |
| 'backgroundcolor',GD.col.mainfig,... | |
| 'callback',@checkbox_callback); | |
| pos = get(H.hp_checkbox,'position'); | |
| H.hp_tx = uicontrol('parent',H.uipanel_preprocessing,... | |
| 'style','text',... | |
| 'string','High-pass filter cut-off (sec.):',... | |
| 'position',[pos(1)+20 pos(2)-25-5 230 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.hp_tx,'position'); | |
| H.hp_edit = uicontrol('parent',H.uipanel_preprocessing,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 100 25],... | |
| 'backgroundcolor','w'); | |
| set(H.hp_checkbox,'userdata',[H.hp_tx,H.hp_edit]) | |
| set(H.smooth_checkbox,'userdata',[H.smooth_tx,H.smooth_edit]) | |
| % Design tab -------------------------------------- | |
| pos = get(H.uipanel_preprocessing,'position'); | |
| H.uipanel_design = uipanel('parent',H.fig,... | |
| 'units','pixel',... | |
| 'position',pos,... | |
| 'title','Design',... | |
| 'visible','off',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| H.hrf_tx = uicontrol('parent',H.uipanel_design,... | |
| 'style','text',... | |
| 'string','Hemodynamic response function:',... | |
| 'position',[20 pos(4)-25-25-10 250 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.hrf_tx,'position'); | |
| H.hrf_popup = uicontrol('parent',H.uipanel_design,... | |
| 'style','popupmenu',... | |
| 'string',{'Human','Rodent'},... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 170 25],... | |
| 'backgroundcolor','w'); | |
| H.omit_volumes_tx = uicontrol('parent',H.uipanel_design,... | |
| 'style','text',... | |
| 'string','Omit volumes from analysis (indices):',... | |
| 'position',[pos(1) pos(2)-25-10 250 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.omit_volumes_tx,'position'); | |
| H.omit_volumes_edit = uicontrol('parent',H.uipanel_design,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 170 25],... | |
| 'backgroundcolor','w'); | |
| H.conditions_tx = uicontrol('parent',H.uipanel_design,... | |
| 'style','text',... | |
| 'string','Conditions:',... | |
| 'position',[pos(1) pos(2)-15-10 250 15],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.conditions_tx,'position'); | |
| H.first_condition_tx = uicontrol('parent',H.uipanel_design,... | |
| 'style','text',... | |
| 'string','First condition:',... | |
| 'position',[pos(1)+20 pos(2)-15-5 230 15],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.first_condition_tx,'position'); | |
| H.onsets_tx = uicontrol('parent',H.uipanel_design,... | |
| 'style','text',... | |
| 'string','Onsets (scans):',... | |
| 'position',[pos(1)+20 pos(2)-25-5 210 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.onsets_tx,'position'); | |
| H.onsets_edit = uicontrol('parent',H.uipanel_design,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 170 25],... | |
| 'backgroundcolor','w'); | |
| H.durations_tx = uicontrol('parent',H.uipanel_design,... | |
| 'style','text',... | |
| 'string','Durations (scans):',... | |
| 'position',[pos(1) pos(2)-25-5 210 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.durations_tx,'position'); | |
| H.durations_edit = uicontrol('parent',H.uipanel_design,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 170 25],... | |
| 'backgroundcolor','w'); | |
| H.second_condition_cb = uicontrol('parent',H.uipanel_design,... | |
| 'style','checkbox',... | |
| 'string','Second condition:',... | |
| 'position',[pos(1)-20 pos(2)-20-20 230 20],... | |
| 'horizontalalign','left',... | |
| 'value',0,... | |
| 'backgroundcolor',GD.col.mainfig,... | |
| 'callback',@checkbox_callback); | |
| pos = get(H.second_condition_cb,'position'); | |
| H.onsets2_tx = uicontrol('parent',H.uipanel_design,... | |
| 'style','text',... | |
| 'string','Onsets (scans):',... | |
| 'position',[pos(1)+20 pos(2)-25-5 210 25],... | |
| 'horizontalalign','left',... | |
| 'enable','off',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.onsets2_tx,'position'); | |
| H.onsets2_edit = uicontrol('parent',H.uipanel_design,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 170 25],... | |
| 'backgroundcolor','w',... | |
| 'enable','off'); | |
| H.durations2_tx = uicontrol('parent',H.uipanel_design,... | |
| 'style','text',... | |
| 'string','Durations (scans):',... | |
| 'position',[pos(1) pos(2)-25-5 210 25],... | |
| 'horizontalalign','left',... | |
| 'enable','off',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.durations2_tx,'position'); | |
| H.durations2_edit = uicontrol('parent',H.uipanel_design,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 170 25],... | |
| 'backgroundcolor','w',... | |
| 'enable','off'); | |
| set(H.second_condition_cb,'userdata',... | |
| [H.onsets2_tx,H.onsets2_edit,H.durations2_tx,H.durations2_edit]) | |
| % Results tab ------------------------------------- | |
| pos = get(H.uipanel_preprocessing,'position'); | |
| H.uipanel_results = uipanel('parent',H.fig,... | |
| 'units','pixel',... | |
| 'position',pos,... | |
| 'title','Results',... | |
| 'visible','off',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| H.t_contrast_tx = uicontrol('parent',H.uipanel_results,... | |
| 'style','text',... | |
| 'string','Contrast vector for t-statistics:',... | |
| 'position',[20 pos(4)-25-25-10 250 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.t_contrast_tx,'position'); | |
| H.t_contrast_edit = uicontrol('parent',H.uipanel_results,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 170 25],... | |
| 'backgroundcolor','w'); | |
| H.threshold_tx = uicontrol('parent',H.uipanel_results,... | |
| 'style','text',... | |
| 'string','Threshold (p < value):',... | |
| 'position',[pos(1) pos(2)-25-10 250 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig); | |
| pos = get(H.threshold_tx,'position'); | |
| H.threshold_edit = uicontrol('parent',H.uipanel_results,... | |
| 'style','edit',... | |
| 'string','0.05',... | |
| 'position',[pos(1)+pos(3)+20 pos(2) 170 25],... | |
| 'backgroundcolor','w'); | |
| H.th_fdr_radio = uicontrol('parent',H.uipanel_results,... | |
| 'style','radio',... | |
| 'string','Use FDR-corrected threshold',... | |
| 'value',1,... | |
| 'position',[pos(1)+20 pos(2)-25-5 230 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig,... | |
| 'callback',@radiobutton_callback); | |
| pos = get(H.th_fdr_radio,'position'); | |
| H.th_uncorr_radio = uicontrol('parent',H.uipanel_results,... | |
| 'style','radio',... | |
| 'value',0,... | |
| 'string','Use uncorrected threshold',... | |
| 'position',[pos(1) pos(2)-25-5 230 25],... | |
| 'horizontalalign','left',... | |
| 'backgroundcolor',GD.col.mainfig,... | |
| 'callback',@radiobutton_callback); | |
| pos = get(H.th_uncorr_radio,'position'); | |
| H.use_mask_cb = uicontrol('parent',H.uipanel_results,... | |
| 'style','checkbox',... | |
| 'string','Use brain mask (ROI labeled "mask")',... | |
| 'position',[pos(1)-20 pos(2)-20-20 250 20],... | |
| 'horizontalalign','left',... | |
| 'value',0,... | |
| 'backgroundcolor',GD.col.mainfig); | |
| if ~isempty(Dat.mask) | |
| set(H.use_mask_cb,'value',1) | |
| else | |
| set(H.use_mask_cb,'enable','off') | |
| end | |
| pos = get(H.use_mask_cb,'position'); | |
| H.save_results_cb = uicontrol('parent',H.uipanel_results,... | |
| 'style','checkbox',... | |
| 'string','Save results in a MAT-file in folder:',... | |
| 'position',[pos(1) pos(2)-20-20 250 20],... | |
| 'horizontalalign','left',... | |
| 'value',1,... | |
| 'backgroundcolor',GD.col.mainfig,... | |
| 'callback',@checkbox_callback); | |
| pos = get(H.save_results_cb,'position'); | |
| H.save_results_edit = uicontrol('parent',H.uipanel_results,... | |
| 'style','edit',... | |
| 'string','',... | |
| 'position',[pos(1)+20 pos(2)-25-5 340 25],... | |
| 'backgroundcolor','w',... | |
| 'horizontalalign','left'); | |
| pos = get(H.save_results_edit,'position'); | |
| H.save_results_browse = uicontrol('parent',H.uipanel_results,... | |
| 'style','pushbutton',... | |
| 'string','Browse...',... | |
| 'position',[pos(1)+pos(3)+10 pos(2) 70 25],... | |
| 'callback',@l_BrowserFolder); | |
| pos = get(H.save_results_edit,'position'); | |
| H.view_results_cb = uicontrol('parent',H.uipanel_results,... | |
| 'style','checkbox',... | |
| 'string','View results in Aedes',... | |
| 'position',[pos(1)-20 pos(2)-20-20 250 20],... | |
| 'horizontalalign','left',... | |
| 'value',1,... | |
| 'backgroundcolor',GD.col.mainfig,... | |
| 'callback',@checkbox_callback); | |
| set(H.save_results_cb,'userdata',... | |
| [H.save_results_edit,H.save_results_browse]) | |
| set(H.th_fdr_radio,'userdata',... | |
| [H.th_fdr_radio,H.th_uncorr_radio]) | |
| set(H.th_uncorr_radio,'userdata',... | |
| [H.th_fdr_radio,H.th_uncorr_radio]) | |
| % Start and Close buttons ------------------------- | |
| H.close_btn = uicontrol('parent',H.fig,... | |
| 'style','pushbutton','position',[fig_w-10-100 10 100 30],... | |
| 'string','Close',... | |
| 'callback',@l_Close); | |
| pos = get(H.close_btn,'position'); | |
| H.start_btn = uicontrol('parent',H.fig,... | |
| 'style','pushbutton','position',[pos(1)-10-pos(3) pos(2:4)],... | |
| 'string','Start',... | |
| 'callback',@l_Start); | |
| end | |
| % Enable/disable uicontrols | |
| function checkbox_callback(h,evd) | |
| % Make sure that results are either save or viewed or both | |
| val_save = get(H.save_results_cb,'value'); | |
| val_view = get(H.view_results_cb,'value'); | |
| if ~val_save && ~val_view | |
| if h == H.save_results_cb | |
| set(H.save_results_cb,'value',1) | |
| else | |
| set(H.view_results_cb,'value',1) | |
| end | |
| end | |
| if get(h,'value') | |
| set(get(h,'userdata'),'enable','on') | |
| else | |
| set(get(h,'userdata'),'enable','off') | |
| end | |
| end | |
| function radiobutton_callback(h,evd) | |
| set(get(h,'userdata'),'value',0) | |
| set(h,'value',1) | |
| end | |
| function l_BrowserFolder(h,evd) | |
| d = uigetdir; | |
| if isequal(d,0) | |
| return | |
| end | |
| set(H.save_results_edit,'string',d) | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Change tab | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function l_ChangeTab(h,evd) | |
| panels = [H.uipanel_preprocessing,H.uipanel_design,... | |
| H.uipanel_results]; | |
| btns = [H.preprocessing_toggle,H.design_toggle,... | |
| H.results_toggle]; | |
| set(btns,'value',0) | |
| ind = find(btns == h); | |
| set(h,'value',1) | |
| set(panels(ind),'visible','on') | |
| set(panels(setdiff([1 2 3],ind)),'visible','off') | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Close GUI | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function l_Close(h,evd) | |
| delete(H.fig) | |
| return | |
| resp = questdlg('Are you sure you want to close the fMRI Analysis Tool?',... | |
| 'Close fMRI Analysis Tool',... | |
| 'Yes','No','No'); | |
| if isempty(resp) || strcmpi(resp,'No') | |
| return | |
| end | |
| delete(H.fig) | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Get all inputted values and selections | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function out = l_GetValues() | |
| out = struct; | |
| % Get preprocessing values | |
| out.prep.TR = str2num(get(H.TR_edit,'string')); | |
| out.prep.smooth.do_smooth = get(H.smooth_checkbox,'value'); | |
| out.prep.smooth.kernel = str2num(get(H.smooth_edit,'string')); | |
| out.prep.hp.do_filt = get(H.hp_checkbox,'value'); | |
| out.prep.hp.cutoff = str2num(get(H.hp_edit,'string')); | |
| % Get design values | |
| str=get(H.hrf_popup,'string'); | |
| out.design.hrf = str{get(H.hrf_popup,'value')}; | |
| out.design.omit_volumes = str2num(get(H.omit_volumes_edit,'string')); | |
| out.design.first_condition.onsets =str2num(get(H.onsets_edit,'string')); | |
| out.design.first_condition.durations = str2num(get(H.durations_edit,'string')); | |
| out.design.second_condition.use_second_condition = get(H.second_condition_cb,'value'); | |
| out.design.second_condition.onsets =str2num(get(H.onsets2_edit,'string')); | |
| out.design.second_condition.durations = str2num(get(H.durations2_edit,'string')); | |
| % Get results values | |
| out.results.contrast = str2num(get(H.t_contrast_edit,'string')); | |
| out.results.threshold.p_value = str2num(get(H.threshold_edit,'string')); | |
| if get(H.th_fdr_radio,'value') | |
| out.results.threshold.corr = 'FDR'; | |
| else | |
| out.results.threshold.corr = 'uncorr'; | |
| end | |
| out.results.use_mask = get(H.use_mask_cb,'value'); | |
| out.results.save_results = get(H.save_results_cb,'value'); | |
| out.results.save_results_folder = get(H.save_results_edit,'string'); | |
| out.results.view_in_aedes = get(H.view_results_cb,'value'); | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Set all values from a structure | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function l_SetValues(in_struct) | |
| % Set preprocessing values | |
| set(H.TR_edit,'string',num2str(in_struct.prep.TR)) | |
| set(H.smooth_checkbox,'value',in_struct.prep.smooth.do_smooth); | |
| set(H.smooth_edit,'string',num2str(in_struct.prep.smooth.kernel)); | |
| set(H.hp_checkbox,'value',in_struct.prep.hp.do_filt); | |
| set(H.hp_edit,'string',num2str(in_struct.prep.hp.cutoff)) | |
| % Set design values | |
| if strcmpi(in_struct.design.hrf,'human') | |
| set(H.hrf_popup,'value',1); | |
| else | |
| set(H.hrf_popup,'value',2); | |
| end | |
| set(H.omit_volumes_edit,'string',num2str(in_struct.design.omit_volumes)) | |
| set(H.onsets_edit,'string',num2str(in_struct.design.first_condition.onsets)) | |
| set(H.durations_edit,'string',num2str(in_struct.design.first_condition.durations)) | |
| set(H.second_condition_cb,'value',in_struct.design.second_condition.use_second_condition); | |
| set(H.onsets2_edit,'string',num2str(in_struct.design.second_condition.onsets)); | |
| set(H.durations2_edit,'string',num2str(in_struct.design.second_condition.durations)); | |
| % Set results values | |
| set(H.t_contrast_edit,'string',num2str(in_struct.results.contrast)); | |
| set(H.threshold_edit,'string',num2str(in_struct.results.threshold.p_value)) | |
| if strcmpi(in_struct.results.threshold.corr,'FDR') | |
| set(H.th_fdr_radio,'value',1) | |
| set(H.th_uncorr_radio,'value',0) | |
| else | |
| set(H.th_uncorr_radio,'value',1) | |
| set(H.th_fdr_radio,'value',0) | |
| end | |
| if strcmpi(get(H.use_mask_cb,'enable'),'on') | |
| set(H.use_mask_cb,'value',in_struct.results.use_mask) | |
| end | |
| set(H.save_results_cb,'value',in_struct.results.save_results); | |
| set(H.save_results_edit,'string',in_struct.results.save_results_folder); | |
| set(H.view_results_cb,'value',in_struct.results.view_in_aedes); | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Do sanity check for input values | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function [ok,msg] = l_SanityCheck(in_struct) | |
| ok = false; | |
| msg = ''; | |
| % Check TR | |
| TR = in_struct.prep.TR; | |
| if length(TR) ~= 1 | |
| msg = 'TR'; | |
| return | |
| end | |
| % Check smoothing | |
| if in_struct.prep.smooth.do_smooth | |
| kr_sz = in_struct.prep.smooth.kernel; | |
| if length(kr_sz) ~= 3 | |
| msg = 'smoothing kernel size'; | |
| return | |
| end | |
| end | |
| % Check high-pass filtering | |
| if in_struct.prep.hp.do_filt | |
| co = in_struct.prep.hp.cutoff; | |
| if length(co) ~= 1 | |
| msg = 'high-pass filter cut-off'; | |
| return | |
| end | |
| end | |
| % Check omit volumes | |
| ov = in_struct.design.omit_volumes; | |
| if ~isempty(ov) && any(ov < 1 | ov > Dat.nVolumes) | |
| msg = 'index/indices in omit volumes'; | |
| return | |
| end | |
| % Check first condition onsets and durations | |
| onsets = in_struct.design.first_condition.onsets; | |
| durations = in_struct.design.first_condition.durations; | |
| if length(onsets) ~= length(durations) || isempty(onsets) ... | |
| || any(onsets<1) || any(onsets>Dat.nVolumes) || isempty(durations) ... | |
| || any(durations<1) || any((onsets+durations)>Dat.nVolumes) | |
| msg = 'first condition onsets or durations'; | |
| return | |
| end | |
| % Check 2nd condition onsets and durations | |
| if in_struct.design.second_condition.use_second_condition | |
| onsets = in_struct.design.second_condition.onsets; | |
| durations = in_struct.design.second_condition.durations; | |
| if length(onsets) ~= length(durations) || isempty(onsets) ... | |
| || any(onsets<1) || any(onsets>Dat.nVolumes) || isempty(durations) ... | |
| || any(durations<1) || any((onsets+durations)>Dat.nVolumes) | |
| msg = 'second condition onsets or durations'; | |
| return | |
| end | |
| end | |
| % Check contrast vector | |
| c=in_struct.results.contrast; | |
| if in_struct.design.second_condition.use_second_condition | |
| cols = 3; | |
| else | |
| cols = 2; | |
| end | |
| if length(c) ~= cols | |
| msg = 'contrast vector length'; | |
| return | |
| end | |
| % Check p value | |
| p_val = in_struct.results.threshold.p_value; | |
| if length(p_val) ~= 1 || p_val <= 0 || p_val >= 1 | |
| msg = 'threshold p-value'; | |
| return | |
| end | |
| % Check save folder | |
| if get(H.save_results_cb,'value') | |
| if ~isdir(get(H.save_results_edit,'string')) | |
| msg = 'save directory' | |
| return | |
| end | |
| end | |
| % All passed | |
| ok = true; | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Save parameter template | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function l_SaveTemplate(h,evd) | |
| % Prompt for a name for the template | |
| popup_str = get(H.popup_tmpl,'string'); | |
| popup_val = get(H.popup_tmpl,'value'); | |
| save_new = true; | |
| if popup_val ~= 1 | |
| % Prompt if current template should be overwritten | |
| qResp = questdlg(['Save a new template or overwrite "',popup_str{popup_val},'"?'],... | |
| 'Save a new template or overwrite existing',... | |
| 'Save new','Overwrite','Save new'); | |
| if strcmp(qResp,'Overwrite') | |
| save_new = false; | |
| end | |
| end | |
| if save_new | |
| done = false; | |
| while ~done | |
| resp=aedes_inputdlg('Please write a name for the template',... | |
| 'Template name'); | |
| if isempty(resp) | |
| % Canceled | |
| break | |
| elseif any(strcmpi(resp{1},popup_str)) | |
| h=errordlg(['A template named "',resp{1},'" already exists. Please select unique name.'],... | |
| 'Template already exists','modal'); | |
| uiwait(h) | |
| elseif isempty(strtrim(resp{1})) | |
| h=errordlg(['Template name cannot be empty'],... | |
| 'Template name cannot be empty','modal'); | |
| uiwait(h) | |
| else | |
| done = true; | |
| end | |
| end | |
| if ~done | |
| return | |
| end | |
| resp = resp{1}; | |
| else | |
| resp = popup_str{popup_val}; | |
| end | |
| % Get current values | |
| vals = l_GetValues; | |
| % Save to preferences | |
| if ispref('Aedes','fMRIToolTemplates') | |
| tmp = getpref('Aedes','fMRIToolTemplates'); | |
| else | |
| tmp = {}; | |
| end | |
| if ~save_new | |
| ind = find(strcmp(resp,{tmp{:,1}})); | |
| tmp{ind,2} = vals; | |
| else | |
| tmp(end+1,:) = {resp,vals}; | |
| % Add template to popup list | |
| if iscell(popup_str) | |
| popup_str{end+1} = resp; | |
| else | |
| popup_str = {popup_str,resp}; | |
| end | |
| set(H.popup_tmpl,'string',popup_str,'value',length(popup_str)) | |
| end | |
| setpref('Aedes','fMRIToolTemplates',tmp) | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Load parameter template | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function l_LoadTemplate(h,evd) | |
| popup_str = get(H.popup_tmpl,'string'); | |
| popup_val = get(H.popup_tmpl,'value'); | |
| if popup_val == 1 | |
| return | |
| end | |
| load_name = popup_str{popup_val}; | |
| tmp = getpref('Aedes','fMRIToolTemplates'); | |
| ind = strcmp(load_name,{tmp{:,1}}); | |
| tmpl_values = tmp{ind,2}; | |
| l_SetValues(tmpl_values) | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Delete parameter template | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function l_DeleteTemplate(h,evd) | |
| popup_str = get(H.popup_tmpl,'string'); | |
| popup_val = get(H.popup_tmpl,'value'); | |
| if popup_val == 1 | |
| return | |
| end | |
| resp = questdlg(['Really delete template "',popup_str{popup_val},'"?'],... | |
| 'Confirm template deletion','Yes','No','No'); | |
| if isempty(resp) || strcmpi(resp,'No') | |
| return | |
| end | |
| del_name = popup_str{popup_val}; | |
| tmp = getpref('Aedes','fMRIToolTemplates'); | |
| ind = strcmp(del_name,{tmp{:,1}}); | |
| tmp(ind,:)=[]; | |
| if isempty(tmp) | |
| rmpref('Aedes','fMRIToolTemplates') | |
| else | |
| setpref('Aedes','fMRIToolTemplates',tmp) | |
| end | |
| popup_str(popup_val)=[]; | |
| set(H.popup_tmpl,'string',popup_str,'value',1) | |
| end | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| % Start fMRI analysis | |
| %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% | |
| function l_Start(h,evd) | |
| % Get input values | |
| vals = l_GetValues; | |
| % Do sanity check | |
| [ok,msg] = l_SanityCheck(vals); | |
| if ~ok | |
| errordlg(['Input value error. Invalid ',msg,'.'],... | |
| 'Input value error','modal'); | |
| return | |
| end | |
| % Close GUI | |
| delete(H.fig) | |
| TR = vals.prep.TR; | |
| if vals.design.second_condition.use_second_condition | |
| onset = {vals.design.first_condition.onsets,... | |
| vals.design.second_condition.onsets}; | |
| durat = {vals.design.first_condition.durations,... | |
| vals.design.second_condition.durations}; | |
| else | |
| onset = vals.design.first_condition.onsets; | |
| durat = vals.design.first_condition.durations; | |
| end | |
| if vals.prep.smooth.do_smooth | |
| smooth_sz = vals.prep.smooth.kernel; | |
| else | |
| smooth_sz = []; | |
| end | |
| qFDR = vals.results.threshold.p_value; | |
| contr = vals.results.contrast; | |
| if vals.prep.hp.do_filt | |
| hipass = vals.prep.hp.cutoff; | |
| else | |
| hipass = []; | |
| end | |
| hrf_type = vals.design.hrf; | |
| omitVols = vals.design.omit_volumes; | |
| if vals.results.use_mask | |
| mask = Dat.mask; | |
| else | |
| mask = []; | |
| end | |
| % Do the fMRI analysis | |
| [maps,th] = aedes_fmri_analysis(Dat.data,'TR',TR,... | |
| 'onsets',onset,'durations',durat,... | |
| 'contrast',contr,'smooth',smooth_sz,... | |
| 'p-value',qFDR,... | |
| 'hipass',hipass,'omitvolumes',omitVols,... | |
| 'mask',mask,'hrf',hrf_type,... | |
| 'multicomp',vals.results.threshold.corr); | |
| % Save results to MAT-file | |
| if vals.results.save_results | |
| opts = vals; | |
| fname = ['results_',datestr(now,'YYYY_mm_dd_HHMMSS.FFF'),'.mat']; | |
| save(fullfile(vals.results.save_results_folder,fname),'maps','th','opts') | |
| end | |
| % View results in Aedes | |
| if vals.results.view_in_aedes | |
| overlay.FTDATA = maps.tmap; | |
| overlay.ImageOverlayCmapStr = 'hot'; | |
| overlay.ImageOverlayTholdDirPos = 1; | |
| overlay.ImageOverlayAlpha = 1; | |
| if iscell(onset) | |
| overlay.fMRIonsets = onset{1}; | |
| overlay.fMRIdurats = durat{1}; | |
| else | |
| overlay.fMRIonsets = onset; | |
| overlay.fMRIdurats = durat; | |
| end | |
| if ~isempty(th) | |
| overlay.ImageOverlayThold = th; | |
| overlay.ImOverlayMin = 0; | |
| else | |
| overlay.ImageOverlayAlpha = 0; | |
| end | |
| aedes(DATA,[],overlay); | |
| end | |
| end | |
| end |