SVMCrossVal.git

@@ -0,0 +1,9 @@

+function addStudyToMenu(menu,label,callbackargs)

+uimenu(menu,...

+    'Label',label,...

+    'Callback',{@mcb_load_study,label,callbackargs});

+end

+

+function mcb_load_study(src,blah,filename,uimodel)

+    load_study(filename,uimodel);

+end

@@ -0,0 +1,45 @@

+function ret = bootstrap(studyID)

+

+StudyArgs.baseDir             = 'D:\';

+StudyArgs.subjectSelectString = 'noSubject';

+StudyArgs.subjectSelectValue	= 1;

+StudyArgs.classdefString      = '';

+

+StudyArgs.pststart            = '0';

+StudyArgs.pstend              = '0';

+StudyArgs.baselinestart       = '0';

+StudyArgs.baselineend         = '0';

+StudyArgs.trfactor            = '0';

+StudyArgs.trlabel             = '2';

+

+StudyArgs.imageTypeSelectionString = 'noImages';

+StudyArgs.imageTypeSelectionValue  = 1;

+

+StudyArgs.voxelString         = '';

+

+StudyArgs.selNormPSTValue     = 1;

+StudyArgs.chkColBiasValue     = 1;

+

+%%%%%%%%%%%%%%%

+

+StudyArgs.frameshiftstart = '0';

+StudyArgs.frameshiftend = '0';

+StudyArgs.frameshiftdur = '0';

+

+StudyArgs.svmoptstring = '';

+StudyArgs.svmnfold = '0';

+StudyArgs.svmrnd = 1;

+

+StudyArgs.somM = '0';

+StudyArgs.somN = '0';

+StudyArgs.latticeModelValue = 1;

+StudyArgs.somnfold = '0';

+

+StudyArgs.searchlightradius = '0';

+StudyArgs.searchlightTimeline = '';

+

+

+% file = strcat(studyID,'.mat');

+% save(fullfile('D:\SPM\spm2\toolbox\SVMCrossVal\study',file),'-Struct','StudyArgs') ;

+ret=StudyArgs;

+end

\ No newline at end of file

@@ -0,0 +1,5 @@

+function label = createLabel(parent,  pos, labelText)

+    label = uicontrol(parent,'Style','text','Units','normalized','String',labelText,'Position',pos);

+    set(label,'HorizontalAlignment','left');

+    set(label,'BackgroundColor','w');

+end

@@ -0,0 +1,6 @@

+function txt = createTextField(parent,pos,string)

+%     textfieldcolor = [0.9 0.9 0.0];

+    textfieldcolor = 'w';

+    txt = uicontrol(parent,'Style','edit','Units','normalized','String',string,'Position',pos);

+    set(txt,'BackgroundColor',textfieldcolor);

+end

@@ -1,4 +1,11 @@

 function defineGlobals()

+global SVMCROSSVAL_SPMDIR;

+global SVMCROSSVAL_TOOLBOXPATH;

+SVMCROSSVAL_TOOLBOXPATH = fullfile(SVMCROSSVAL_SPMDIR,'toolbox','SVMCrossVal');

+

+global SVMCROSSVAL_STUDYDIR;

+SVMCROSSVAL_STUDYDIR = fullfile(SVMCROSSVAL_TOOLBOXPATH,'study');

+

 %define global constants

 global SVMCROSSVAL_USE_DRIVE_CHECK_HACK;

 %enables subroutine to check if image path starts with 'D'

@@ -0,0 +1,15 @@

+function fillStudyMenu(studymenu,uimodel)

+studydir = fullfile(getTbxPath,'study');

+    files = dir(studydir);

+    for fileidx = 1: numel(files)

+        if ~files(fileidx).isdir

+%         && ~strcmp(files(fileidx).name,'default.mat')

+%             uimenu(studymenu,...

+%                 'Label',files(fileidx).name,...

+%                 'Callback',{@mcb_load_study,files(fileidx).name,uimodel});

+            addStudyToMenu(studymenu,files(fileidx).name,uimodel);

+        end

+    end

+end

+

+

@@ -0,0 +1,3 @@

+function bd = getBaseDir(model)

+bd = get(model.txtBaseDir,'String');

+end

\ No newline at end of file

@@ -0,0 +1,3 @@

+function id = getPreviousStudyID

+id = 'default';

+end

\ No newline at end of file

@@ -0,0 +1,4 @@

+function p = getStudyPath

+global SVMCROSSVAL_STUDYDIR;

+p = SVMCROSSVAL_STUDYDIR;

+end

\ No newline at end of file

@@ -0,0 +1,35 @@

+function StudyArgs = load_study(studyFile,model)

+    studyID = strrep(studyFile,'.mat','');

+    display(['LOAD STUDY ' studyID]);

+

+    global SVMCROSSVAL_STUDYDIR;

+    StudyArgs = load(fullfile(SVMCROSSVAL_STUDYDIR,studyFile));

+

+    set(model.txtBaseDir,'String',StudyArgs.baseDir);

+    set(model.txtStudyID,'String',studyID);

+        

+    set(model.subjectSelector,'String',StudyArgs.subjectSelectString);

+    set(model.subjectSelector,'UserData',StudyArgs.subjectSelectString);

+    set(model.subjectSelector,'Value',StudyArgs.subjectSelectValue);

+    

+    set(model.txtClassDef,'String',sprintf(StudyArgs.classdefString));

+    

+    set(model.txtPSTHStart,     'String',sprintf(StudyArgs.pststart));

+    set(model.txtPSTHEnd,       'String',sprintf(StudyArgs.pstend));

+    set(model.txtBaselineStart, 'String',sprintf(StudyArgs.baselinestart));

+    set(model.txtBaselineEnd,   'String',sprintf(StudyArgs.baselineend));

+    set(model.txtTrFactor,      'String',sprintf(StudyArgs.trfactor));

+    set(model.labelTR,          'String',sprintf(StudyArgs.trlabel));

+    

+    set(model.imageTypeSelection, 'String'  ,StudyArgs.imageTypeSelectionString);

+    set(model.imageTypeSelection, 'UserData',StudyArgs.imageTypeSelectionString);

+    set(model.imageTypeSelection, 'Value'   ,StudyArgs.imageTypeSelectionValue);

+    

+    set(model.txtVoxelDef,'String',sprintf(StudyArgs.voxelString));

+    

+    set(model.selNormPST, 'Value',StudyArgs.selNormPSTValue);

+    set(model.chkColBias, 'Value',StudyArgs.chkColBiasValue);

+end

+

+

+

@@ -0,0 +1,46 @@

+function ret = saveStudy(studyID,model)

+display(['SAVE ' studyID]);

+

+StudyArgs.baseDir             = getBaseDir(model);

+StudyArgs.subjectSelectString = get(model.subjectSelector,'String');

+StudyArgs.subjectSelectValue  = get(model.subjectSelector,'Value');

+StudyArgs.classdefString      = get(model.txtClassDef,'String');

+

+StudyArgs.pststart            = get(model.txtPSTHStart,'String');

+StudyArgs.pstend              = get(model.txtPSTHEnd,'String');

+StudyArgs.baselinestart       = get(model.txtBaselineStart,'String');

+StudyArgs.baselineend         = get(model.txtBaselineEnd,'String');

+StudyArgs.trfactor            = get(model.txtTrFactor,'String');

+StudyArgs.trlabel             = get(model.labelTR,'String');

+

+StudyArgs.imageTypeSelectionString = get(model.imageTypeSelection,'String');

+StudyArgs.imageTypeSelectionValue  = get(model.imageTypeSelection,'Value');

+

+StudyArgs.voxelString         = get(model.txtVoxelDef,'String');

+

+StudyArgs.selNormPSTValue     = get(model.selNormPST, 'Value');

+StudyArgs.chkColBiasValue     = get(model.chkColBias, 'Value');

+

+% %%%%%%%%%%%%%%%

+

+StudyArgs.frameshiftstart       = get(model.txtFrameShiftStart,'String');

+StudyArgs.frameshiftend         = get(model.txtFrameShiftEnd,'String');

+StudyArgs.frameshiftdur         = get(model.txtFrameShiftDur,'String');

+

+StudyArgs.svmoptstring          = get(model.txtSVMopts,'String');

+StudyArgs.svmnfold              = get(model.txtSVMnfold,'String');

+StudyArgs.svmrnd                = get(model.chkSVMrnd,'Value');

+

+StudyArgs.somM                  = get(model.txtSomM,'String');

+StudyArgs.somN                  = get(model.txtSomN,'String');

+StudyArgs.latticeModelValue     = get(model.selSomLattice,'Value');

+StudyArgs.somnfold              = get(model.txtSOMnfold,'String');

+

+StudyArgs.searchlightradius     = get(model.txtSearchlightRadius,'String');

+StudyArgs.searchlightTimeline   = get(model.txtSearchlightTimeline,'String');

+

+

+file = strcat(studyID,'.mat');

+save(fullfile(getStudyPath,file),'-Struct','StudyArgs') ;

+ret=1;

+end

\ No newline at end of file

@@ -1,18 +1,19 @@

 function model = scanDirs(model)

-disp('scan dir');

-subjectNames = listDirNames(model.baseDir);

+% disp('scan dir');

+baseDir = getBaseDir(model);

+subjectNames = listDirNames(baseDir);

 set(model.subjectSelector,'String',subjectNames);

 set(model.subjectSelector,'UserData',subjectNames);

 set(model.subjectSelector,'Value',model.selectedSubject);

 %subjectNames(model.selectedSubject)

-imageMask = imageMaskNames(fullfile(model.baseDir,cell2mat(subjectNames(model.selectedSubject))));

+imageMask = imageMaskNames(fullfile(baseDir,cell2mat(subjectNames(model.selectedSubject))));

 set(model.imageTypeSelection,'String',imageMask);

 set(model.imageTypeSelection,'UserData',imageMask);

-set(model.txtBaseDir,'String',model.baseDir);

+% set(model.txtBaseDir,'String',baseDir);

 % des = 

 % tr = des.xsDes.Interscan_interval(1:end-3);

@@ -1,9 +1,9 @@

-function ui_createStudy()

-    frameWidth=450;

-    frameHeight=450;

+function ui_createStudy(menu,uimodel)

+    frameWidth=300;

+    frameHeight=200;

-    frame = figure('Visible','off','Position',[0,0,frameWidth,frameHeight]);

-    movegui(frame,'west'); % get this thing visible on smaller displays.

+    frame = figure('Visible','on','Position',[0,0,frameWidth,frameHeight]);

+    movegui(frame,'center'); % get this thing visible on smaller displays.

     set(frame,'Name','Create Study');

     set(frame,'NumberTitle','off');

     set(frame,'MenuBar','none');

@@ -13,4 +13,54 @@ function ui_createStudy()

     set(frame,'Color','y');

+    study= struct();

+    % name

+    namelabel = createLabel(frame,[0 0.6 1 0.1],'Identifier for new study (the name):');

+    study.name = createTextField(frame,[0 0.5 1 .1],'');

+    % base-dir

+    dirlabel = createLabel(frame,[0 0.4 1 0.1],'Full path to the directory containing the data:');

+    study.basedir = createTextField(frame,[0 0.3 1 .1],'');

+    

+    %fertig-button

+        btnSwitchPreprocessing = uicontrol(frame,'Style','pushbutton',...

+            'String','create',...

+            'Units','normalized','Position',[0.0 0.0 1 0.1]);

+        set(btnSwitchPreprocessing,'Callback',{@cbCreateStudy,study,frame,uimodel,menu}); 

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

+    

+end

+

+function uimodel = cbCreateStudy(src,evnt,study,window,uimodel,menu)

+% global SVMCROSSVAL_STUDYDIR;

+disp('Creating new Study');

+if strcmp(get(study.name,'String'),'') || strcmp(get(study.basedir,'String'),'')

+    error('spm_SVMCrossVal:createStudy','please provide Name and Path');

+end

+studyID = get(study.name,'String');

+baseDir = get(study.basedir,'String');

+

+set(uimodel.txtBaseDir,'String',baseDir);

+set(uimodel.txtStudyID,'String',studyID);

+

+StudyArgs.subjectSelectString = listDirNames(baseDir);

+StudyArgs.subjectSelectValue = 1;

+set(uimodel.subjectSelector,'String',StudyArgs.subjectSelectString);

+set(uimodel.subjectSelector,'UserData',StudyArgs.subjectSelectString);

+set(uimodel.subjectSelector,'Value',StudyArgs.subjectSelectValue);

+

+StudyArgs.imageTypeSelectionString = imageMaskNames(fullfile(baseDir,cell2mat(StudyArgs.subjectSelectString(StudyArgs.subjectSelectValue))));

+StudyArgs.imageTypeSelectionValue = 1;

+set(uimodel.imageTypeSelection, 'String'  ,StudyArgs.imageTypeSelectionString);

+set(uimodel.imageTypeSelection, 'UserData',StudyArgs.imageTypeSelectionString);

+set(uimodel.imageTypeSelection, 'Value'   ,StudyArgs.imageTypeSelectionValue);

+

+% des = 

+% tr = des.xsDes.Interscan_interval(1:end-3);

+StudyArgs.trlabel = '2';

+set(uimodel.labelTR, 'String',sprintf(StudyArgs.trlabel));

+ 

+studyfile = [studyID '.mat'];

+saveStudy(studyID,uimodel);

+addStudyToMenu(menu,studyfile,uimodel);

+close(window);

 end

\ No newline at end of file

@@ -9,21 +9,25 @@ function ui_main(varargin)

     set(frame,'Name','SVMCrossVal Decode Performance 4 SPM');

     set(frame,'NumberTitle','off');

     set(frame,'MenuBar','none');

-%     set(frame,'Color',get(0,'defaultUicontrolBackgroundColor'));

     set(frame,'Resize','on');

     set(frame,'Units','normalized');

     set(frame,'Color','y');

     task = struct;

-    DEFAULT = mcb_load_study(0,0,fullfile(getTbxPath,'study/stimolos.mat'));

+%     studyID = getPreviousStudyID();

-    model1 = struct;

-    model1.baseDir = DEFAULT.wd;

+%     StudyArgs = load_study(studyID);

-    model1.txtBaseDir = createLabel(frame,[0 0.97 1 0.03],model1.baseDir);

-    set(model1.txtBaseDir,'BackgroundColor','w');

-    set(model1.txtBaseDir,'ForegroundColor','b');

+    model = struct;

+    

+    model.txtBaseDir = createLabel(frame,[0 0.97 0.8 0.03],'');

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

+    set(model.txtBaseDir,'ForegroundColor','b');

+    

+    model.txtStudyID = createLabel(frame,[0.8 0.97 0.2 0.03],'');

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

+    set(model.txtStudyID,'ForegroundColor','r');    

     TASK_HEIGHT = 1-0.13;

@@ -32,80 +36,68 @@ function ui_main(varargin)

     set(task.preprocessing,'BackgroundColor','w');

     set(task.preprocessing,'Units','normalized');

-    model1.selectedSubject = DEFAULT.selectedSubject;

-    model1 = createFirstStepPanel(model1,task.preprocessing,DEFAULT);

+    model = createFirstStepPanel(model,task.preprocessing);

     % fill with data

-    model1 = scanDirs(model1);

+%     model = scanDirs(model);

     % CLASSIFICATION

-    model2 = struct;

-    

     task.classification = uipanel(frame,'Title','Classification','Position',[0 0.0 1 TASK_HEIGHT]);

     set(task.classification,'BackgroundColor','w');

-    model2 = createSecondStepPanel(model2,task.classification,DEFAULT);

+    model = createSecondStepPanel(model,task.classification);

     % PLOT

-    model3 = struct;

     task.plot = uipanel(frame,'Title','Plot','Position',[0 0.0 1 TASK_HEIGHT]);

     set(task.plot,'BackgroundColor','w');

-    model3 = createVisualStepPanel(model3,task.plot,DEFAULT);

+    model = createVisualStepPanel(model,task.plot);

     % TASK

     task.taskSwitch = uibuttongroup(frame,'Position',[0 1-0.13 1 0.10]);

     % controlls togglebuttons

-%         set(task.taskSwitch,'Title','TASK');

         set(task.taskSwitch,'BackgroundColor','w');

         set(task.taskSwitch,'Units','normalized');

         btnSwitchPreprocessing = uicontrol(task.taskSwitch,'Style','pushbutton',...

             'String','ImageProcessing',...

             'Units','normalized','Position',[0.0 0.0 0.33 1]);

-        set(btnSwitchPreprocessing,'Callback',{@cbSwitchTask,'PRE',task,model1}); 

+        set(btnSwitchPreprocessing,'Callback',{@cbSwitchTask,'PRE',task}); 

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

         btnSwitchClassify = uicontrol(task.taskSwitch,'Style','pushbutton',...

             'String','Decode',...

             'Units','normalized','Position',[0.33 0.0 0.33 1]);

-        set(btnSwitchClassify,'Callback',{@cbSwitchTask,'CLASSIFY',task,model2}); 

+        set(btnSwitchClassify,'Callback',{@cbSwitchTask,'CLASSIFY',task}); 

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

         btnSwitchPlot = uicontrol(task.taskSwitch,'Style','pushbutton',...

             'String','Plot',...

             'Units','normalized','Position',[0.66 0.0 0.33 1]);

-        set(btnSwitchPlot,'Callback',{@cbSwitchTask,'PLOT',task,model3}); 

+        set(btnSwitchPlot,'Callback',{@cbSwitchTask,'PLOT',task}); 

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

-    % menu

-    savemenu = uimenu(frame,'Label','Save/Load','Enable','off');

-        uimenu(savemenu,'Label','Save Preprocessing Parameter','Callback',{@mcb_save,model1},'Enable','off');

-        uimenu(savemenu,'Label','Load Preprocessing Parameter','Callback',{@mcb_load,model1},'Enable','off');

-        uimenu(savemenu,'Label','Save Decode Parameter','Callback',{@mcb_save,model2},'Enable','off');

-        uimenu(savemenu,'Label','Load Decode Parameter','Callback',{@mcb_load,model2},'Enable','off');

-        uimenu(savemenu,'Label','Save All','Callback',{@mcb_save,model1},'Enable','off');

-        uimenu(savemenu,'Label','Load All','Callback',{@mcb_load,model1},'Enable','off');

+    % menus

-    studymenu = uimenu(frame,'Label','change Study','Enable','on');

-        fillStudyMenu(studymenu);

+    savemenu = uimenu(frame,'Label','Save ...','Enable','on');

+        uimenu(savemenu,'Label','Save All','Callback',{@mcb_save,model},'Enable','on');

-    cbSwitchTask(0,0,'PRE',task,model1);

+    studySelectMenu = uimenu(frame,'Label','Study ...','Enable','on');

+        uimenu(studySelectMenu,'Label','*new Study*','Callback',{@mcb_new_study,studySelectMenu,model});

+        fillStudyMenu(studySelectMenu,model);

-    set(frame,'Visible','on');

+    updateMenu = uimenu(frame,'Label','update ...','Enable','off');

+        uimenu(updateMenu,'Label','scan dirs','Callback',{@ssss,studySelectMenu});

-end

+%     newStudyMenu = uimenu(frame,'Label','new Study','Enable','on');

+

+    load_study([getPreviousStudyID '.mat'],model);

+    cbSwitchTask(0,0,'PRE',task);

+    set(frame,'Visible','on');

-function fillStudyMenu(studymenu)

-    studydir = fullfile(getTbxPath,'study');

-    files = dir(studydir);

-    for fileidx = 1: numel(files)

-        if ~files(fileidx).isdir

-            uimenu(studymenu,'Label',files(fileidx).name,'Callback',{@mcb_load_study,fullfile(studydir,files(fileidx).name)});

-        end

-    end

 end

-function model = createFirstStepPanel(model,parent,DEFAULT)

+%%%%% ui elements

+function model = createFirstStepPanel(model,parent)

     main_grid = cell(2,4);

     main_grid{1,1} = [0 0.7 0.4 0.3];

@@ -122,11 +114,9 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

     set(pSubject,'Title','Subjects');

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

-    subjectList = {'DUMMY Subj1','DUMMY Subj2','DUMMY Subj3','DUMMY Subj4'};

+%     subjectNames = listDirNames(getBaseDir(model));

     model.subjectSelector = uicontrol(pSubject,'Style','listbox',...

                     'Min',1, 'Max',3,...

-                    'String',subjectList,...

-                    'UserData',subjectList,...

                     'Units','normalized',...

                     'Position',[0 0 1 1]);

     set(model.subjectSelector, 'FontName', 'FixedWidth');

@@ -144,8 +135,8 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

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

         set(lClassDef,'HorizontalAlignment','left');

+        

         model.txtClassDef = uicontrol(pClasses,'Style','edit',...

-            'String',sprintf(DEFAULT.classdefstring),...

             'Units','normalized',...

             'Position',[0 0 1 0.8]);

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

@@ -193,11 +184,11 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

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

         lTRF        = createLabel(pPSTH, cell2mat(tl_grid(1,5)) ,'TR Factor');

-        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.txtTrFactor          = createTextField(pPSTH,cell2mat(tl_grid(2,5)),DEFAULT.trfactor);

+        model.txtPSTHStart         = createTextField(pPSTH,cell2mat(tl_grid(2,2)),'');

+        model.txtPSTHEnd           = createTextField(pPSTH,cell2mat(tl_grid(3,2)),'');

+        model.txtBaselineStart     = createTextField(pPSTH,cell2mat(tl_grid(2,3)),'');

+        model.txtBaselineEnd       = createTextField(pPSTH,cell2mat(tl_grid(3,3)),'');

+        model.txtTrFactor          = createTextField(pPSTH,cell2mat(tl_grid(2,5)),'');

         model.labelTR              = createTextField(pPSTH,cell2mat(tl_grid(3,5)),'');

         % images

@@ -206,22 +197,16 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

         createLabel(pImage,[0.0 0.5 1 0.5],'Select Image Base');

-        imageRegExList = {'DUMMY f*.IMG','DUMMY swrf*.IMG','DUMMY wrf*.IMG'};

         model.imageTypeSelection = uicontrol(pImage,'Style','popupmenu',...

         'Units','normalized',...

-        'Position',[0.0 0.0 1 0.5],...

-        'String',imageRegExList,...

-        'UserData',imageRegExList,...

-        'Value',1);

+        'Position',[0.0 0.0 1 0.5]);

         set(model.imageTypeSelection,'BackgroundColor','w');

-        

         % 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> [+ radius (mm)];');

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

-            sprintf(DEFAULT.voxelstring));

+        model.txtVoxelDef = createTextField(pVoxel,[0 0 1 0.9],'');

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

         set(model.txtVoxelDef,'Max',20);

         set(model.txtVoxelDef,'Min',0);

@@ -237,18 +226,14 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

             'Units','normalized',...

             'Position',[0.0 0.5 1 0.25],...

             'String',norm1Model,...

-            'UserData',norm1Model,...

-            'Value',2);

+            'UserData',norm1Model);

          set(model.selNormPST,'BackgroundColor','w');   

-%         createLabel(pNorm,[0 0.25 1 0.25],'Col Bias removal');

-%         norm2Model = {'on','off'};

         model.chkColBias = uicontrol(pNorm,'Style','checkbox',...

             'Units','normalized',...

             'Position',[0.0 0.1 1 0.25],...

             'String','column Bias removal',...

-            'Enable','on',...

-            'Value',1);

+            'Enable','on');

          set(model.chkColBias,'BackgroundColor','w');   

         %buttons

@@ -271,7 +256,7 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

         set(btnRunButton3,'Enable','on');

 end

-function model = createSecondStepPanel(model,parent,DEFAULT)

+function model = createSecondStepPanel(model,parent)

 basecolor = 'w';

 pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.8 1 0.2]);

@@ -295,25 +280,25 @@ pTime = uipanel(parent,'Units','normalized','Position',[0.0 0.8 1 0.2]);

     lFrameShift = createLabel(pTime, cell2mat(time_grid(1,2)),'Frame Shift');

     lFramsSize  = createLabel(pTime, cell2mat(time_grid(1,3)),'Frame Size');

-    model.txtFrameShiftStart   = createTextField(pTime,cell2mat(time_grid(2,2)),DEFAULT.frameshiftstart);

-    model.txtFrameShiftEnd     = createTextField(pTime,cell2mat(time_grid(3,2)),DEFAULT.frameshiftend);

-    model.txtFrameShiftDur     = createTextField(pTime,cell2mat(time_grid(2,3)),DEFAULT.frameshiftdur);

+    model.txtFrameShiftStart   = createTextField(pTime,cell2mat(time_grid(2,2)),'');

+    model.txtFrameShiftEnd     = createTextField(pTime,cell2mat(time_grid(3,2)),'');

+    model.txtFrameShiftDur     = createTextField(pTime,cell2mat(time_grid(2,3)),'');

 pSVM = uipanel(parent,'Units','normalized','Position',[0 0.4 0.5 0.4]);

     set(pSVM,'Title','SVM Classification');

     set(pSVM,'BackgroundColor',basecolor);

-    model.txtSVMopts = createTextField(pSVM,[0 0.83 1 0.16],DEFAULT.svmoptstring);

+    model.txtSVMopts = createTextField(pSVM,[0 0.83 1 0.16],'');

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

-    model.txtSVMnfold = createTextField(pSVM,[0.0 0.66 0.5 0.16],DEFAULT.svmnfold);

+    model.txtSVMnfold = createTextField(pSVM,[0.0 0.66 0.5 0.16],'');

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

     model.chkSVMrnd = uicontrol(pSVM,'Style','checkbox','Units','normalized','Position',[0.1 0.50 0.9 0.16]);

     set(model.chkSVMrnd,'String','Randomize Datapoints');

     set(model.chkSVMrnd,'BackgroundColor','w');

-    set(model.chkSVMrnd,'Value',DEFAULT.svmrnd);

+%     set(model.chkSVMrnd,'Value',StudyArgs.svmrnd);

     btnRunSVM = uicontrol(pSVM,'String','run batchmode SVM Crossvalidation',...

         'Units','normalized',...

@@ -330,21 +315,19 @@ pSOM = uipanel(parent,'Units','normalized','Position',[0.5 0.4 0.5 0.4]);

     set(pSOM,'BackgroundColor',basecolor);

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

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

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

     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);

- 

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

     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);

+        'UserData',latticeModel);

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

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

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

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

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

@@ -364,10 +347,10 @@ pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 0.5 0.3])

     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);

+    model.txtSearchlightRadius = createTextField(pSearchlight,[0.5 0.6 0.5 0.3],'');

     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);

+    model.txtSearchlightTimeline = createTextField(pSearchlight,[0.5 0.3 0.5 0.3],'');

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

         'Units','normalized',...

@@ -383,7 +366,7 @@ pSearchlight = uipanel(parent,'Units','normalized','Position',[0.0 0.1 0.5 0.3])

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

 end

-function model = createVisualStepPanel(model,parent,DEFAULT)

+function model = createVisualStepPanel(model,parent)

     grid_h = 0.25;

     grid_w = 0.5;

@@ -420,8 +403,9 @@ function model = createVisualStepPanel(model,parent,DEFAULT)

 end

+%%%%% ui callbacks

-function cbSwitchTask(src,evnt,task,taskpanel,model)

+function cbSwitchTask(src,evnt,task,taskpanel)

 set(taskpanel.preprocessing,'Visible','off');

 set(taskpanel.classification,'Visible','off');

 set(taskpanel.plot,'Visible','off');

@@ -436,14 +418,10 @@ switch task

     case 'PLOT'

         set(taskpanel.plot,'Visible','on');

-        

 end

-

-assignin('base','model',model);

-

+% assignin('base','model',model);

 end

-

 function cbRunPreprocessing(src,evnt,model,task)

 main(model,'pre',task);

 end

@@ -456,51 +434,23 @@ function cbPlot(src,evnt,model,type)

 main(model,'plot',type);

 end

-function default = mcb_load_study(src,evnt,studyfile)

-    default = load(studyfile);

-end

+%%%%%%%%%% menu callbacks

-function model = mcb_cd(src,evnt,model)

-disp('CD');

-directory_name = uigetdir(model.baseDir,'Select Study Base Directory ...');

-model.baseDir = directory_name;

-model = scanDirs(model);

+function mcb_save(src,evnt,model)

+studyID = get(model.txtStudyID,'String');

+saveStudy(studyID,model);

 end

-function mcb_save(src,evnt,model)

-disp('SAVE');

-baseDir  = model.baseDir;

-timeLine = getTimeLineParams(model);

-classDefString = getClassDefString(model);

-coordDefString = getCoordDefString(model);

-

-[file path] = uiputfile('*.mat','Save current Params ...',model.baseDir);

-save( fullfile(path,file),'baseDir','timeLine','classDefString','coordDefString') ;

+function mcb_new_study(src,evnt,studymenu,uimodel)

+display('CREATE STUDY');

+    ui_createStudy(studymenu,uimodel);

 end

-function model = mcb_load(src,evnt,model)

-disp('LOAD');

-[file path] = uigetfile('*.mat','Load Params ...',model.baseDir);

-l = load(fullfile(path,file));

-% assignin('base','l',l);

-model = setTimeLineParams(model,l.timeLine);

-model = setClassDefString(model,l.classDefString);

-model = setCoordDefString(model,l.coordDefString);

-model.baseDir = l.baseDir;

-model = scanDirs(model);

-end

-function label = createLabel(parent,  pos, labelText)

-    label = uicontrol(parent,'Style','text','Units','normalized','String',labelText,'Position',pos);

-    set(label,'HorizontalAlignment','left');

-    set(label,'BackgroundColor','w');

-end

-function txt = createTextField(parent,pos,model)

-%     textfieldcolor = [0.9 0.9 0.0];

-    textfieldcolor = 'w';

-    txt = uicontrol(parent,'Style','edit','Units','normalized','String',model,'Position',pos);

-    set(txt,'BackgroundColor',textfieldcolor);

-end

+

+

+

+

@@ -1,16 +1,20 @@

 function spm_SVMCrossVal(varargin)

-defineGlobals();

-

+%Enter the base directory of your SPM installation

 global SVMCROSSVAL_SPMDIR;

-global SVMCROSSVAL_SPMVERSION;

-global SVMCROSSVAL_TOOLBOXPATH;

-global SVMCROSSVAL_DEBUG;

-% SPMDIR = 'D:\SPM\spm5human'

 SVMCROSSVAL_SPMDIR = 'D:\SPM\spm2';

+%Enter the SPM version string. Like 'SPM2', 'SPM5', 'SPM8'

+global SVMCROSSVAL_SPMVERSION;

 SVMCROSSVAL_SPMVERSION = 'SPM2';

-% SVMCROSSVAL_TOOLBOXPATH = fullfile('C:\Dokumente und Einstellungen\Christoph\Eigene Dateien\MATLAB\spmtoolbox\SVMCrossVal\','');

-SVMCROSSVAL_TOOLBOXPATH = fullfile(SVMCROSSVAL_SPMDIR,'toolbox','SVMCrossVal');

+

+% No Config from here

+if strcmp(SVMCROSSVAL_SPMDIR,'') || strcmp(SVMCROSSVAL_SPMVERSION,'')

+    error('spm_SVMCrossVal:main:noinstall','installation not complete!');

+end

+

+global SVMCROSSVAL_DEBUG;

+

+defineGlobals();

 switch nargin

     case 0