SVMCrossVal.git

@@ -32,12 +32,19 @@ function coordinates = computeRoiImageCoordinates(V,Vm)

     for iVolImage = 1:nVolImage

         coordinates{iVolImage} = [];

         for jRoiImage = 1:nRoiImage

+            [x,y,z] = computeCoordinateVector(V(iVolImage),Vm(jRoiImage));

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

+        end

+    end

+end

+

+function [x,y,z] = computeCoordinateVector(VolumeImage,RoiImage)

             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)

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

+            for p = 1:VolumeImage.dim(3) % resample mask RoiImage in space of VolumeImage

                 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));

+                M = inv(B*inv(VolumeImage.mat)*RoiImage.mat);

+                msk = find(spm_slice_vol(RoiImage,M,VolumeImage.dim(1:2),0));

                 if ~isempty(msk)

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

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

@@ -45,7 +52,4 @@ function coordinates = computeRoiImageCoordinates(V,Vm)

                     z = [z; z1];

                 end;

             end;

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

-        end

-    end

 end

@@ -0,0 +1,22 @@

+function defineGlobals()

+%define global constants

+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';

+end

\ No newline at end of file

@@ -1,22 +1,27 @@

-function retVal = main(action,parameterModel)

-

-% if nargs ~=2 

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

-% end

-

-StudyID = 'CHOICE24';

-

+function main(action,parameterModel)

+timeline = getTimeLineParams(parameterModel);

+switch action

+    case 'COORD-LOOKUP-TABLE'

+        runCoordTable(timeline,parameterModel);

+    case 'ROI-IMAGE-MASK'

+        runROIImageMaskMode(parameterModel)

+    case 'FULL-BRAIN'

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

+    otherwise 

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

+end

+end

-        loadParams.StudyID = StudyID;

+function runROIImageMaskMode(parameterModel)

+        loadParams.StudyID = 'CHOICE24';

         loadParams.use_smoothed_image_hack = 1;

         loadParams.subjectCellArray = getSubjectIDString(parameterModel);

         imageStruct = loadImageFileNamesData(loadParams);

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

-        coordinateStruct = computeCoordinates(imageStruct);

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

-

+%         coordinateStruct = computeCoordinates(imageStruct);

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

 end

 % generate parameter structs for subroutines

@@ -1,25 +1,8 @@

 function spm_SVMCrossVal(varargin)

-%define global constants

-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';

+SVMCROSSVAL_BASEDIR = fullfile('D:','Analyse','Choice');

+

+defineGlobals();

 switch nargin

 case 0

@@ -32,6 +15,9 @@ error('spm_SVMCrossVal:main','wrong nargin');

 end

 end

+function loadStudies(basedir)

+

+end