refactored to arg-structs! (untested) (c54095b) - SVMCrossVal.git

refactored to arg-structs! (untested)

Christoph Budziszewski commited on 2009-01-29 16:25:27
Zeige 9 geänderte Dateien mit 223 Einfügungen und 102 Löschungen.

git-svn-id: https://svn.discofish.de/MATLAB/spmtoolbox/SVMCrossVal@122 83ab2cfd-5345-466c-8aeb-2b2739fb922d

private/buildTimePointMatrix.m fa65ee8..b864278
private/calculateDecodePerformance.m 131af5c..661f7ab
private/calculateImageData.m 3354881..bc19a71
private/calculatePST.m eb54660..b7cec94
private/classify.m 579d553..819b53d
private/getImageFileList.m 0000000..df9596f
private/main_UI.m ce1a312..cd08a9e
private/readRoiImage.m 0000000..ffccd19
spm_SVMCrossVal.m ba26bdf..dbb255a

private/buildTimePointMatrix.m

Zeige Datei @ c54095b

@@ -1,14 +1,14 @@
-function timePointMatrix = buildTimePointMatrix(argStruct)
+function timePointMatrix = buildTimePointMatrix(timeline,argStruct)
 
-pst             = argStruct.pst;
 
-timeLineStart   = argStruct.timeLineStart;
-timeLineEnd     = argStruct.timeLineEnd;
-globalStart     = argStruct.globalStart;
-globalEnd       = argStruct.globalEnd;
-decodeDuration  = argStruct.decodeDuration;
-eventList       = argStruct.eventList;
+timeLineStart   = timeline.frameShiftStart;
+timeLineEnd     = timeline.frameShiftEnd;
+globalStart     = timeline.psthStart;
+globalEnd       = timeline.psthEnd;
+decodeDuration  = timeline.decodeDuration;
 
+pst             = argStruct.pst;
+eventList       = argStruct.eventList;
 labelMap        = argStruct.labelMap;
 
 timePointMatrix = {};

private/calculateDecodePerformance.m

Zeige Datei @ c54095b

@@ -1,5 +1,5 @@
 % function [decodePerformance rawTimecourse ] = calculateDecodePerformance(des,timeLineStart, timeLineEnd, decodeDuration, svmargs, conditionList, sessionList, voxelList, classList, labelMap,normalize)
-function outputStruct = calculateDecodePerformance(timeline,inputStruct,SubjectID)
+function outputStruct = calculateDecodePerformance(timeline,inputStruct,subjectParams)
 
 global CROSSVAL_METHOD_DEF;
 
@@ -10,13 +11,16 @@ METHOD              = inputStruct.CROSSVAL_METHOD;
 
 RANDOMIZE_DATAPOINTS = inputStruct.RANDOMIZE;
 
+% SubjectID       = subjectParams.SubjectID;
+% namehelper      = subjectParams.namehelper;
+voxelList       = subjectParams.voxelList;
+des             = subjectParams.des;
+
 outputStruct = struct;
 
-namehelper      = strcat('s',SubjectID);
-des             = inputStruct.(namehelper).des;
 svmargs         = inputStruct.svmargs;
 sessionList     = inputStruct.sessionList;
-voxelList       = inputStruct.(namehelper).voxelList;
+
 % classList       = inputStruct.classList;
 % labelMap        = inputStruct.labelMap;
 smoothed        = inputStruct.smoothed;
@@ -24,33 +28,45 @@ eventList       = inputStruct.eventList;
 
 timeLineStart   = timeline.frameShiftStart;
 timeLineEnd     = timeline.frameShiftEnd;
-decodeDuration  = timeline.decodeDuration;
-globalStart     = timeline.psthStart;
-globalEnd       = timeline.psthEnd;
-baselineStart   = timeline.baselineStart;
-baselineEnd     = timeline.baselineEnd;
+% decodeDuration  = timeline.decodeDuration;
+% globalStart     = timeline.psthStart;
+% globalEnd       = timeline.psthEnd;
+% baselineStart   = timeline.baselineStart;
+% baselineEnd     = timeline.baselineEnd;
 
 
 minPerformance = inf;
 maxPerformance = -inf;
 
-        %% ERSETZEN DURCH ROI-IMAGE!
-        for voxel = 1:size(voxelList,1)  % [[x;x],[y;y],[z;z]]
-                extr        = calculateImageData(voxelList(voxel,:),des,smoothed); 
-                rawdata     = cell2mat({extr.mean}); % Raw Data
-                pst{voxel}  = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,rawdata,sessionList);
+imageFiles = getImageFileList(des,~smoothed);
+
+
+extr = calculateImageData(imageFiles,voxelList);
+rawdata = extr.dat;
+
+nVoxel = size(voxelList,1);
+
+calculatePstOpts = struct;
+calculatePstOpts.des = des;
+calculatePstOpts.eventList = eventList;
+calculatePstOpts.sessionList = sessionList;
+
+for iVoxel = 1:nVoxel
+    pst{nVoxel} = calculatePST(timeline,calculatePstOpts,rawdata(iVoxel));
 end
 
+%         for voxel = 1:size(voxelList,1)  % [[x;x],[y;y],[z;z]]
+%             extr        = calculateImageData(imageFiles,voxelList(voxel,:));
+%             rawdata     = cell2mat({extr.mean}); % Raw Data
+%             pst{voxel}  = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,rawdata,sessionList);
+%         end
+
 timePointArgs.pst = pst;
-        timePointArgs.timeLineStart = timeLineStart;
-        timePointArgs.timeLineEnd   = timeLineEnd;
-        timePointArgs.globalStart   = globalStart;
-        timePointArgs.globalEnd     = globalEnd;
-        timePointArgs.decodeDuration= decodeDuration;
+
 timePointArgs.labelMap      = inputStruct.labelMap;
 timePointArgs.eventList     = eventList;
 
-        timePointMatrix = buildTimePointMatrix(timePointArgs);
+timePointMatrix = buildTimePointMatrix(timeline,timePointArgs);
 
 decodePerformance = [];
 for index = 1:timeLineEnd-timeLineStart+1

private/calculateImageData.m

Zeige Datei @ c54095b

@@ -1,79 +1,102 @@
-function extr = calculateImageData(voxelList,des,smoothed)
+% filenameList as in SPM.xY.VY
+% voxelList in [x y z], 1 coordinate per row
 
-dtype='PSTH';
+function extr = calculateImageData(filenameList, voxelList)
+%function extr = calculateImageData(voxelList,des,smoothed)
+% global USE_DRIVE_CHECK_HACK;
 
-switch dtype 
-    case 'PSTH'
-        V=des.xY.VY;
-    case 'betas'
-        V=des.Vbeta;
-end;
+% dtype='PSTH';
 
-if V(1).fname(1)~='D'
-     for z=1:length(V) % Change Drive Letter!\
-      	V(z).fname(1) = 'D';
-     end; 
-end
+% switch dtype 
+%     case 'PSTH'
+%         V=des.xY.VY;
+%     case 'betas'
+%         V=des.Vbeta;
+% end;
 
-if (~smoothed)
-  for z=1:length(V) % Change Drive Letter!\
-      % 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
+% 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
 
-% rad = 0; % one voxel
-% opt = 1; % xyz coordinates [mm]
+% 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
 
+V = filenameList;
 
 vox = voxelList;
-nRoi = size(vox,1);
+nVoxel = size(vox,1);
+nImage = numel(V);
+
+for kImage=1:nImage
+	extr(kImage) = struct(...
+        'val',   repmat(NaN, [1 nVoxel]),...
+		'mean',  repmat(NaN, [1 nVoxel]),...
+		'sum',   repmat(NaN, [1 nVoxel]),...
+		'nvx',   repmat(NaN, [1 nVoxel]),...
+		'posmm', repmat(NaN, [3 nVoxel]),...
+		'posvx', repmat(NaN, [3 nVoxel]));
 
-nImg = numel(V);
+    switch TRANSFORM_METHOD
+        case 'single'
+            roicenter = round(inv(V(kImage).mat)*[vox, ones(nVoxel,1)]');
+            x = roicenter(1,:);
+            y = roicenter(2,:);
+            z = roicenter(3,:);
+        case 'image'
+             x = []; y = []; z = [];
+            for iRoiFile = 1:nRoiFiles 
+                [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;
 
-for k=1:nImg
-	extr(k) = struct(...
-        'val',   repmat(NaN, [1 nRoi]),...
-		'mean',  repmat(NaN, [1 nRoi]),...
-		'sum',   repmat(NaN, [1 nRoi]),...
-		'nvx',   repmat(NaN, [1 nRoi]),...
-		'posmm', repmat(NaN, [3 nRoi]),...
-		'posvx', repmat(NaN, [3 nRoi]));
+            end
+    end
     
-    roicenter = round(inv(V(k).mat)*[vox, ones(nRoi,1)]');
 
-	for l = 1:nRoi
+	for iVoxel = 1:nVoxel
 
 %         if rad==0
-            x = roicenter(1,l);
-            y = roicenter(2,l);
-            z = roicenter(3,l);
+            x = roicenter(1,iVoxel);
+            y = roicenter(2,iVoxel);
+            z = roicenter(3,iVoxel);
 %         else
-%             tmp = spm_imatrix(V(k).mat);
+%             tmp = spm_imatrix(V(kImage).mat);
 %             vdim = tmp(7:9);
-%             vxrad = ceil((rad*ones(1,3))./(ones(nRoi,1)*vdim))';
-%             [x y z] = ndgrid(-vxrad(1,l):sign(vdim(1)):vxrad(1,l), ...
-%                       -vxrad(2,l):sign(vdim(2)):vxrad(2,l), ...
-%                       -vxrad(3,l):sign(vdim(3)):vxrad(3,l));
-%             sel = (x./vxrad(1,l)).^2 + (y./vxrad(2,l)).^2 + ...
-%                   (z./vxrad(3,l)).^2 <= 1;
-%             x = roicenter(1,l)+x(sel(:));
-%             y = roicenter(2,l)+y(sel(:));
-%             z = roicenter(3,l)+z(sel(:));
+%             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(k), x, y, z,0);
-		[maxv maxi]         = max(dat);
-		tmp                 = V(k).mat*[x(maxi); y(maxi); z(maxi);1]; % Max Pos
-		extr(k).val(l)      = maxv;
-		extr(k).sum(l)      = sum(dat);
-		extr(k).mean(l)     = nanmean(dat);
-        extr(k).nvx(l)      = numel(dat);
-		extr(k).posmm(:,l)  = tmp(1:3);
-		extr(k).posvx(:,l)  = [x(maxi); y(maxi); z(maxi)]; % Max Pos
+		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;

private/calculatePST.m

Zeige Datei @ c54095b

@@ -1,9 +1,14 @@
-function pst = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,data,sessionList)
-    bstart          = baselineStart;
-    bend            = baselineEnd;
+%function pst = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,data,sessionList)
+function pst = calculatePST(timeline,pstopts,data)
+    des         = pstopts.des;
+    eventList   = pstopts.eventList;
+    sessionList = pstopts.sessionList;
+
+    bstart          = timeline.baselineStart;
+    bend            = timeline.baselineEnd;
     edur            = 12;
-    pre             =  globalStart;
-    post            =  globalEnd;
+    pre             = timeline.psthStart;
+    post            = timeline.psthEnd;
     res             = 1;
 
     normz           = 'file';

private/classify.m

Zeige Datei @ c54095b

@@ -1,6 +1,7 @@
 function classify(varargin)
 
 global CROSSVAL_METHOD_DEF;
+global VOXEL_SELECTION_MODE_DEF;
 
 switch nargin
     case 1
@@ -28,6 +29,7 @@ end
         
 %         calculateParams.CROSSVAL_METHOD_DEF = CROSSVAL_METHOD_DEF;
         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;
         
@@ -76,11 +78,13 @@ end
 
 %% subject loop
 function decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams)
+global VOXEL_SELECTION_MODE_DEF;
+
 decode = struct;
 decode.decodePerformance = [];
 decode.rawTimeCourse     = [];
 
-for subjectCell = subjectSelection
+for subjectCell = calculateParams.subjectSelection
     SubjectID = cell2mat(subjectCell);
     namehelper = strcat('s',SubjectID); %Vars can not start with numbers.
 
@@ -88,16 +92,29 @@ for subjectCell = subjectSelection
     spm = load(fullfile(calculateParams.PROJECT_BASE_PATH,SubjectID,calculateParams.PROJECT_RESULT_PATH));
     display('... done.');
 
-    % calculate
-    calculateParams.(namehelper).des             = spm.SPM;
-    calculateParams.(namehelper).voxelList       = parseVoxelList(paramModel,SubjectID);
-    assignin('base','calculateParams',calculateParams);
+    % per subject params..
+    subjectParams = struct;
+    
+    subjectParams.des             = spm.SPM;
+
+    switch calculateParams.VOXEL_SELECTION_MODE 
+        case VOXEL_SELECTION_MODE_DEF.manualGui
+            subjectParams.voxelList       = parseVoxelList(paramModel,SubjectID);
+            
+        case VOXEL_SELECTION_MODE_DEF.roiImage
+            subjectParams.voxelList       = readRoiImage();
+    end
+    
+    
+    subjectParams.SubjectID       = SubjectID;
+    subjectParams.namehelper      = namehelper;
+%     assignin('base','calculateParams',calculateParams);
 
     display(sprintf('calculating cross-validation performance time-shift for Subject %s. Please Wait. ...',SubjectID));
     display('switching off all warnings');
     warning_state               = warning('off','all');
     display('calculating ...');
-    decode.(namehelper)         = calculateDecodePerformance(timelineParams,calculateParams,SubjectID);
+    decode.(namehelper)         = calculateDecodePerformance(timelineParams,calculateParams,subjectParams);
 
     display('... done');
     display('restoring warnings');

private/getImageFileList.m

Zeige Datei @ c54095b

...	...	@@ -0,0 +1,24 @@
	1	+function fileList = getImageFileList(des,use_unsmoothed_hack)
	2	+
	3	+global USE_DRIVE_CHECK_HACK;
	4	+
	5	+fileList = des.xY.VY;
	6	+nFiles = length(fileList);
	7	+
	8	+if USE_DRIVE_CHECK_HACK
	9	+ if fileList(1).fname(1)~='D'
	10	+ for z=1:nFiles % Change Drive Letter - HACK!
	11	+ fileList(z).fname(1) = 'D';
	12	+ end;
	13	+ end
	14	+end
	15	+if use_unsmoothed_hack
	16	+ for z=1:nFiles % Change smoothed Filename - HACK!
	17	+ % D:....SUBJECTID\session\swfanders...
	18	+ % D:....SUBJECTID\session\wfanders...
	19	+ tmp = findstr(filesep,fileList(z).fname);
	20	+ fileList(z).fname = strcat(fileList(z).fname(1:tmp(end)),fileList(z).fname(tmp(end)+2:end));
	21	+ end;
	22	+end
	23	+
	24	+end
0	25	\ No newline at end of file

private/main_UI.m

Zeige Datei @ c54095b

@@ -1,5 +1,7 @@
 function main_UI(args)
 
+global CROSSVAL_METHOD_DEF;
+
 %     project = args.project;
 %     DEFAULT = project.default;
 
@@ -61,12 +63,17 @@ DEFAULT.svmoptstring    = '-s 0 -t 0 -v 6 -c 1';
                     'Position',[firstColumn firstRow 0.66*frameWidth controlElementHeight*6]);
     set(model.subjectSelector,'BackgroundColor','w');
     
-    createLabel(pSubject,[0.68*frameWidth firstRow*2  0.25*frameWidth controlElementHeight],'Smooth Data');
     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');
     
-    createLabel(pSubject,[0.68*frameWidth firstRow*4  0.25*frameWidth controlElementHeight],'Crossvalidation');
-    model.txtMultisubject = createTextField(pSubject,[0.68*frameWidth firstRow*3  0.25*frameWidth controlElementHeight],DEFAULT.multisubject);
-    set(model.txtMultisubject,'enable','off');
+    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;

private/readRoiImage.m

Zeige Datei @ c54095b

...	...	@@ -0,0 +1,24 @@
	1	+function voxelList = readRoiImage()
	2	+
	3	+Vm = spm_vol(spm_select([1 Inf],'image','Select ROI image'));
	4	+nRoiFiles = size(Vm,2);
	5	+
	6	+% for iRoiFile = 1:nRoiFiles
	7	+% x = []; y = []; z = [];
	8	+% [x1 y1] = ndgrid(1:V(k).dim(1),1:V(k).dim(2));
	9	+% for p = 1:V(k).dim(3) % resample mask Vm(iRoiFile) in space of V(k)
	10	+% B = spm_matrix([0 0 -p 0 0 0 1 1 1]);
	11	+% M = inv(Binv(V(k).mat)Vm(iRoiFile).mat);
	12	+% msk = find(spm_slice_vol(Vm(iRoiFile),M,V(k).dim(1:2),0));
	13	+% if ~isempty(msk)
	14	+% z1 = p*ones(size(msk(:)));
	15	+% x = [x; x1(msk(:))];
	16	+% y = [y; y1(msk(:))];
	17	+% z = [z; z1];
	18	+% end;
	19	+% end;
	20	+%
	21	+% end
	22	+voxelList = Vm;
	23	+
	24	+end
0	25	\ No newline at end of file

spm_SVMCrossVal.m

Zeige Datei @ c54095b

@@ -1,13 +1,19 @@
 function spm_SVMCrossVal(varargin)
 
 %define global constants
-global CROSSVAL_METHOD_DEF;
+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 cross subject testing';
+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';
+
 switch nargin
 case 0
 % 	project_UI;


...	...	@@ -1,14 +1,14 @@
1		-function timePointMatrix = buildTimePointMatrix(argStruct)
	1	+function timePointMatrix = buildTimePointMatrix(timeline,argStruct)
2	2
3		-pst = argStruct.pst;
4	3
5		-timeLineStart = argStruct.timeLineStart;
6		-timeLineEnd = argStruct.timeLineEnd;
7		-globalStart = argStruct.globalStart;
8		-globalEnd = argStruct.globalEnd;
9		-decodeDuration = argStruct.decodeDuration;
10		-eventList = argStruct.eventList;
	4	+timeLineStart = timeline.frameShiftStart;
	5	+timeLineEnd = timeline.frameShiftEnd;
	6	+globalStart = timeline.psthStart;
	7	+globalEnd = timeline.psthEnd;
	8	+decodeDuration = timeline.decodeDuration;
11	9
	10	+pst = argStruct.pst;
	11	+eventList = argStruct.eventList;
12	12	labelMap = argStruct.labelMap;
13	13
14	14	timePointMatrix = {};

...	...	@@ -1,5 +1,5 @@
1	1	% function [decodePerformance rawTimecourse ] = calculateDecodePerformance(des,timeLineStart, timeLineEnd, decodeDuration, svmargs, conditionList, sessionList, voxelList, classList, labelMap,normalize)
2		-function outputStruct = calculateDecodePerformance(timeline,inputStruct,SubjectID)
	2	+function outputStruct = calculateDecodePerformance(timeline,inputStruct,subjectParams)
3	3
4	4	global CROSSVAL_METHOD_DEF;
5	5
...	...	@@ -10,13 +11,16 @@ METHOD = inputStruct.CROSSVAL_METHOD;
10	11
11	12	RANDOMIZE_DATAPOINTS = inputStruct.RANDOMIZE;
12	13
	14	+% SubjectID = subjectParams.SubjectID;
	15	+% namehelper = subjectParams.namehelper;
	16	+voxelList = subjectParams.voxelList;
	17	+des = subjectParams.des;
	18	+
13	19	outputStruct = struct;
14	20
15		-namehelper = strcat('s',SubjectID);
16		-des = inputStruct.(namehelper).des;
17	21	svmargs = inputStruct.svmargs;
18	22	sessionList = inputStruct.sessionList;
19		-voxelList = inputStruct.(namehelper).voxelList;
	23	+
20	24	% classList = inputStruct.classList;
21	25	% labelMap = inputStruct.labelMap;
22	26	smoothed = inputStruct.smoothed;
...	...	@@ -24,33 +28,45 @@ eventList = inputStruct.eventList;
24	28
25	29	timeLineStart = timeline.frameShiftStart;
26	30	timeLineEnd = timeline.frameShiftEnd;
27		-decodeDuration = timeline.decodeDuration;
28		-globalStart = timeline.psthStart;
29		-globalEnd = timeline.psthEnd;
30		-baselineStart = timeline.baselineStart;
31		-baselineEnd = timeline.baselineEnd;
	31	+% decodeDuration = timeline.decodeDuration;
	32	+% globalStart = timeline.psthStart;
	33	+% globalEnd = timeline.psthEnd;
	34	+% baselineStart = timeline.baselineStart;
	35	+% baselineEnd = timeline.baselineEnd;
32	36
33	37
34	38	minPerformance = inf;
35	39	maxPerformance = -inf;
36	40
37		- %% ERSETZEN DURCH ROI-IMAGE!
38		- for voxel = 1:size(voxelList,1) % [[x;x],[y;y],[z;z]]
39		- extr = calculateImageData(voxelList(voxel,:),des,smoothed);
40		- rawdata = cell2mat({extr.mean}); % Raw Data
41		- pst{voxel} = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,rawdata,sessionList);
	41	+imageFiles = getImageFileList(des,~smoothed);
	42	+
	43	+
	44	+extr = calculateImageData(imageFiles,voxelList);
	45	+rawdata = extr.dat;
	46	+
	47	+nVoxel = size(voxelList,1);
	48	+
	49	+calculatePstOpts = struct;
	50	+calculatePstOpts.des = des;
	51	+calculatePstOpts.eventList = eventList;
	52	+calculatePstOpts.sessionList = sessionList;
	53	+
	54	+for iVoxel = 1:nVoxel
	55	+ pst{nVoxel} = calculatePST(timeline,calculatePstOpts,rawdata(iVoxel));
42	56	end
43	57
	58	+% for voxel = 1:size(voxelList,1) % [[x;x],[y;y],[z;z]]
	59	+% extr = calculateImageData(imageFiles,voxelList(voxel,:));
	60	+% rawdata = cell2mat({extr.mean}); % Raw Data
	61	+% pst{voxel} = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,rawdata,sessionList);
	62	+% end
	63	+
44	64	timePointArgs.pst = pst;
45		- timePointArgs.timeLineStart = timeLineStart;
46		- timePointArgs.timeLineEnd = timeLineEnd;
47		- timePointArgs.globalStart = globalStart;
48		- timePointArgs.globalEnd = globalEnd;
49		- timePointArgs.decodeDuration= decodeDuration;
	65	+
50	66	timePointArgs.labelMap = inputStruct.labelMap;
51	67	timePointArgs.eventList = eventList;
52	68
53		- timePointMatrix = buildTimePointMatrix(timePointArgs);
	69	+timePointMatrix = buildTimePointMatrix(timeline,timePointArgs);
54	70
55	71	decodePerformance = [];
56	72	for index = 1:timeLineEnd-timeLineStart+1

...	...	@@ -1,79 +1,102 @@
1		-function extr = calculateImageData(voxelList,des,smoothed)
	1	+% filenameList as in SPM.xY.VY
	2	+% voxelList in [x y z], 1 coordinate per row
2	3
3		-dtype='PSTH';
	4	+function extr = calculateImageData(filenameList, voxelList)
	5	+%function extr = calculateImageData(voxelList,des,smoothed)
	6	+% global USE_DRIVE_CHECK_HACK;
4	7
5		-switch dtype
6		- case 'PSTH'
7		- V=des.xY.VY;
8		- case 'betas'
9		- V=des.Vbeta;
10		-end;
	8	+% dtype='PSTH';
11	9
12		-if V(1).fname(1)~='D'
13		- for z=1:length(V) % Change Drive Letter!\
14		- V(z).fname(1) = 'D';
15		- end;
16		-end
	10	+% switch dtype
	11	+% case 'PSTH'
	12	+% V=des.xY.VY;
	13	+% case 'betas'
	14	+% V=des.Vbeta;
	15	+% end;
17	16
18		-if (~smoothed)
19		- for z=1:length(V) % Change Drive Letter!\
20		- % D:....SUBJECTID\session\swfanders...
21		- % D:....SUBJECTID\session\wfanders...
22		- tmp = findstr(filesep,V(z).fname);
23		- V(z).fname = strcat(V(z).fname(1:tmp(end)),V(z).fname(tmp(end)+2:end));
24		- end;
25		-end
	17	+% if USE_DRIVE_CHECK_HACK
	18	+% if V(1).fname(1)~='D'
	19	+% for z=1:length(V) % Change Drive Letter - HACK!
	20	+% V(z).fname(1) = 'D';
	21	+% end;
	22	+% end
	23	+% end
26	24
27		-% rad = 0; % one voxel
28		-% opt = 1; % xyz coordinates [mm]
	25	+% if (~smoothed)
	26	+% for z=1:length(V) % Change smoothed Filename - HACK!
	27	+% % D:....SUBJECTID\session\swfanders...
	28	+% % D:....SUBJECTID\session\wfanders...
	29	+% tmp = findstr(filesep,V(z).fname);
	30	+% V(z).fname = strcat(V(z).fname(1:tmp(end)),V(z).fname(tmp(end)+2:end));
	31	+% end;
	32	+% end
29	33
	34	+V = filenameList;
30	35
31	36	vox = voxelList;
32		-nRoi = size(vox,1);
	37	+nVoxel = size(vox,1);
	38	+nImage = numel(V);
	39	+
	40	+for kImage=1:nImage
	41	+ extr(kImage) = struct(...
	42	+ 'val', repmat(NaN, [1 nVoxel]),...
	43	+ 'mean', repmat(NaN, [1 nVoxel]),...
	44	+ 'sum', repmat(NaN, [1 nVoxel]),...
	45	+ 'nvx', repmat(NaN, [1 nVoxel]),...
	46	+ 'posmm', repmat(NaN, [3 nVoxel]),...
	47	+ 'posvx', repmat(NaN, [3 nVoxel]));
33	48
34		-nImg = numel(V);
	49	+ switch TRANSFORM_METHOD
	50	+ case 'single'
	51	+ roicenter = round(inv(V(kImage).mat)*[vox, ones(nVoxel,1)]');
	52	+ x = roicenter(1,:);
	53	+ y = roicenter(2,:);
	54	+ z = roicenter(3,:);
	55	+ case 'image'
	56	+ x = []; y = []; z = [];
	57	+ for iRoiFile = 1:nRoiFiles
	58	+ [x1 y1] = ndgrid(1:V(k).dim(1),1:V(k).dim(2));
	59	+ for p = 1:V(k).dim(3) % resample mask Vm(iRoiFile) in space of V(k)
	60	+ B = spm_matrix([0 0 -p 0 0 0 1 1 1]);
	61	+ M = inv(Binv(V(k).mat)Vm(iRoiFile).mat);
	62	+ msk = find(spm_slice_vol(Vm(iRoiFile),M,V(k).dim(1:2),0));
	63	+ if ~isempty(msk)
	64	+ z1 = p*ones(size(msk(:)));
	65	+ x = [x; x1(msk(:))];
	66	+ y = [y; y1(msk(:))];
	67	+ z = [z; z1];
	68	+ end;
	69	+ end;
35	70
36		-for k=1:nImg
37		- extr(k) = struct(...
38		- 'val', repmat(NaN, [1 nRoi]),...
39		- 'mean', repmat(NaN, [1 nRoi]),...
40		- 'sum', repmat(NaN, [1 nRoi]),...
41		- 'nvx', repmat(NaN, [1 nRoi]),...
42		- 'posmm', repmat(NaN, [3 nRoi]),...
43		- 'posvx', repmat(NaN, [3 nRoi]));
	71	+ end
	72	+ end
44	73
45		- roicenter = round(inv(V(k).mat)*[vox, ones(nRoi,1)]');
46	74
47		- for l = 1:nRoi
	75	+ for iVoxel = 1:nVoxel
48	76
49	77	% if rad==0
50		- x = roicenter(1,l);
51		- y = roicenter(2,l);
52		- z = roicenter(3,l);
	78	+ x = roicenter(1,iVoxel);
	79	+ y = roicenter(2,iVoxel);
	80	+ z = roicenter(3,iVoxel);
53	81	% else
54		-% tmp = spm_imatrix(V(k).mat);
	82	+% tmp = spm_imatrix(V(kImage).mat);
55	83	% vdim = tmp(7:9);
56		-% vxrad = ceil((radones(1,3))./(ones(nRoi,1)vdim))';
57		-% [x y z] = ndgrid(-vxrad(1,l):sign(vdim(1)):vxrad(1,l), ...
58		-% -vxrad(2,l):sign(vdim(2)):vxrad(2,l), ...
59		-% -vxrad(3,l):sign(vdim(3)):vxrad(3,l));
60		-% sel = (x./vxrad(1,l)).^2 + (y./vxrad(2,l)).^2 + ...
61		-% (z./vxrad(3,l)).^2 <= 1;
62		-% x = roicenter(1,l)+x(sel(:));
63		-% y = roicenter(2,l)+y(sel(:));
64		-% z = roicenter(3,l)+z(sel(:));
	84	+% vxrad = ceil((radones(1,3))./(ones(nVoxel,1)vdim))';
	85	+% [x y z] = ndgrid(-vxrad(1,iVoxel):sign(vdim(1)):vxrad(1,iVoxel), ...
	86	+% -vxrad(2,iVoxel):sign(vdim(2)):vxrad(2,iVoxel), ...
	87	+% -vxrad(3,iVoxel):sign(vdim(3)):vxrad(3,iVoxel));
	88	+% sel = (x./vxrad(1,iVoxel)).^2 + (y./vxrad(2,iVoxel)).^2 + ...
	89	+% (z./vxrad(3,iVoxel)).^2 <= 1;
	90	+% x = roicenter(1,iVoxel)+x(sel(:));
	91	+% y = roicenter(2,iVoxel)+y(sel(:));
	92	+% z = roicenter(3,iVoxel)+z(sel(:));
65	93	% end;
66	94
67	95
68		- dat = spm_sample_vol(V(k), x, y, z,0);
69		- [maxv maxi] = max(dat);
70		- tmp = V(k).mat*[x(maxi); y(maxi); z(maxi);1]; % Max Pos
71		- extr(k).val(l) = maxv;
72		- extr(k).sum(l) = sum(dat);
73		- extr(k).mean(l) = nanmean(dat);
74		- extr(k).nvx(l) = numel(dat);
75		- extr(k).posmm(:,l) = tmp(1:3);
76		- extr(k).posvx(:,l) = [x(maxi); y(maxi); z(maxi)]; % Max Pos
	96	+ dat = spm_sample_vol(V(kImage), x, y, z,0);
	97	+ extr(kImage).dat(iVoxel) = dat;
	98	+ extr(kImage).mean(iVoxel) = nanmean(dat);
	99	+ extr(kImage).nvx(iVoxel) = numel(dat);
77	100	end;
78	101
79	102	end;

...	...	@@ -1,9 +1,14 @@
1		-function pst = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,data,sessionList)
2		- bstart = baselineStart;
3		- bend = baselineEnd;
	1	+%function pst = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,eventList,data,sessionList)
	2	+function pst = calculatePST(timeline,pstopts,data)
	3	+ des = pstopts.des;
	4	+ eventList = pstopts.eventList;
	5	+ sessionList = pstopts.sessionList;
	6	+
	7	+ bstart = timeline.baselineStart;
	8	+ bend = timeline.baselineEnd;
4	9	edur = 12;
5		- pre = globalStart;
6		- post = globalEnd;
	10	+ pre = timeline.psthStart;
	11	+ post = timeline.psthEnd;
7	12	res = 1;
8	13
9	14	normz = 'file';

...	...	@@ -1,6 +1,7 @@
1	1	function classify(varargin)
2	2
3	3	global CROSSVAL_METHOD_DEF;
	4	+global VOXEL_SELECTION_MODE_DEF;
4	5
5	6	switch nargin
6	7	case 1
...	...	@@ -28,6 +29,7 @@ end
28	29
29	30	% calculateParams.CROSSVAL_METHOD_DEF = CROSSVAL_METHOD_DEF;
30	31	calculateParams.CROSSVAL_METHOD = CROSSVAL_METHOD_DEF.svmcrossval;
	32	+ calculateParams.VOXEL_SELECTION_MODE = VOXEL_SELECTION_MODE_DEF.roiImage;
31	33	calculateParams.PROJECT_BASE_PATH = PROJECT_BASE_PATH;
32	34	calculateParams.PROJECT_RESULT_PATH = PROJECT_RESULT_PATH;
33	35
...	...	@@ -76,11 +78,13 @@ end
76	78
77	79	%% subject loop
78	80	function decode = claculateMultiSubjectDecodePerformance(timelineParams,calculateParams)
	81	+global VOXEL_SELECTION_MODE_DEF;
	82	+
79	83	decode = struct;
80	84	decode.decodePerformance = [];
81	85	decode.rawTimeCourse = [];
82	86
83		-for subjectCell = subjectSelection
	87	+for subjectCell = calculateParams.subjectSelection
84	88	SubjectID = cell2mat(subjectCell);
85	89	namehelper = strcat('s',SubjectID); %Vars can not start with numbers.
86	90
...	...	@@ -88,16 +92,29 @@ for subjectCell = subjectSelection
88	92	spm = load(fullfile(calculateParams.PROJECT_BASE_PATH,SubjectID,calculateParams.PROJECT_RESULT_PATH));
89	93	display('... done.');
90	94
91		- % calculate
92		- calculateParams.(namehelper).des = spm.SPM;
93		- calculateParams.(namehelper).voxelList = parseVoxelList(paramModel,SubjectID);
94		- assignin('base','calculateParams',calculateParams);
	95	+ % per subject params..
	96	+ subjectParams = struct;
	97	+
	98	+ subjectParams.des = spm.SPM;
	99	+
	100	+ switch calculateParams.VOXEL_SELECTION_MODE
	101	+ case VOXEL_SELECTION_MODE_DEF.manualGui
	102	+ subjectParams.voxelList = parseVoxelList(paramModel,SubjectID);
	103	+
	104	+ case VOXEL_SELECTION_MODE_DEF.roiImage
	105	+ subjectParams.voxelList = readRoiImage();
	106	+ end
	107	+
	108	+
	109	+ subjectParams.SubjectID = SubjectID;
	110	+ subjectParams.namehelper = namehelper;
	111	+% assignin('base','calculateParams',calculateParams);
95	112
96	113	display(sprintf('calculating cross-validation performance time-shift for Subject %s. Please Wait. ...',SubjectID));
97	114	display('switching off all warnings');
98	115	warning_state = warning('off','all');
99	116	display('calculating ...');
100		- decode.(namehelper) = calculateDecodePerformance(timelineParams,calculateParams,SubjectID);
	117	+ decode.(namehelper) = calculateDecodePerformance(timelineParams,calculateParams,subjectParams);
101	118
102	119	display('... done');
103	120	display('restoring warnings');

...	...	@@ -1,5 +1,7 @@
1	1	function main_UI(args)
2	2
	3	+global CROSSVAL_METHOD_DEF;
	4	+
3	5	% project = args.project;
4	6	% DEFAULT = project.default;
5	7
...	...	@@ -61,12 +63,17 @@ DEFAULT.svmoptstring = '-s 0 -t 0 -v 6 -c 1';
61	63	'Position',[firstColumn firstRow 0.66frameWidth controlElementHeight6]);
62	64	set(model.subjectSelector,'BackgroundColor','w');
63	65
64		- createLabel(pSubject,[0.68frameWidth firstRow2 0.25*frameWidth controlElementHeight],'Smooth Data');
65	66	model.chkSmoothed = uicontrol(pSubject,'Style','checkbox','Position',[0.68frameWidth firstRow 0.25frameWidth controlElementHeight],'Value',DEFAULT.smoothed);
	67	+ createLabel(pSubject,[0.75frameWidth firstRow 0.25frameWidth controlElementHeight],'Smooth Data?');
	68	+
	69	+ createLabel(pSubject,[0.68frameWidth firstRow4 0.25*frameWidth controlElementHeight],'Analysis Method');
66	70
67		- createLabel(pSubject,[0.68frameWidth firstRow4 0.25*frameWidth controlElementHeight],'Crossvalidation');
68		- model.txtMultisubject = createTextField(pSubject,[0.68frameWidth firstRow3 0.25*frameWidth controlElementHeight],DEFAULT.multisubject);
69		- set(model.txtMultisubject,'enable','off');
	71	+ model.analysisMethodSelector = uicontrol(pSubject,'Style','popupmenu',...
	72	+ 'Position',[0.68frameWidth firstRow3 0.25*frameWidth controlElementHeight],...
	73	+ 'String',{CROSSVAL_METHOD_DEF.svmcrossval, CROSSVAL_METHOD_DEF.classPerformance},...
	74	+ 'Value',1);
	75	+ set(model.analysisMethodSelector,'BackgroundColor','w');
	76	+% set(model.analysisMethodSelector,'enable','off');
70	77
71	78	% PSTH
72	79	firstColumn = 5.00;

...	...	@@ -1,13 +1,19 @@
1	1	function spm_SVMCrossVal(varargin)
2	2
3	3	%define global constants
4		-global CROSSVAL_METHOD_DEF;
	4	+global USE_DRIVE_CHECK_HACK;
	5	+USE_DRIVE_CHECK_HACK = 1; %enables subroutine to check if image path starts with 'D'
5	6
	7	+global CROSSVAL_METHOD_DEF;
6	8	CROSSVAL_METHOD_DEF.svmcrossval = 'svm crossval';
7	9	CROSSVAL_METHOD_DEF.classPerformance = 'svm class performance';
8		-CROSSVAL_METHOD_DEF.crossSubject = 'svm cross subject testing';
	10	+CROSSVAL_METHOD_DEF.crossSubject = 'svm across subject testing';
9	11	CROSSVAL_METHOD_DEF.somTraining = 'som Training';
10	12
	13	+global VOXEL_SELECTION_MODE_DEF;
	14	+VOXEL_SELECTION_MODE_DEF.manualGui = 'manually defined in GUI';
	15	+VOXEL_SELECTION_MODE_DEF.roiImage = 'use ROI image and popup image selector';
	16	+
11	17	switch nargin
12	18	case 0
13	19	% project_UI;
14	20