SVMCrossVal.git

@@ -0,0 +1,51 @@

+function coordinateStruct = computeCoordinates(imageStruct)

+%imageStruct.(someName).images

+%imageStruct.(someName).roiImages

+coordinateStruct = struct;

+

+subjectCellList = fieldnames(imageStruct);

+

+for subject = 1:length(subjectCellList)

+    subjectFieldName = cell2mat(subjectCellList(subject));

+    % ROI Image Coordinates

+    V  = imageStruct.(subjectFieldName).images;

+    Vm = imageStruct.(subjectFieldName).roiImages;

+    coordinateStruct.(subjectFieldName) = ...

+        computeRoiImageCoordinates(V,Vm);

+    % Parsed Voxel Definitions

+    coordinateStruct.(subjectFieldName) = ...

+        appendManualVoxelCoordinates(coordinateStruct.(subjectFieldName),V);

+    

+end

+end

+

+function coordinates = appendManualVoxelCoordinates(coordinateStruct,V)

+    coordinates =coordinateStruct;

+end

+

+function coordinates = computeRoiImageCoordinates(V,Vm)

+    nVolImage = length(V);

+    nRoiImage = length(Vm);

+    

+    coordinates = cell(nVolImage,1);

+ 

+    for iVolImage = 1:nVolImage

+        coordinates{iVolImage} = [];

+        for jRoiImage = 1:nRoiImage

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

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

+            for p = 1:V(iVolImage).dim(3) % resample mask Vm(jRoiImage) in space of V(iVolImage)

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

+                M = inv(B*inv(V(iVolImage).mat)*Vm(jRoiImage).mat);

+                msk = find(spm_slice_vol(Vm(jRoiImage),M,V(iVolImage).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;

+            coordinates{iVolImage} = [coordinates{iVolImage}; x, y, z];

+        end

+    end

+end

\ No newline at end of file

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

+function path = getStudyBasePath(studyID)

+switch studyID

+    case 'CHOICE24'

+        path = fullfile('D:','Analyze','Choice','24pilot');

+    otherwise

+        error('SVMCrossVal:getBasePath:noid',...

+            'Please specify a base path in ''getStudyBasePath'' or check the studyID');

+end

+end

@@ -0,0 +1,23 @@

+function datastruct = loadImageFileNamesData(loadParams)

+

+global SVMCROSSVAL_SUBJECT_PREFIX;

+

+RESULT_PATH = fullfile('results','SPM.mat');

+

+for subjectCell = loadParams.subjectCellArray

+    SubjectID   = cell2mat(subjectCell);

+    subjectString = strcat(SVMCROSSVAL_SUBJECT_PREFIX,SubjectID); 

+    

+    display('loading SPM.mat ...');

+    des = load(fullfile(getStudyBasePath(loadParams.StudyID),SubjectID,RESULT_PATH));

+    des = des.SPM;

+    display('... done.');

+    

+    datastruct.(subjectString).images      = getImageFileList(des,loadParams.use_smoothed_image_hack);

+    

+    ROIIMAGE = 1;

+    if ROIIMAGE

+        %load ROI Image Header

+        datastruct.(subjectString).roiImages = readRoiImage(sprintf('Select ROI Images for Subject %s',SubjectID));

+    end

+end

\ No newline at end of file

@@ -0,0 +1,54 @@

+function retVal = main(action,parameterModel)

+

+% if nargs ~=2 

+%     error('SVMCrossVal:main:argument','wrong number of arguments');

+% end

+

+StudyID = 'CHOICE24';

+

+

+        loadParams.StudyID = StudyID;

+        loadParams.use_smoothed_image_hack = 1;

+        loadParams.subjectCellArray = getSubjectIDString(parameterModel);

+

+        imageStruct = loadImageFileNamesData(loadParams);

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

+        

+        coordinateStruct = computeCoordinates(imageStruct);

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

+

+end

+

+% generate parameter structs for subroutines

+function timelineParams = getTimeLineParams(paramModel)

+timelineParams = struct;

+timelineParams.frameShiftStart = getDouble(paramModel.txtFrameShiftStart);  % -20;

+timelineParams.frameShiftEnd   = getDouble(paramModel.txtFrameShiftEnd); %15;

+timelineParams.decodeDuration  = getDouble(paramModel.txtFrameShiftDur);

+timelineParams.psthStart       = getDouble(paramModel.txtPSTHStart); % -25;

+timelineParams.psthEnd         = getDouble(paramModel.txtPSTHEnd); % 20;

+timelineParams.baselineStart   = getDouble(paramModel.txtBaselineStart); % -22;

+timelineParams.baselineEnd     = getDouble(paramModel.txtBaselineEnd); % -20;

+

+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

@@ -1,45 +1,19 @@

-% filenameList as in SPM.xY.VY

-% voxelList in [x y z], 1 coordinate per row

+% filenameList (e.g. as in SPM.xY.VY)

+% voxelList in [x y z], 1 coordinate per row, untransformed

-function extr = calculateImageData(filenameList, voxelList)

-%function extr = calculateImageData(voxelList,des,smoothed)

-% global USE_DRIVE_CHECK_HACK;

-

-% dtype='PSTH';

-

-% switch dtype 

-%     case 'PSTH'

-%         V=des.xY.VY;

-%     case 'betas'

-%         V=des.Vbeta;

-% end;

-

-% if USE_DRIVE_CHECK_HACK

-% if V(1).fname(1)~='D'

-%      for z=1:length(V) % Change Drive Letter - HACK!

-%       	V(z).fname(1) = 'D';

-%      end; 

-% end

-% end

-

-% if (~smoothed)

-%   for z=1:length(V) % Change smoothed Filename - HACK!

-%       % D:....SUBJECTID\session\swfanders...

-%       % D:....SUBJECTID\session\wfanders...

-%       tmp = findstr(filesep,V(z).fname);

-%       V(z).fname = strcat(V(z).fname(1:tmp(end)),V(z).fname(tmp(end)+2:end));

-%   end;

-% end

+function extr = calculateImageData(filenameList, voxelList, imageOpts)

+TRANSFORM_METHOD = 'image';

 V = filenameList;

 vox = voxelList;

 nVoxel = size(vox,1);

 nImage = numel(V);

+nRoiFiles = ;

 for kImage=1:nImage

     extr(kImage) = struct(...

-        'val',   repmat(NaN, [1 nVoxel]),...

+        'dat',   repmat(NaN, [1 nVoxel]),...

         'mean',  repmat(NaN, [1 nVoxel]),...

         'sum',   repmat(NaN, [1 nVoxel]),...

         'nvx',   repmat(NaN, [1 nVoxel]),...

@@ -71,33 +44,10 @@ for kImage=1:nImage

             end

     end

-

-	for iVoxel = 1:nVoxel

-

-%         if rad==0

-            x = roicenter(1,iVoxel);

-            y = roicenter(2,iVoxel);

-            z = roicenter(3,iVoxel);

-%         else

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

-%             vdim = tmp(7:9);

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

-%             [x y z] = ndgrid(-vxrad(1,iVoxel):sign(vdim(1)):vxrad(1,iVoxel), ...

-%                       -vxrad(2,iVoxel):sign(vdim(2)):vxrad(2,iVoxel), ...

-%                       -vxrad(3,iVoxel):sign(vdim(3)):vxrad(3,iVoxel));

-%             sel = (x./vxrad(1,iVoxel)).^2 + (y./vxrad(2,iVoxel)).^2 + ...

-%                   (z./vxrad(3,iVoxel)).^2 <= 1;

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

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

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

-%         end;

-

-

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

     extr(kImage).dat(iVoxel)      = dat;

     extr(kImage).mean(iVoxel)     = nanmean(dat);

     extr(kImage).nvx(iVoxel)      = numel(dat);

 end;

-end;

 end

\ No newline at end of file

@@ -96,13 +96,20 @@ for subjectCell = calculateParams.subjectSelection

     subjectParams = struct;

     subjectParams.des             = spm.SPM;

+    smoothed = calculateParams.smoothed;

+    

+    DataImageFilenames      = getImageFileList(des,~smoothed);

+    subjectParams.voxelList = getTransformedCoordinates(...

+        calculateParams.VOXEL_SELECTION_MODE,

     switch calculateParams.VOXEL_SELECTION_MODE 

         case VOXEL_SELECTION_MODE_DEF.manualGui

-            subjectParams.voxelList       = parseVoxelList(paramModel,SubjectID);

+            parsedVoxelList          = parseVoxelList(paramModel,SubjectID);

+              = transformVoxelList(parsedVoxelList);

+            

         case VOXEL_SELECTION_MODE_DEF.roiImage

-            subjectParams.voxelList       = readRoiImage();

+            subjectParams.voxelList       = readRoiImage(); % image for subject!

     end

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

-function fileList = getImageFileList(des,use_unsmoothed_hack)

+function fileList = getImageFileList(des,use_smoothed_image_hack)

 global USE_DRIVE_CHECK_HACK;

@@ -12,7 +12,7 @@ if USE_DRIVE_CHECK_HACK

         end;

     end

 end

-if use_unsmoothed_hack

+if ~use_smoothed_image_hack

     for z=1:nFiles % Change smoothed Filename - HACK!

         % D:....SUBJECTID\session\swfanders...

         % D:....SUBJECTID\session\wfanders...

@@ -166,7 +166,8 @@ end

 function cbRunSVM(src,evnt,model)

     display('RUN');

     if isSane(model)

-        classify(model)

+%         classify(model)

+        main('all',model);

     else

         error('spmtoolbox:SVMCrossVal:paramcheck','please verify all parameters');

     end

@@ -1,24 +1,4 @@

-function voxelList = readRoiImage()

-

-Vm = spm_vol(spm_select([1 Inf],'image','Select ROI image'));

-nRoiFiles = size(Vm,2);

-

-% for iRoiFile = 1:nRoiFiles

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

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

-%     for p = 1:V(k).dim(3) % resample mask Vm(iRoiFile) 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;

-% 

-% end

-voxelList = Vm;

-

+function imageList = readRoiImage(formatstring)

+wd = 'C:\Dokumente und Einstellungen\Christoph\Eigene Dateien\Diplomarbeit\data';

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

 end

\ No newline at end of file

@@ -1,18 +1,25 @@

 function spm_SVMCrossVal(varargin)

 %define global constants

-global USE_DRIVE_CHECK_HACK;

-USE_DRIVE_CHECK_HACK = 1;  %enables subroutine to check if image path starts with 'D'

-

-global CROSSVAL_METHOD_DEF;

-CROSSVAL_METHOD_DEF.svmcrossval       = 'svm crossval';

-CROSSVAL_METHOD_DEF.classPerformance  = 'svm class performance';

-CROSSVAL_METHOD_DEF.crossSubject      = 'svm across subject testing';

-CROSSVAL_METHOD_DEF.somTraining       = 'som Training';

-

-global VOXEL_SELECTION_MODE_DEF;

-VOXEL_SELECTION_MODE_DEF.manualGui    = 'manually defined in GUI';

-VOXEL_SELECTION_MODE_DEF.roiImage     = 'use ROI image and popup image selector';

+global SVMCROSSVAL_USE_DRIVE_CHECK_HACK;

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

+SVMCROSSVAL_USE_DRIVE_CHECK_HACK                  = 1;  

+

+global SVMCROSSVAL_CROSSVAL_METHOD_DEF;

+% supported classification methods

+SVMCROSSVAL_CROSSVAL_METHOD_DEF.svmcrossval       = 'svm crossval';

+SVMCROSSVAL_CROSSVAL_METHOD_DEF.classPerformance  = 'svm class performance';

+SVMCROSSVAL_CROSSVAL_METHOD_DEF.crossSubject      = 'svm across subject testing';

+SVMCROSSVAL_CROSSVAL_METHOD_DEF.somTraining       = 'som Training';

+

+global SVMCROSSVAL_VOXEL_SELECTION_MODE_DEF;

+% supported voxel selection methods

+SVMCROSSVAL_VOXEL_SELECTION_MODE_DEF.manualGui    = 'manually defined in GUI';

+SVMCROSSVAL_VOXEL_SELECTION_MODE_DEF.roiImage     = 'use ROI image by pop-up image selector';

+

+global SVMCROSSVAL_SUBJECT_PREFIX;

+% internally used to prefix subject-ids starting with numbers.

+SVMCROSSVAL_SUBJECT_PREFIX                        = 'subject';

 switch nargin

 case 0