SVMCrossVal.git

@@ -1,27 +1,32 @@

-function [extr voxelcount] = calculateImageData(filenameList, voxelList, rad)

+function [extr voxelcount] = calculateImageData(filenameList, coordlist)

+

+vox = [];

+% radius = [];

+nCoords = size(coordlist,1);

+for iCoord = 1:nCoords

+   vox = [vox ; coordlist(iCoord).coord];

+%    radius = [radius , coordlist(iCoord).rad];

+end

+

 voxelcount = 0;

 V = filenameList;

-

-vox = voxelList;

-nVoxel = size(vox,1);

 nImage = numel(V);

-

-% rad = 0;

-

+nVoxel = nCoords;

 for kImage=1:nImage

     roicenter = round(inv(V(kImage).mat)*[vox, ones(nVoxel,1)]');

-    x = roicenter(1,:);

-    y = roicenter(2,:);

-    z = roicenter(3,:);

+%     x = roicenter(1,:);

+%     y = roicenter(2,:);

+%     z = roicenter(3,:);

+    subvoxelcount = 0;

+    for iVoxel = 1:nVoxel

+

+        rad = coordlist(iVoxel).rad;

         tmp = spm_imatrix(V(kImage).mat);

         vdim = tmp(7:9);

         vxrad = ceil((rad*ones(nVoxel,3))./(ones(nVoxel,1)*vdim))';

-    subvoxelcount = 0;

-    for iVoxel = 1:nVoxel

-

         if rad==0

             x = roicenter(1,iVoxel);

             y = roicenter(2,iVoxel);

@@ -1,19 +1,24 @@

 function scoords = getSubjectCoordinates(gcoords,map)

 m = java.util.HashMap ;

+%build lookuptable

 for i = 1:numel(map.names)

     key = cell2mat(map.names(i));

     val = map.coords(i,:);

     m.put(key,val);

 end

+% do the lookup

 scoords = [];

-

 for c = 1:numel(gcoords)

     key = strtrim(gcoords(c).name);

     val = m.get(key)';

-    mod = gcoords(c).mod;

-    scoords = [scoords; val+mod];

+%     mod = gcoords(c).mod;

+%     scoords = [scoords; val+mod];

+    co = struct;

+    co.coord = val;

+    co.rad = gcoords(c).rad;

+    scoords = [scoords; co];

 end

 end

\ No newline at end of file

@@ -45,7 +45,6 @@ switch task

         coordargs.eventList     = classDef.eventMatrix;

         coordargs.coords        = parseCoordinateTextField(model);

         coordargs.mask          = mask;

-        coordargs.radius        = getSearchlightRadius(model);

         coordargs.psthOpts      = psthOpts;

@@ -114,6 +113,9 @@ switch task

         assignin('base','decode',decode);

     case 'X-SOM'

         disp('not implemented')

+    case 'FBS'

+        disp('not implemented')

+        fbs.radius        = getSearchlightRadius(model);

 end

@@ -7,10 +7,17 @@ voxelList = [];

         continue;

     end

     line = s(i,:);

+    if (strfind(line,'+'))

+        % has radius

         [roi rem] = strtok(line,'+');

-        roimod = eval(str2mat(rem(2:end)));

+        rad = eval(str2mat(rem(2:end)));

+    else

+        % radius set to 0

+        roi = line;

+        rad = 0;

+    end

     coord.name = roi;

-        coord.mod = roimod;

+    coord.rad = rad;

     voxelList = [voxelList; coord];

 end

@@ -7,7 +7,6 @@ function subjectData = runCoordTable(args)

     subjects = args.subjects;

     nSubjects = numel(subjects);

     sessionlist = args.sessionList;

-    radius = args.radius;

     pstopts = args.psthOpts;

     disp(sprintf('batch processing %g subjects.',nSubjects));

@@ -26,7 +25,7 @@ function subjectData = runCoordTable(args)

         disp('fetching volume definitions, please wait');

         subjectStruct{s}.volumes = spm_vol(getImageFileList(subjectStruct{s}.dir,sessionlist,args.mask));

-        [extr nExtractedVoxel] = calculateImageData(subjectStruct{s}.volumes,subjectStruct{s}.coords,radius);

+        [extr nExtractedVoxel] = calculateImageData(subjectStruct{s}.volumes,subjectStruct{s}.coords);

         pstopts.des = subjectStruct{s}.des;

         pstopts.eventList = args.eventList;

@@ -10,7 +10,7 @@ DEFAULT.frameshiftstart = -5;

 DEFAULT.frameshiftend   = 35;

 DEFAULT.frameshiftdur   = 0;

 DEFAULT.classdefstring  = 'left,\t[9,11,13]\nright,\t[10,12,14]';

-DEFAULT.voxelstring     = 'SPL l + [ 0, 0, 0] \nSPL r + [ 0, 0, 0]\n';

+DEFAULT.voxelstring     = 'M1 l + 3 \nM1 r + 3\n';

 DEFAULT.svmoptstring    = '-s 0 -t 0 -c 1';

 DEFAULT.svmnfold        = '6';

 DEFAULT.svmrnd          = 1;

@@ -200,14 +200,11 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

         lPSTH       = createLabel(pPSTH, cell2mat(tl_grid(1,2)),'PSTH Range');

         lBaseline   = createLabel(pPSTH, cell2mat(tl_grid(1,3)),'Baseline');

-        lSearchligh = createLabel(pPSTH, cell2mat(tl_grid(1,5)),'Searchlight Radius');

-

-

         model.txtPSTHStart         = createTextField(pPSTH,cell2mat(tl_grid(2,2)),DEFAULT.pststart);

         model.txtPSTHEnd           = createTextField(pPSTH,cell2mat(tl_grid(3,2)),DEFAULT.pstend);

         model.txtBaselineStart     = createTextField(pPSTH,cell2mat(tl_grid(2,3)),DEFAULT.baselinestart);

         model.txtBaselineEnd       = createTextField(pPSTH,cell2mat(tl_grid(3,3)),DEFAULT.baselineend);

-        model.txtSearchlightRadius = createTextField(pPSTH,cell2mat(tl_grid(2,5)),DEFAULT.searchlightradius);

+

         % images

         pImage = uipanel(parent,'Title','Image Options','Position',cell2mat(main_grid(2,2)));

@@ -228,7 +225,7 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

         % coordinate Table

         pVoxel = uipanel(parent,'Title','ROI','Position',cell2mat(main_grid(1,3)));

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

-        lVoxelDef = createLabel(pVoxel, [0 0.9 1 0.1],'<ROI Name>+[offset];');

+        lVoxelDef = createLabel(pVoxel, [0 0.9 1 0.1],'<ROI Name> [+ radius (mm)];');

         model.txtVoxelDef = createTextField(pVoxel,[0 0 1 0.9],...

             sprintf(DEFAULT.voxelstring));

         set(model.txtVoxelDef,'HorizontalAlignment','left');

@@ -269,7 +266,7 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

         set(btnRunButton1,'Callback',{@cbRunPreprocessing,model,'COORD'}); % set here, because of model.    

         set(btnRunButton1,'Enable','on');

-        btnRunButton2 = uicontrol(pButtons,'String','run full Brain Searchlight',...

+        btnRunButton2 = uicontrol(pButtons,'String','run full-brain Searchlight',...

             'Units','normalized','Position',[0.33 0 0.33 1]);

         set(btnRunButton2,'Callback',{@cbRunPreprocessing,model,'FBS'}); % set here, because of model.  

         set(btnRunButton2,'Enable','off');

@@ -356,11 +353,25 @@ 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','off');

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

+    

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

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

+        'Position',[0.0 0.0 1 0.3]);

+    set(btnRunFBS,'Enable','off');

+    

+

 % button callbacks set here, because of model.

     set(btnRunSVM, 'Callback',{@cbRunDecode,model,'SVM'}); 

     set(btnRunXSVM,'Callback',{@cbRunDecode,model,'XSVM'}); 

     set(btnRunSOM, 'Callback',{@cbRunDecode,model,'SOM'});

     set(btnRunXSOM,'Callback',{@cbRunDecode,model,'XSOM'});

+    set(btnRunFBS,'Callback',{@cbRunDecode,model,'FBS'});

 end

 function model = createVisualStepPanel(model,parent,DEFAULT)