SVMCrossVal.git

@@ -1,20 +0,0 @@

-function vValue = VoxelValueAtTimepoint (coordinate, timepoint)

-% single Voxel for single coordinate

-

-if(size(coordinate,2)>1)

-    error('VoxelValueAtTimepoint:CoordinateError','only single Coordinate permitted.');

-end

-

-imageNumber = timePointToImageNumber(timepoint, 's');

-V           = evalin('base','SPM.xY.VY'); % Memory Mapped Images

-center      = round(inv(V(imageNumber).mat)*[coordinate; 1]);

-

-x           = center(1,1);

-y           = center(2,1);

-z           = center(3,1);

-

-vValue      = spm_sample_vol(V(imageNumber), x, y, z, 0);

-

-end

-

-

@@ -0,0 +1,30 @@

+function extr = calculateRoiImageData(filenameList,roiImageList)

+

+V = filenameList;

+nImage = numel(V);

+Vm = roiImageList;

+nRoi = numel(Vm);

+

+for kImage=1:nImage

+    x = []; y = []; z = [];

+    dat = [];

+    for iRoiFile = 1:nRoi

+        [x1 y1] = ndgrid(1:V(kImage).dim(1),1:V(kImage).dim(2));

+        for p = 1:V(kImage).dim(3) % resample mask Vm(i) in space of V(k)

+            B = spm_matrix([0 0 -p 0 0 0 1 1 1]);

+            M = inv(B*inv(V(kImage).mat)*Vm(iRoiFile).mat);

+            msk = find(spm_slice_vol(Vm(iRoiFile),M,V(kImage).dim(1:2),0));

+            if ~isempty(msk)

+                z1 = p*ones(size(msk(:)));

+                x = [x; x1(msk(:))];

+                y = [y; y1(msk(:))];

+                z = [z; z1];

+            end

+        end

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

+        

+    end

+    extr(kImage).dat = dat;

+end

+

+end

\ No newline at end of file

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

 function fileList = getImageFileList(subjectdir,sessionlist,mask)

 fileList = [];

-for session = 1:numel(sessionlist)    

-    [sessionFileList dd] = spm_select('FPList',fullfile(subjectdir,sessionlist{session}),mask);

+for session = sessionlist;    

+    [sessionFileList dd] = spm_select('FPList',fullfile(subjectdir,getSessionDirName(session)),mask);

     fileList = [fileList; sessionFileList];

 end

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

+function msk = getImageFileMask(model)

+hdl = model.imageTypeSelection;

+ud = get(hdl,'UserData');

+msk = ud(get(hdl,'Value'));

+end

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

+function s = getSessionDirName(sessionNumber)

+ASCII_OFFSET = 96;

+s = char(sessionNumber+ASCII_OFFSET);

+end

\ No newline at end of file

@@ -1,5 +1,4 @@

 function fileList = getVolumeImageFileHeader(basedir,filemask)

-regexp = sprintf('^%s.*\\.img$',filemask)

+regexp = sprintf('^%s.*\\.img$',filemask);

 fileList = spm_select('List',basedir,regexp);

-

 end

\ No newline at end of file

@@ -15,51 +13,27 @@ switch task

         disp('COORD');

         coordinates= 'parse me';

         runCoordTable()

+        

     case 'ROI'

         disp('ROI');

-        runROIImageMaskMode(subjects,timeLine)

-    case 'FBS'

-        disp('FBS')

-end

-

-return

-

-timeline = getTimeLineParams(parameterModel);

-switch action

-    case 'COORD-LOOKUP-TABLE'

-        runCoordTable(timeline,parameterModel);

-    case 'ROI-IMAGE-MASK'

-        runROIImageMaskMode(timeline,parameterModel);

-        disp('DONE');

-    case 'FULL-BRAIN'

-        error('SVMCrossVal:main:notImplemented','Feature not yet implemented');

-    otherwise 

-        error('SVMCrossVal:main:actionError','Wrong ''action''. Use the GUI.');

-end

-end

+        roiargs = struct;

+        roiargs.subjects = subjects;

+        roiargs.timeline = timeLine;

+        roiargs.classes  = classDef;

+        roiargs.mask     = getImageFileMask(model);

+        roiargs.basedir  = model.baseDir;

+        assignin('base','roiargs',roiargs);

+        runROIImageMaskMode(roiargs);

+    case 'FBS'

+        disp('FBS')

+end

+end

-function calculateParams = parseCalculateParams(paramModel)

-calculateParams  = struct;

-calculateParams.smoothed        = getChkValue(paramModel.chkSmoothed);

-calculateParams.svmargs         = get(paramModel.txtSVMopts,'String');

-calculateParams.sessionList     = 1:3;

-calculateParams.CROSSVAL_METHOD      = CROSSVAL_METHOD_DEF.svmcrossval;

-calculateParams.VOXEL_SELECTION_MODE = VOXEL_SELECTION_MODE_DEF.roiImage;

-calculateParams.PROJECT_BASE_PATH    = PROJECT_BASE_PATH;

-calculateParams.PROJECT_RESULT_PATH  = PROJECT_RESULT_PATH;

-calculateParams.RANDOMIZE       = 0;

-classStruct = parseClassDef(paramModel);

-calculateParams.labelMap        = LabelMap(classStruct.labelCells , classStruct.conditionCells, 'auto'); % LabelMap({'<','>','<+<','>+>','<+>','>+<'},{-2,-1,1,2,3,4}); 0 is autolabel

-calculateParams.classList       = getClasses(calculateParams.labelMap);

-calculateParams.eventList       = classStruct.eventMatrix; %[9,11,13; 10,12,14];

-calculateParams.subjectSelection = subjectSelection;

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

-end

@@ -1,179 +0,0 @@

-function main_UI(args)

-

-global CROSSVAL_METHOD_DEF;

-

-DEFAULT.selectedSubject = 1;

-DEFAULT.smoothed        = 1;

-DEFAULT.multisubject    = 'single';

-DEFAULT.pststart        = -15;

-DEFAULT.pstend          = 40;

-DEFAULT.baselinestart   = -3;

-DEFAULT.baselineend     = -1;

-DEFAULT.frameshiftstart = -5;

-DEFAULT.frameshiftend   = 35;

-DEFAULT.frameshiftdur   = 0;

-DEFAULT.classdefstring  = 'left,\t[9,11,13],\t -2 ;\nright,\t[10,12,14],\t -1;';

-DEFAULT.voxelstring     = 'SPL l,\t[ 0, 0, 0];\nSPL r,\t[ 0, 0, 0];\n';

-DEFAULT.svmoptstring    = '-s 0 -t 0 -v 6 -c 1';

-

-%  Initialize and hide the GUI as it is being constructed.

-    frameWidth=450;

-    frameHeight=600;

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

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

-    

-    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','off');

-    set(frame,'Units','normalize');

-    

-    

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

-    

-%     model.subjectMap = SubjectRoiMapping(project);

-    model.subjectMap = SubjectRoiMapping;

-    

-    nElementRows = 24;

-    optionLineHeight = 1.0/nElementRows;

-    controlElementHeight=optionLineHeight*(1.0/1.5)*frameHeight;

-    pSubject     = uipanel(frame,'Title','Subject',          'Position',[0 optionLineHeight*19 frameWidth optionLineHeight*5]);

-    pPSTH        = uipanel(frame,'Title','PSTH Options',     'Position',[0 optionLineHeight*14 frameWidth optionLineHeight*5]); 

-    pCLASS       = uipanel(frame,'Title','Class Definitions','Position',[0 optionLineHeight*9  frameWidth optionLineHeight*5]); 

-    pVOXEL       = uipanel(frame,'Title','Voxel Selector',   'Position',[0 optionLineHeight*3  frameWidth optionLineHeight*6]); 

-    pSVM         = uipanel(frame,'Title','SVM Options',      'Position',[0 optionLineHeight*1  frameWidth optionLineHeight*2]); 

-    btnRunButton1 = uicontrol(frame,'Tag','Coord-Table','String','run coord-Table','Position',[2 optionLineHeight*0  (frameWidth/2) controlElementHeight*1.6]);

-    btnRunButton2 = uicontrol(frame,'Tag','ROI-Image','String','run ROI-Image processing','Position',[2+(frameWidth/2) optionLineHeight*0  (frameWidth/2) controlElementHeight*1.6]);

-

-

-    % Subject

-    firstColumn  =  5.00;

-    firstRow     =  1.00 * controlElementHeight;

-    

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

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

-                    'String',getSubjectCellList(model.subjectMap),...

-                    'Value',DEFAULT.selectedSubject,...  % default selected item

-                    'Position',[firstColumn firstRow 0.66*frameWidth controlElementHeight*6]);

-    set(model.subjectSelector,'BackgroundColor','w');

-    

-    model.chkSmoothed     = uicontrol(pSubject,'Style','checkbox','Position',[0.68*frameWidth firstRow  0.25*frameWidth controlElementHeight],'Value',DEFAULT.smoothed);

-    createLabel(pSubject,[0.75*frameWidth firstRow  0.25*frameWidth controlElementHeight],'Smooth Data?');

-

-    createLabel(pSubject,[0.68*frameWidth firstRow*4  0.25*frameWidth controlElementHeight],'Analysis Method');

-    

-    model.analysisMethodSelector = uicontrol(pSubject,'Style','popupmenu',...

-        'Position',[0.68*frameWidth firstRow*3  0.25*frameWidth controlElementHeight],...

-        'String',{CROSSVAL_METHOD_DEF.svmcrossval, CROSSVAL_METHOD_DEF.classPerformance},...

-        'Value',1);

-    set(model.analysisMethodSelector,'BackgroundColor','w');

-%     set(model.analysisMethodSelector,'enable','off');

-

-    % PSTH

-    firstColumn  = 5.00;

-    secondColumn = 0.33*frameWidth;

-    thirdColumn  = 0.66*frameWidth;

-%     fourthColumn = 0.84*frameWidth;

-    

-    firstRow    = 5.5*controlElementHeight;

-    secondRow   = 4.5*controlElementHeight;

-    thirdRow    = 3.5*controlElementHeight;

-    fourthRow   = 2.5*controlElementHeight;

-    fifthRow    = 1.0*controlElementHeight;

-    

-    lStart      = createLabel(pPSTH, [secondColumn firstRow  0.33*frameWidth controlElementHeight],'Start [sec]');

-    lEnd        = createLabel(pPSTH, [thirdColumn  firstRow  0.33*frameWidth controlElementHeight],'End [sec]');

-    lPSTH       = createLabel(pPSTH, [firstColumn  secondRow 0.33*frameWidth controlElementHeight],'PSTH Range');

-    lBaseline   = createLabel(pPSTH, [firstColumn  thirdRow  0.33*frameWidth controlElementHeight],'Baseline');

-    lFrameShift = createLabel(pPSTH, [firstColumn  fourthRow 0.33*frameWidth controlElementHeight],'SVM Frame Shift');

-    lFramsSize  = createLabel(pPSTH, [firstColumn  fifthRow  0.33*frameWidth controlElementHeight],'SVM Frame Size');

-    

-    

-    model.txtPSTHStart       = createTextField(pPSTH,[secondColumn secondRow 0.25*frameWidth controlElementHeight],DEFAULT.pststart);

-    model.txtPSTHEnd         = createTextField(pPSTH,[thirdColumn  secondRow 0.25*frameWidth controlElementHeight],DEFAULT.pstend);

-    model.txtBaselineStart   = createTextField(pPSTH,[secondColumn thirdRow  0.25*frameWidth controlElementHeight],DEFAULT.baselinestart);

-    model.txtBaselineEnd     = createTextField(pPSTH,[thirdColumn  thirdRow  0.25*frameWidth controlElementHeight],DEFAULT.baselineend);

-    model.txtFrameShiftStart = createTextField(pPSTH,[secondColumn fourthRow 0.25*frameWidth controlElementHeight],DEFAULT.frameshiftstart);

-    model.txtFrameShiftEnd   = createTextField(pPSTH,[thirdColumn  fourthRow 0.25*frameWidth controlElementHeight],DEFAULT.frameshiftend);

-    model.txtFrameShiftDur   = createTextField(pPSTH,[secondColumn fifthRow  0.25*frameWidth controlElementHeight],DEFAULT.frameshiftdur);

-

-                

-    %Classes

-    nClassRows = 6;

-    firstColumn  = 5.00;

-    

-    firstRow    = (nClassRows-0.5)*controlElementHeight;

-    secondRow   = (nClassRows-4.5)*controlElementHeight;

-

-    lClassDef = createLabel(pCLASS, [firstColumn firstRow  0.66*frameWidth controlElementHeight],'<Label>,<[Event,Event,..]>,<SVM-Value>;');

-    model.txtClassDef = createTextField(pCLASS,[firstColumn secondRow 0.98*frameWidth 4*controlElementHeight],sprintf(DEFAULT.classdefstring));

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

-    set(model.txtClassDef,'Max',20);

-    set(model.txtClassDef,'Min',0);

-    set(model.txtClassDef, 'FontName', 'FixedWidth')

-    

-    %Voxel

-    nVoxelRows = 8;

-    firstColumn  = 5.00;

-    

-    firstRow    = (nVoxelRows-0.5)*controlElementHeight;

-    secondRow   = (nVoxelRows-7.5)*controlElementHeight;

-

-    lVoxelDef = createLabel(pVOXEL, [firstColumn firstRow  0.66*frameWidth controlElementHeight],'<ROI Name>,<ROI Modifier>;');

-    model.txtVoxelDef = createTextField(pVOXEL,[firstColumn secondRow 0.98*frameWidth 6*controlElementHeight],...

-        sprintf(DEFAULT.voxelstring));

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

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

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

-    set(model.txtVoxelDef, 'FontName', 'FixedWidth')

-                

-    % SVM

-    firstColumn  =  5.00;

-    firstRow     =  1.00 * controlElementHeight;

-

-    model.txtSVMopts = createTextField(pSVM,[firstColumn firstRow  0.66*frameWidth controlElementHeight],DEFAULT.svmoptstring);

-    %model.txtSVMopts = createTextField(pSVM,[firstColumn firstRow  0.66*frameWidth controlElementHeight],'-s 0 -t 2 -v 6 -c 10 -g .1');

-    set(model.txtSVMopts,'Enable','on'); %inactive

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

-

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

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

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

-    uimenu(savemenu,'Label','Save','Callback',{@mcb_save,model});

-    uimenu(savemenu,'Label','Load','Callback',{@mcb_load,model});

-

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

-end

-

-function mcb_save(src,event,model)

-display('SAVE');

-

-end

-

-function mcb_load(src,event,model)

-display('LOAD');

-end

-

-function cbRunCoordTable(src,evnt,model)

-    display('RUN Coord-Table Mode');

-    main('COORD-LOOKUP-TABLE',model);

-end

-function cbRunROIImage(src,evnt,model)

-    display('RUN Image-Mask Mode');

-    main('ROI-IMAGE-MASK', model);

-end

-    

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

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

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

-    set(label,'Units','characters');

-%     set(label,'BackgroundColor','r');

-end

-

-

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

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

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

-end

-

@@ -1,43 +0,0 @@

-function project_UI(args)

-    PROJECTPATH = 'projects';

-    

-    frameWidth=450;

-    frameHeight=50;

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

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

-

-    set(model.frame,'Name','SVM CrossVal Decode Performance 4 SPM, Projectchooser');

-    set(model.frame,'NumberTitle','off');

-    set(model.frame,'MenuBar','none');

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

-    set(model.frame,'Resize','off');

-    set(model.frame,'Units','normalize');

-

-    newProjectMenu = uimenu(model.frame,'Label','Define New Project');

-    set(newProjectMenu,'Enable','off');

-

-    d = dir(fullfile(PROJECTPATH,'*.m'));

-    

-    model.projectSelection = uicontrol(model.frame,'Style','popupmenu',...

-                    'String',{d.name},...

-                    'Value',1,...  % default selected item

-                    'Position',[0.33*frameWidth 40 0.66*frameWidth 20]);

-    set(model.projectSelection,'BackgroundColor','w');

-    

-    

-    btnSelectButton = uicontrol(model.frame,'Tag','select','String','continue','Position',[2 0  frameWidth 20]);

-    

-%    model.projectSelector = 

-

-	model.val = 1;

-

-    set(btnSelectButton,'Callback',{@cbChooseProject,model}); % set here, because of model.    

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

-end

-

-function cbChooseProject(src,evnts,args)

-

-	spm_SVMCrossVal(args);

-	display(args);

-	close(args.frame)

-end

@@ -1,37 +1,35 @@

-function runROIImageMaskMode(subjects,timeline)

+function runROIImageMaskMode(args)

-%         imageStruct = loadImageFileNamesData(loadParams);

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

+subjects = args.subjects;

+mask     = ['^' cell2mat(args.mask) '.*\.img$'];

-%         coordinateStruct = computeCoordinates(imageStruct);

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

-end

+nSubjects = size(subjects);

+sessionlist = 1:3;

-function extr = claculateRoiImageData(filenameList,roiImageList)

-

-V = filenameList;

-nImage = numel(V);

-Vm = roiImageList;

-nRoi = numel(Vm);

-for kImage=1:nImage

-    x = []; y = []; z = [];

-    for iRoiFile = 1:nRoi

-        [x1 y1] = ndgrid(1:V(k).dim(1),1:V(k).dim(2));

-        for p = 1:V(k).dim(3) % resample mask Vm(i) in space of V(k)

-            B = spm_matrix([0 0 -p 0 0 0 1 1 1]);

-            M = inv(B*inv(V(k).mat)*Vm(iRoiFile).mat);

-            msk = find(spm_slice_vol(Vm(iRoiFile),M,V(k).dim(1:2),0));

-            if ~isempty(msk)

-                z1 = p*ones(size(msk(:)));

-                x = [x; x1(msk(:))];

-                y = [y; y1(msk(:))];

-                z = [z; z1];

-            end

-        end

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

-        extr(kImage).dat(iRoiFile) = dat;

+for s = 1:nSubjects

+    subjectStruct{s}.dir = fullfile(args.basedir,cell2mat(subjects(s)));

+    subjectStruct{s}.name = cell2mat(subjects(s));

+    subjectStruct{s}.roiFile = ui_selectRoiImage(...

+        sprintf('Select ROI Files for %s',subjectStruct{s}.name),...

+        fullfile(subjectStruct{s}.dir,'results','roi'));

 end

+

+

+

+for s = 1:nSubjects

+    % load image data

+   

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

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

+

+    disp('computing volume values, please wait');

+    subjectStruct{s}.rawData = calculateRoiImageData(subjectStruct{s}.volumes,subjectStruct{s}.roiFile);

+    % calculate psth

+          

 end

+assignin('base','subjectStruct',subjectStruct);

+

 end

+

@@ -1,18 +0,0 @@

-%timePointToImageNumber type is optional

-function imgNumber = timePointToImageNumber(timepoint, type)% timepoint in ms

-    switch type

-        case 's'

-            imgNumber = timePointToImageNumber(timepoint*1000,'ms');

-            return;

-        case 'ms'

-            imageTimeResolution   = 2000; %ms

-            imgNumber = round(timepoint/imageTimeResolution);

-            return;

-        case 'image'

-            imgNumber = timepoint;

-            return;

-        otherwise

-            imgNumber = timePointToImageNumber(timepoint,'ms');

-            return;

-    end

-end

\ No newline at end of file

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

 function ui_main(varargin)

 DEFAULT.selectedSubject = 2;

-DEFAULT.smoothed        = 1;

-DEFAULT.multisubject    = 'single';

+

 DEFAULT.pststart        = -15;

 DEFAULT.pstend          = 40;

 DEFAULT.baselinestart   = -3;

@@ -97,7 +96,7 @@ model = setTimeLineParams(model,l.timeLine);

 model = setClassDefString(model,l.classDefString);

 model = setCoordDefString(model,l.coordDefString);

 model.baseDir = l.baseDir;

-model = scanDirs(model)

+model = scanDirs(model);

 end

@@ -278,8 +277,6 @@ function model = createFirstStepPanel(model,parent,DEFAULT)

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

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

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

-        

         %normalizations

         pNorm = uipanel(parent,'Title','Normalization','Position',cell2mat(main_grid(2,3)));

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

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

-function imageList = readRoiImage(formatstring,wd)

+function imageList = ui_selectRoiImage(formatstring,wd)

 imageList = spm_vol(spm_select([1 Inf],'image',formatstring,[],wd));

 end

\ No newline at end of file