SVMCrossVal.git

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

+function dirs = listDirs(wd)

+% d = listDirs(dir) returns all directories below dir as a cell array. 

+% the Structure is the same as from the 'dir' command (because this

+% function relies on 'dir'

+% . and .. are filterd. no intetion to include an option switch for those

+% special dirs.

+allfiles = dir(wd);

+nDirs = 1;

+for i = 1:size(allfiles)

+    file = allfiles(i);

+    if file.isdir && file.name(1)~='.'

+        dirs{nDirs}=file;

+        nDirs = nDirs +1;

+    end

+end

@@ -15,9 +15,13 @@ for subjectCell = loadParams.subjectCellArray

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

+    subjectPath = fullfile(getStudyBasePath(loadParams.StudyID),SubjectID);

+    

     ROIIMAGE = 1;

     if ROIIMAGE

         %load ROI Image Header

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

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

+        wd = subjectPath;

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

     end

 end

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@@ -4,7 +4,8 @@ switch action

     case 'COORD-LOOKUP-TABLE'

         runCoordTable(timeline,parameterModel);

     case 'ROI-IMAGE-MASK'

-        runROIImageMaskMode(parameterModel)

+        runROIImageMaskMode(parameterModel);

+        disp('DONE');

     case 'FULL-BRAIN'

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

     otherwise 

@@ -12,17 +13,7 @@ switch action

 end

 end

-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);

-end

 % generate parameter structs for subroutines

 function timelineParams = getTimeLineParams(paramModel)

@@ -139,7 +139,7 @@ DEFAULT.svmoptstring    = '-s 0 -t 0 -v 6 -c 1';

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

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

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

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

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

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

@@ -1,4 +1,3 @@

-function imageList = readRoiImage(formatstring)

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

+function imageList = readRoiImage(formatstring,wd)

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

 end

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@@ -0,0 +1,40 @@

+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);

+end

+

+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;

+    end

+end

+

+end

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