SVMCrossVal.git

@@ -40,7 +40,7 @@ for kImage=1:nImage

             x = roicenter(1,iVoxel)+x(sel(:));

             y = roicenter(2,iVoxel)+y(sel(:));

             z = roicenter(3,iVoxel)+z(sel(:));

-            [x y z]

+%             [x y z]

         end;

         dat = spm_sample_vol(V(kImage), x, y, z,0);

@@ -16,6 +16,8 @@ end

 function preprocess(model,task)

 % parse the GUI and pass parameters as structure

+evalin('base','clear(''preprocessedData'')');

+

 timeLine = getTimeLineParams(model);

 subjects = getSubjectCellList(model);

 classDef = parseClassDef(model);

@@ -112,7 +114,7 @@ if(~(isa(preprocessedData,'struct')))

     display('you need to preprocess some data before this step');

     return

 end

-

+warn = warning('off','all');

 header            = preprocessedData.header;

 header.frameShift = getFrameShiftParams(model);

 data              = preprocessedData.subjectdata;

@@ -163,8 +165,8 @@ switch task

 end

-% disp('warings restored');

-% warning('on',warn);

+disp('warings restored');

+warning(warn);

 end

 function decode_plot(model,type)

@@ -1,7 +1,8 @@

 function output =  runFBSImageMaskMode(header,subjectdata,fbsargs)

 addpath('NIFTI_20090325');

-DEBUG = 1;

+DEBUG = 0;

+NORM_DECODE = 0; % 1: normalize to [-1:1], 0: normalize to [0:1]

 savePath = fullfile('output',datestr(now,30));

 mkdir(savePath);

@@ -196,7 +197,6 @@ for timeShiftIdx = fbsTimeLine

                     svmdata   = svmdata(rndindex,:);

                     svmlabel  = svmlabel(rndindex);

                 end

-                decode = 0;

                 decode = svm_single_crossval(svmlabel,svmdata,svmopts);

                 % save the decode value to the corresponding coordinate

@@ -205,7 +205,12 @@ for timeShiftIdx = fbsTimeLine

                 y = coord(2);

                 z = coord(3);

+                if NORM_DECODE

                     img3D{rIdx}(x,y,z) = ((decode/100)-0.5)*2; % range [-1:1]

+                else

+                    img3D{rIdx}(x,y,z) = (decode/100); % range [0:1]

+                end

+

             end %for each radius

         end %for each voxel

@@ -17,6 +17,9 @@ DEFAULT.svmnfold        = '6';

 DEFAULT.svmrnd          = 1;

 DEFAULT.searchlightradius = 3;

 DEFAULT.searchlightTimeline = '';

+DEFAULT.somM = 3;

+DEFAULT.somN = 3;

+DEFAULT.somLattice = 1;

 DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');

@@ -339,13 +342,25 @@ pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.4 0.5 0.4]);

     set(pSOM,'Title','SOM Classification');

     set(pSOM,'BackgroundColor',basecolor);

-    model.txtSOMopts = createTextField(pSOM,[0 0.75 1 0.25],'3x3 rect');

-    set(model.txtSOMopts,'HorizontalAlignment','left');

-    set(model.txtSOMopts,'Enable','off');

+    createLabel(pSOM,[0 0.75 0.3 0.20],'Size:');

+    model.txtSomM = createTextField(pSOM,[0.3 0.75 0.25 0.2],DEFAULT.somM);

+    somsizemal = createLabel(pSOM,[0.55 0.75 0.2 0.20],'x');

+    set(somsizemal,'HorizontalAlignment','center');

+    model.txtSomN = createTextField(pSOM,[0.75 0.75 0.25 0.20],DEFAULT.somN);

+ 

+    latticeModel = {'rect','hexa'};

+    model.selSomLattice = uicontrol(pSOM,'Style','popupmenu',...

+        'Units','normalized',...

+        'Position',[0.0 0.5 0.3 0.20],...

+        'String',latticeModel,...

+        'UserData',latticeModel,...

+        'Value',1);

+    set(model.selSomLattice,'BackgroundColor','w');

+

+    model.txtSOMnfold = createTextField(pSOM,[0.5 0.50 0.25 0.20],DEFAULT.svmnfold);

+%     set(model.txtSOMnfold,'Enable','off');

+    createLabel(pSOM,[0.75 0.5 0.25 0.20 ],'-Fold CrossVal');

-    model.txtSOMnfold = createTextField(pSOM,[0.0 0.50 0.5 0.25],DEFAULT.svmnfold);

-    set(model.txtSOMnfold,'Enable','off');

-    createLabel(pSOM,[0.5 0.50 0.5 0.25 ],'-Fold CrossVal');

     btnRunSOM = uicontrol(pSOM,'String','run SOM Crossvalidation',...

         'Units','normalized',...

@@ -357,14 +372,14 @@ pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.4 0.5 0.4]);

         'Position',[0.0 0.0 1 0.25]);

     set(btnRunXSOM,'Enable','on');

-pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 1 0.3]);

+pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 0.5 0.3]);

     set(pSearchlight,'Title','Spatiotemporal FB classification');

     set(pSearchlight,'BackgroundColor',basecolor);

     lSearchligh = createLabel(pSearchlight, [0 0.6 0.5 0.3],'Searchlight Radius');

     model.txtSearchlightRadius = createTextField(pSearchlight,[0.5 0.6 0.5 0.3],DEFAULT.searchlightradius);

-    lFBSTiming = createLabel(pSearchlight, [0 0.3 0.5 0.3],'Optional Timeline ( e.g. ''-5 0 5 10 15''');

+    lFBSTiming = createLabel(pSearchlight, [0 0.3 0.5 0.3],'Optional Timeline ( e.g. ''-5 0 5 10 15'')');

     model.txtSearchlightTimeline = createTextField(pSearchlight,[0.5 0.3 0.5 0.3],DEFAULT.searchlightTimeline);

     btnRunFBS = uicontrol(pSearchlight,'String','run Spatiotemporal FB classification',...

@@ -389,17 +404,23 @@ function model = createVisualStepPanel(model,parent,DEFAULT)

     plot_grid{1,1} = [0.0 0.63 grid_w grid_h];

     plot_grid{1,2} = [0.0 0.33 grid_w grid_h];

     plot_grid{1,3} = [0.0 0.03 grid_w grid_h];

-    plot_grid{2,1} = [0.5 0.63 grid_w grid_h];

-    plot_grid{2,2} = [0.5 0.33 grid_w grid_h];

-    plot_grid{2,3} = [0.5 0.03 grid_w grid_h];

+    plot_grid{2,1} = [0.25 0.63 grid_w grid_h];

+    plot_grid{2,2} = [0.25 0.33 grid_w grid_h];

+    plot_grid{2,3} = [0.25 0.03 grid_w grid_h];

     pButtonPane = uipanel(parent,'Units','normalized','Position',[0 0.5 1 0.5]);

 %     set(pButtonPane,'Title','Plot');

     set(pButtonPane,'BackgroundColor','w');

+    btnPlot03 = uicontrol(pButtonPane,'String','plot PSTH',...

+        'Units','normalized',...

+        'Position',cell2mat(plot_grid(2,1)));

+    set(btnPlot03,'Callback',{@cbPlot,model,'psth'}); 

+    set(btnPlot03,'Enable','on');

+  

     btnPlot01 = uicontrol(pButtonPane,'String','plot performance and SE',...

         'Units','normalized',...

-        'Position',cell2mat(plot_grid(1,3)));

+        'Position',cell2mat(plot_grid(2,2)));

     set(btnPlot01,'Callback',{@cbPlot,model,'simple'});

     set(btnPlot01,'Enable','on');

@@ -409,11 +430,6 @@ function model = createVisualStepPanel(model,parent,DEFAULT)

     set(btnPlot02,'Callback',{@cbPlot,model,'x-subject-val'});

     set(btnPlot02,'Enable','on');

-    btnPlot03 = uicontrol(pButtonPane,'String','plot PSTH',...

-        'Units','normalized',...

-        'Position',cell2mat(plot_grid(1,2)));

-    set(btnPlot03,'Callback',{@cbPlot,model,'psth'}); 

-    set(btnPlot03,'Enable','on');

 end