Browse code

fbs filename adaption, default fbs radius, delete unneded m-files

git-svn-id: https://svn.discofish.de/MATLAB/spmtoolbox/SVMCrossVal@171 83ab2cfd-5345-466c-8aeb-2b2739fb922d

Christoph Budziszewski authored on 02/04/2009 16:26:51
Showing 7 changed files
1 1
deleted file mode 100644
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@@ -1,7 +0,0 @@
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-function s = boolToYesNoString(bool)
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-    if bool
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-        s = 'yes';
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-    else
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-        s = 'no';
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-    end
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-end
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9 1
deleted file mode 100644
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@@ -1,55 +0,0 @@
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-function coordinateStruct = computeCoordinates(imageStruct)
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-%imageStruct.(someName).images
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-%imageStruct.(someName).roiImages
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-coordinateStruct = struct;
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-
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-subjectCellList = fieldnames(imageStruct);
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-
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-for subject = 1:length(subjectCellList)
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-    subjectFieldName = cell2mat(subjectCellList(subject));
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-    % ROI Image Coordinates
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-    V  = imageStruct.(subjectFieldName).images;
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-    Vm = imageStruct.(subjectFieldName).roiImages;
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-    coordinateStruct.(subjectFieldName) = ...
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-        computeRoiImageCoordinates(V,Vm);
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-    % Parsed Voxel Definitions
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-    coordinateStruct.(subjectFieldName) = ...
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-        appendManualVoxelCoordinates(coordinateStruct.(subjectFieldName),V);
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-    
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-end
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-end
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-
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-function coordinates = appendManualVoxelCoordinates(coordinateStruct,V)
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-    coordinates =coordinateStruct;
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-end
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-
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-function coordinates = computeRoiImageCoordinates(V,Vm)
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-    nVolImage = length(V);
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-    nRoiImage = length(Vm);
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-    
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-    coordinates = cell(nVolImage,1);
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- 
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-    for iVolImage = 1:nVolImage
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-        coordinates{iVolImage} = [];
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-        for jRoiImage = 1:nRoiImage
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-            [x,y,z] = computeCoordinateVector(V(iVolImage),Vm(jRoiImage));
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-            coordinates{iVolImage} = [coordinates{iVolImage}; x, y, z];
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-        end
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-    end
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-end
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-
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-function [x,y,z] = computeCoordinateVector(VolumeImage,RoiImage)
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-            x = []; y = []; z = [];
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-            [x1 y1] = ndgrid(1:VolumeImage.dim(1),1:VolumeImage.dim(2));
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-            for p = 1:VolumeImage.dim(3) % resample mask RoiImage in space of VolumeImage
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-                B = spm_matrix([0 0 -p 0 0 0 1 1 1]);
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-                M = inv(B*inv(VolumeImage.mat)*RoiImage.mat);
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-                msk = find(spm_slice_vol(RoiImage,M,VolumeImage.dim(1:2),0));
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-                if ~isempty(msk)
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-                    z1 = p*ones(size(msk(:)));
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-                    x = [x; x1(msk(:))];
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-                    y = [y; y1(msk(:))];
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-                    z = [z; z1];
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-                end;
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-            end;
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-end
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deleted file mode 100644
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@@ -1,40 +0,0 @@
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-function decode = fbs_calculateDecodePerformance(header,psth,svmopts)
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-
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-RANDOMIZE_DATAPOINTS = header.svmrnd;
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-
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-timeline = header.timeline;
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-timeline.frameShiftStart = header.frameShift.frameShiftStart;
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-timeline.frameShiftEnd   = header.frameShift.frameShiftEnd;
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-timeline.decodeDuration  = header.frameShift.decodeDuration;
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-
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-timeLineStart  = timeline.frameShiftStart;
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-timeLineEnd    = timeline.frameShiftEnd;
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-
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-timePointArgs.pst           = psth;
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-timePointArgs.labelMap      = LabelMap(header.classDef.labelCells,header.classDef.conditionCells);
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-timePointArgs.eventList     = header.classDef.eventMatrix;
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-
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-timePointMatrix = buildTimePointMatrix(timeline,timePointArgs);
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-
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-decodePerformance = [];
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-for index = 1:timeLineEnd-timeLineStart+1
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-
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-    svmdata      = timePointMatrix{index}(:,2:size(timePointMatrix{index},2));
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-    svmlabel     = timePointMatrix{index}(:,1);
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-
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-    if RANDOMIZE_DATAPOINTS
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-        rndindex  = randperm(length(svmlabel));
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-        svmdata   = svmdata(rndindex,:);
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-        svmlabel  = svmlabel(rndindex);
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-    end
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-
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-    decodePerformance = [decodePerformance; svm_single_crossval(svmlabel,svmdata,svmopts)];
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-    
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-    
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-end
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-
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-decode  = decodePerformance;
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-end
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-
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-
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-
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deleted file mode 100644
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@@ -1,7 +0,0 @@
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-function id = fbs_coordtable_getIndex(table,coord)
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-if table.containsKey(coord)
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-    id = table.get(coord);
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-else
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-     error('FBS:getLabel:noSuchValue','this Mapping does not contain a Value %d',condition);
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-end
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-end
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deleted file mode 100644
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@@ -1,20 +0,0 @@
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-function voxellist = generateVoxelList(center, radius)
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-%     cx = ROICenter(1);
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-%     cy = ROICenter(2);
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-%     cz = ROICenter(3);
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-    
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-    voxellist = [];
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-    
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-    cx = center(1);
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-    cy = center(2);
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-    cz = center(3);
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-
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-    for z=cz-radius+1:cz+radius-1
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-        for y=(cy-radius+1):(cy+radius-1)
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-            for x=(cx-radius+1):(cx+radius-1)
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-                voxellist = [voxellist [x;y;z]];
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-            end
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-        end
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-    end
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-
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-end
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\ No newline at end of file
... ...
@@ -1,6 +1,9 @@
1 1
 function output =  runFBSImageMaskMode(header,subjectdata,fbsargs)
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 addpath('NIFTI_20090325');
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+savePath = fullfile('output',sprintf('%s',date))
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+mkdir(savePath);
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+
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 args = header.args;
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 subjects = subjectdata;
... ...
@@ -108,16 +111,24 @@ for s = 1:nSubjects
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     % tmp = spm_imatrix(V(kImage).mat); %
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     % vdim = tmp(7:9); % Voxel-Size
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-    vdim = [3,3,3.5];
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+    
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+
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     mask_image = load_nii(subjects{s}.roiFile.fname);
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+    vdim = mask_image.hdr.dime.pixdim(2:4);
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+    if mask_image.hdr.dime.pixdim(1) == 1
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+        vdim = vdim .* [-1 1 1];
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+    end
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+
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+    display(sprintf('starting timesliceing'));
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+    
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     for timeShift = 1:timeLineEnd-timeLineStart+1
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     % center timepoint && relative shift
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     frameStart  = floor(-globalStart+1+timeShift - 0.5*decodeDuration);
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     frameEnd    = min(ceil(frameStart+decodeDuration + 0.5*decodeDuration),-globalStart+globalEnd);
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-        img3D = zeros(size(mask_image)); %output image
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+        img3D = zeros(size(mask_image)); %output image prepare
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         for iVoxel = 1:nVoxel % linear structure avoids 3D-Loop.
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             % get surrounding coordinate-IDs within radius
... ...
@@ -151,21 +162,23 @@ for s = 1:nSubjects
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             x = coord(1);
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             y = coord(2);
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             z = coord(3);
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-            img3D(x,y,z) = decode/100; %damn percentage
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-%             mask_image.img(x,y,z) = decode/100;
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+            
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+            img3D(x,y,z) = ((decode/100)-0.5)*2; % range [-1:1]
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         end  %for each voxel
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-        nii = make_nii(img3D,vdim,mask_image.hdr.hist.originator(1:3),16,'decode performance'); %default origin
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-        save_nii(nii,fullfile('output',sprintf('TESTFILE%g',timeShift)));
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-%         save_nii(mask_image,sprintf('MTESTFILE%g',timeShift));
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+        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));
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+        save_nii(nii,fullfile(savePath,sprintf('%s-%03g',subjects{s}.name,timeShift)));
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     end %for each timeslice
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     display('rastering done');
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-    elapsed{s}.decode = toc;
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-    clear pst; %save memory!
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+    elapsed{s}.decode = toc;
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     assignin('base','timing',elapsed);
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+
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+    %save memory!
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+    clear pst; 
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+    clear mask_image;
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 end
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171 184
 end
... ...
@@ -14,7 +14,7 @@ DEFAULT.voxelstring     = 'M1 l + 3 \nM1 r + 3\n';
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 DEFAULT.svmoptstring    = '-s 0 -t 0 -c 1';
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 DEFAULT.svmnfold        = '6';
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 DEFAULT.svmrnd          = 1;
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-DEFAULT.searchlightradius = 0;
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+DEFAULT.searchlightradius = 3;
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 DEFAULT.wd  = fullfile('d:','Analyze','Choice','24pilot');