SVMCrossVal.git

@@ -1,7 +0,0 @@

-function s = boolToYesNoString(bool)

-    if bool

-        s = 'yes';

-    else

-        s = 'no';

-    end

-end

\ No newline at end of file

@@ -1,55 +0,0 @@

-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] = 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: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(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(:))];

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

-                    z = [z; z1];

-                end;

-            end;

-end

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

-function decode = fbs_calculateDecodePerformance(header,psth,svmopts)

-

-RANDOMIZE_DATAPOINTS = header.svmrnd;

-

-timeline = header.timeline;

-timeline.frameShiftStart = header.frameShift.frameShiftStart;

-timeline.frameShiftEnd   = header.frameShift.frameShiftEnd;

-timeline.decodeDuration  = header.frameShift.decodeDuration;

-

-timeLineStart  = timeline.frameShiftStart;

-timeLineEnd    = timeline.frameShiftEnd;

-

-timePointArgs.pst           = psth;

-timePointArgs.labelMap      = LabelMap(header.classDef.labelCells,header.classDef.conditionCells);

-timePointArgs.eventList     = header.classDef.eventMatrix;

-

-timePointMatrix = buildTimePointMatrix(timeline,timePointArgs);

-

-decodePerformance = [];

-for index = 1:timeLineEnd-timeLineStart+1

-

-    svmdata      = timePointMatrix{index}(:,2:size(timePointMatrix{index},2));

-    svmlabel     = timePointMatrix{index}(:,1);

-

-    if RANDOMIZE_DATAPOINTS

-        rndindex  = randperm(length(svmlabel));

-        svmdata   = svmdata(rndindex,:);

-        svmlabel  = svmlabel(rndindex);

-    end

-

-    decodePerformance = [decodePerformance; svm_single_crossval(svmlabel,svmdata,svmopts)];

-    

-    

-end

-

-decode  = decodePerformance;

-end

-

-

-

@@ -1,7 +0,0 @@

-function id = fbs_coordtable_getIndex(table,coord)

-if table.containsKey(coord)

-    id = table.get(coord);

-else

-     error('FBS:getLabel:noSuchValue','this Mapping does not contain a Value %d',condition);

-end

-end

\ No newline at end of file

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

-function voxellist = generateVoxelList(center, radius)

-%     cx = ROICenter(1);

-%     cy = ROICenter(2);

-%     cz = ROICenter(3);

-    

-    voxellist = [];

-    

-    cx = center(1);

-    cy = center(2);

-    cz = center(3);

-

-    for z=cz-radius+1:cz+radius-1

-        for y=(cy-radius+1):(cy+radius-1)

-            for x=(cx-radius+1):(cx+radius-1)

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

-            end

-        end

-    end

-

-end

\ No newline at end of file

@@ -1,6 +1,9 @@

 function output =  runFBSImageMaskMode(header,subjectdata,fbsargs)

 addpath('NIFTI_20090325');

+savePath = fullfile('output',sprintf('%s',date))

+mkdir(savePath);

+

 args = header.args;

 subjects = subjectdata;

@@ -108,16 +111,24 @@ for s = 1:nSubjects

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

     % vdim = tmp(7:9); % Voxel-Size

-    vdim = [3,3,3.5];

+    

+

     mask_image = load_nii(subjects{s}.roiFile.fname);

+    vdim = mask_image.hdr.dime.pixdim(2:4);

+    if mask_image.hdr.dime.pixdim(1) == 1

+        vdim = vdim .* [-1 1 1];

+    end

+

+    display(sprintf('starting timesliceing'));

+    

     for timeShift = 1:timeLineEnd-timeLineStart+1

     % center timepoint && relative shift

     frameStart  = floor(-globalStart+1+timeShift - 0.5*decodeDuration);

     frameEnd    = min(ceil(frameStart+decodeDuration + 0.5*decodeDuration),-globalStart+globalEnd);

-        img3D = zeros(size(mask_image)); %output image

+        img3D = zeros(size(mask_image)); %output image prepare

         for iVoxel = 1:nVoxel % linear structure avoids 3D-Loop.

             % get surrounding coordinate-IDs within radius

@@ -151,21 +162,23 @@ for s = 1:nSubjects

             x = coord(1);

             y = coord(2);

             z = coord(3);

-            img3D(x,y,z) = decode/100; %damn percentage

-%             mask_image.img(x,y,z) = decode/100;

+            

+            img3D(x,y,z) = ((decode/100)-0.5)*2; % range [-1:1]

         end  %for each voxel

-        nii = make_nii(img3D,vdim,mask_image.hdr.hist.originator(1:3),16,'decode performance'); %default origin

-        save_nii(nii,fullfile('output',sprintf('TESTFILE%g',timeShift)));

-%         save_nii(mask_image,sprintf('MTESTFILE%g',timeShift));

+        nii = make_nii(img3D,vdim,mask_image.hdr.hist.originator(1:3),16,sprintf('decode performance, time relative to onset: %g to %g sec',frameStart,frameEnd));

+        save_nii(nii,fullfile(savePath,sprintf('%s-%03g',subjects{s}.name,timeShift)));

     end %for each timeslice

     display('rastering done');

-    elapsed{s}.decode = toc;

-    clear pst; %save memory!

+    elapsed{s}.decode = toc;

     assignin('base','timing',elapsed);

+

+    %save memory!

+    clear pst; 

+    clear mask_image;

 end

 end

@@ -14,7 +14,7 @@ DEFAULT.voxelstring     = 'M1 l + 3 \nM1 r + 3\n';

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

 DEFAULT.svmnfold        = '6';

 DEFAULT.svmrnd          = 1;

-DEFAULT.searchlightradius = 0;

+DEFAULT.searchlightradius = 3;

 DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');