SVMCrossVal.git

@@ -4,14 +4,15 @@ function m = SubjectRoiMapping(argv)

 %   normally called without any arguments

 if nargin == 0

-    m.subject{1}='HIGL5';

-    m.subject{2}='AXLI5';

-    m.subject{3}='SHWA5';

-    m.subject{4}='DAPR5';

-    m.subject{5}='5IGKA';

-    m.subject{6}='5RAEL';

-    m.subject{7}='5JEZI';

-    m.subject{8}='5PK002';

+    m.subject{1} ='AI020';

+    m.subject{2} ='BD001';

+    m.subject{3} ='HG027';

+    m.subject{4} ='IK011';

+    m.subject{5} ='JZ006'; % Guter Proband

+    m.subject{6} ='LB001';

+    m.subject{7} ='SW007';

+    m.subject{8} ='VW005';

+

     m.subjectNameMap = java.util.HashMap;

     for subj = 1:size(m.subject,2)

         m.subjectNameMap.put(m.subject{subj},subj);

@@ -19,14 +20,18 @@ if nargin == 0

-    m.roi_name{1}='SPL l';

-    m.roi_name{2}='SPL r';

-    m.roi_name{3}='dPM l';

-    m.roi_name{4}='dPM r';

-    m.roi_name{5}='DLPFC l';

-    m.roi_name{6}='DLPFC r';

-    m.roi_name{7}='SMA l';

-    m.roi_name{8}='antIPS l';

+    m.roi_name{1}  ='SPL l'; % <-Parietalkortex links 

+    m.roi_name{2}  ='SPL r'; % <-Parietalkortex rechts 

+    m.roi_name{3}  ='PMd l'; 

+    m.roi_name{4}  ='PMd r'; 

+    m.roi_name{5}  ='IPSa l'; 

+    m.roi_name{6}  ='IPSa r'; 

+    m.roi_name{7}  ='SMA'; 

+    m.roi_name{8}  ='DLPFC'; 

+    m.roi_name{9}  ='V1 l'; 

+    m.roi_name{10} ='V1 r'; 

+    m.roi_name{11} ='M1 l'; % <-Motorischer Cortex l 

+    m.roi_name{12} ='M1 r'; % <-Motorischer Cortex r 

     m.roiNameMap = java.util.HashMap;

     for roi = 1:size(m.roi_name,2)

@@ -35,77 +40,103 @@ if nargin == 0

     % Koordinaten aller Probanden A von den ROIS B: rois{A}(B,[x y z in mm]) 

-    m.coordinate{1}(1,:)=[-15 -66 60];

-    m.coordinate{1}(2,:)=[18 -63 63];

-    m.coordinate{1}(3,:)=[-24 -6 57];

-    m.coordinate{1}(4,:)=[27 -9 54];

-    m.coordinate{1}(5,:)=[-42 30 39];

-    m.coordinate{1}(6,:)=[36 45 21];

-    m.coordinate{1}(7,:)=[-3 6 60];

-    m.coordinate{1}(8,:)=[-33 -39 42];

-

-    m.coordinate{2}(1,:)=[-15 -66 66];

-    m.coordinate{2}(2,:)=[15 -69 63];

-    m.coordinate{2}(3,:)=[-30 -9 63];

-    m.coordinate{2}(4,:)=[33 -6 60];

-    m.coordinate{2}(5,:)=[-30 39 42];

-    m.coordinate{2}(6,:)=[36 36 42];

-    m.coordinate{2}(7,:)=[-3 0 63];

-    m.coordinate{2}(8,:)=[-39 -42 60];

-

-    m.coordinate{3}(1,:)=[-18 -63 57];

-    m.coordinate{3}(2,:)=[15 -69 60];

-    m.coordinate{3}(3,:)=[-24 -12 51];

-    m.coordinate{3}(4,:)=[27 -12 51];

-    m.coordinate{3}(5,:)=[-27 36 42];

-    m.coordinate{3}(6,:)=[30 42 42];

-    m.coordinate{3}(7,:)=[-3 -6 63];

-    m.coordinate{3}(8,:)=[-36 -51 60];

-

-    m.coordinate{4}(1,:)=[-30 -54 63];

-    m.coordinate{4}(2,:)=[18 -60 54];

-    m.coordinate{4}(3,:)=[-33 -6 57];

-    m.coordinate{4}(4,:)=[27 -6 57];

-    m.coordinate{4}(5,:)=[-27 33 27];

-    m.coordinate{4}(6,:)=[nan nan nan];

-    m.coordinate{4}(7,:)=[-6 3 60];

-    m.coordinate{4}(8,:)=[-33 -51 54];

-

-    m.coordinate{5}(1,:)=[-21 -63 66];

-    m.coordinate{5}(2,:)=[24 -54 66];

-    m.coordinate{5}(3,:)=[-30 -6 51];

-    m.coordinate{5}(4,:)=[21 0 57];

-    m.coordinate{5}(5,:)=[-33 36 27];

-    m.coordinate{5}(6,:)=[33 45 30];

-    m.coordinate{5}(7,:)=[-6 -3 54];

-    m.coordinate{5}(8,:)=[-39 -42 54];

-

-    m.coordinate{6}(1,:)=[-15 -69 54];

-    m.coordinate{6}(2,:)=[21 -63 57];

-    m.coordinate{6}(3,:)=[-24 -9 66];

-    m.coordinate{6}(4,:)=[33 -6 66];

-    m.coordinate{6}(5,:)=[-33 30 39];

-    m.coordinate{6}(6,:)=[33 45 30];

-    m.coordinate{6}(7,:)=[-3 0 54];

-    m.coordinate{6}(8,:)=[-39 -42 39];

-

-    m.coordinate{7}(1,:)=[-12 -66 63];

-    m.coordinate{7}(2,:)=[15 -66 63];

-    m.coordinate{7}(3,:)=[-21 -9 54];

-    m.coordinate{7}(4,:)=[30 -9 57];

-    m.coordinate{7}(5,:)=[-39 33 33];

-    m.coordinate{7}(6,:)=[39 30 33];

-    m.coordinate{7}(7,:)=[-6 0 54];

-    m.coordinate{7}(8,:)=[-39 -45 54];

+    m.coordinate{1}(1,:)  = [-18, -78, 53];

+    m.coordinate{1}(2,:)  = [12, -69, 46];

+    m.coordinate{1}(3,:)  = [-21, -12, 49];

+    m.coordinate{1}(4,:)  = [30, -12, 53];

+    m.coordinate{1}(5,:)  = [-30, -51, 39];

+    m.coordinate{1}(6,:)  = [ 33, -60, 49];

+    m.coordinate{1}(7,:)  = [ -9, 6, 46];

+    m.coordinate{1}(8,:)  = [-27 27 48];

+    m.coordinate{1}(9,:)  = [-6, -90, -7];

+    m.coordinate{1}(10,:) = [12, -90, -4];

+    m.coordinate{1}(11,:) = [-57, -24, 49];

+    m.coordinate{1}(12,:) = [42, -24, 60];

+    m.coordinate{2}(1,:)  = [-9, -72, 56]; 

+    m.coordinate{2}(2,:)  = [15, -72, 60]; 

+    m.coordinate{2}(3,:)  = [-30, -9, 53]; 

+    m.coordinate{2}(4,:)  = [ 30, -9, 49]; 

+    m.coordinate{2}(5,:)  = [-42 -36 39]; 

+    m.coordinate{2}(6,:)  = [30 -36 42]; 

+    m.coordinate{2}(7,:)  = [ -3, 6, 53];

+    m.coordinate{2}(8,:)  = [-27 30 28];

+    m.coordinate{2}(9,:)  = [-6, -81, -7]; 

+    m.coordinate{2}(10,:) = [9, -78, -7];

+    m.coordinate{2}(11,:) = [-51, -24, 60];

+    m.coordinate{2}(12,:) = [48, -21, 63]; 

+    m.coordinate{3}(1,:)  = [-15, -72, 60];

+    m.coordinate{3}(2,:)  = [15, -66, 63];

+    m.coordinate{3}(3,:)  = [-27, -12, 56];

+    m.coordinate{3}(4,:)  = [24 -15 53];

+    m.coordinate{3}(5,:)  = [-36 -36 42];

+    m.coordinate{3}(6,:)  = [30 -39 35];

+    m.coordinate{3}(7,:)  = [-9, 3, 53]; 

+    m.coordinate{3}(8,:)  = [-30 30 28];

+    m.coordinate{3}(9,:)  = [-3, -90, 4];

+    m.coordinate{3}(10,:) = [15, -99, 14];

+    m.coordinate{3}(11,:) = [-27, -27, 74];

+    m.coordinate{3}(12,:) = [36, -27, 70]; 

+    m.coordinate{4}(1,:)  = [-21, -69, 63]; 

+    m.coordinate{4}(2,:)  = [21, -69, 63];

+    m.coordinate{4}(3,:)  = [-33 -12 53];

+    m.coordinate{4}(4,:)  = [12 -9 60];

+    m.coordinate{4}(5,:)  = [-33 -35 46];

+    m.coordinate{4}(6,:)  = [42 -36 39];

+    m.coordinate{4}(7,:)  = [-3 0 49];

+    m.coordinate{4}(8,:)  = [-33 33 28];

+    m.coordinate{4}(9,:)  = [-3, -90, -7];

+    m.coordinate{4}(10,:) = [9, -81, -7];

+    m.coordinate{4}(11,:) = [-39, -27, 53];

+    m.coordinate{4}(12,:) = [51, -24, 60];

+    m.coordinate{5}(1,:)  = [-12 -66 63];

+    m.coordinate{5}(2,:)  = [12, -75, 60];

+    m.coordinate{5}(3,:)  = [-24, -12, 53];

+    m.coordinate{5}(4,:)  = [27, -9, 60]; 

+    m.coordinate{5}(5,:)  = [-42 -42 35]; 

+    m.coordinate{5}(6,:)  = [33 -48 35];

+    m.coordinate{5}(7,:)  = [ -3, 0, 49];

+    m.coordinate{5}(8,:)  = [-36 33 28];

+    m.coordinate{5}(9,:)  = [-15, -93, -4];

+    m.coordinate{5}(10,:) = [15, -90, 4]; 

+    m.coordinate{5}(11,:) = [-39, -33, 67];

+    m.coordinate{5}(12,:) = [27, -18, 74];

+    m.coordinate{6}(1,:)  = [-21, -69, 60];

+    m.coordinate{6}(2,:)  = [9, -72, 63];

+    m.coordinate{6}(3,:)  = [-24 -12 53];

+    m.coordinate{6}(4,:)  = [32 -12 56]; 

+    m.coordinate{6}(5,:)  = [-36 -39 35];

+    m.coordinate{6}(6,:)  = [42 -33 46]; 

+    m.coordinate{6}(7,:)  = [-6 3 49]; 

+    m.coordinate{6}(8,:)  = [-36 33 28];

+    m.coordinate{6}(9,:)  = [-12, -99, 0];

+    m.coordinate{6}(10,:) = [9, -96, -7];

+    m.coordinate{6}(11,:) = [-48, -27, 60];

+    m.coordinate{6}(12,:) = [33, -33, 60];

+    m.coordinate{7}(1,:)  = [-21, -60, 56]; 

+    m.coordinate{7}(2,:)  = [12, -69, 60]; 

+    m.coordinate{7}(3,:)  = [-24, -12, 49];

+    m.coordinate{7}(4,:)  = [24, -6, 49]; 

+    m.coordinate{7}(5,:)  = [-33 -45 46]; 

+    m.coordinate{7}(6,:)  = [30, -51, 49];

+    m.coordinate{7}(7,:)  = [0, 9, 42]; 

+    m.coordinate{7}(8,:)  = [-30 36 35]; 

+    m.coordinate{7}(9,:)  = [-3, -84, -4];

+    m.coordinate{7}(10,:) = [18, -87, -7];

+    m.coordinate{7}(11,:) = [-36, -30, 63]; 

+    m.coordinate{7}(12,:) = [42, -27, 60];

+    m.coordinate{8}(1,:)  = [-27, -63, 53];

+    m.coordinate{8}(2,:)  = [18, -66, 56];

+    m.coordinate{8}(3,:)  = [-21, -6, 56];

+    m.coordinate{8}(4,:)  = [27 -6 53]; 

+    m.coordinate{8}(5,:)  = [-36, -51, 49];

+    m.coordinate{8}(6,:)  = [45, -39, 53];

+    m.coordinate{8}(7,:)  = [-9, 9, 53];

+    m.coordinate{8}(8,:)  = [-36 24 25]; 

+    m.coordinate{8}(9,:)  = [0, -90, 4]; 

+    m.coordinate{8}(10,:) = [0, -90, 4];

+    m.coordinate{8}(11,:) = [-42, -27, 67]; 

+    m.coordinate{8}(12,:) = [51, -27, 63]; 

-    m.coordinate{8}(1,:)=[-15 -72 51];

-    m.coordinate{8}(2,:)=[15 -75 51];

-    m.coordinate{8}(3,:)=[-27 -12 66];

-    m.coordinate{8}(4,:)=[33 -18 69];

-    m.coordinate{8}(5,:)=[-48 21 33];

-    m.coordinate{8}(6,:)=[42 33 36];

-    m.coordinate{8}(7,:)=[-3 -6 57];

-    m.coordinate{8}(8,:)=[-39 -48 45];

     m = class(m,'SubjectRoiMapping');

 elseif isa(argv,'SubjectRoiMapping') % copy

@@ -5,8 +5,8 @@ function classify(varargin)

 switch nargin

     case 1

         paramModel = varargin{1};

-         PROJECT_BASE_PATH = 'D:\Analyze\Stimolos';

-        %PROJECT_BASE_PATH = 'D:\Analyze\Choice\24pilot';

+        %PROJECT_BASE_PATH = 'D:\Analyze\Stimolos';

+        PROJECT_BASE_PATH = 'D:\Analyze\Choice\24pilot';

         PROJECT_RESULT_PATH = 'results\SPM.mat';

     otherwise

         error('spmtoolbox:SVMCrossVal:arginError','Please Specify action and parameter model');

@@ -93,12 +93,13 @@ function pst = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,

                         n{zr}=n{zr}+1;

                         pst{zr}(n{zr},:)=interp1(stime,sdata(:,sessionID),[des.Sess(sessionID).U(eventList(zr,ze)).ons(zz)+pre:res:des.Sess(sessionID).U(eventList(zr,ze)).ons(zz)+post],'linear');

+                        pstevnt{zr}(n{zr})=eventList(zr,ze); % NEW 090110 Specify #Event/Condition for each PST

                         if strcmp(normz,'epoc')

                             bline=nanmean(pst{zr}(n{zr},round(-pre/res+(bstart)/res+1):round(-pre/res+(bend)/res+1)));

                             if isnan(bline)

                                 pst{zr}(n{zr},1:-pre/res+post/res+1)=nan;

                             else

-%                                     nn{zr}=nn{zr}+1;

+                                nn{zr}=nn{zr}+1;

                                 pst{zr}(n{zr},:)=(pst{zr}(n{zr},:)-bline)/bline*100; % 'epoch-based' normalization

                             end;

                         end;

@@ -122,9 +123,41 @@ function pst = calculatePST(des,globalStart,baselineStart,baselineEnd,globalEnd,

         end;

     end;

+    %%%%COL BIAS REMOVAL, added 090110 %%%%%

+    col_bias_removal=0;

+    if col_bias_removal

+

+        for zr=1:evntrow % Event ROW

+            pst4row(zr,:)=nanmean(pst{zr}); % Average PST for overall ROW

+            n_col=0;

+            for ze=1:evntcol % Even COL

+                if ze==1 || (ze>1 && eventList(zr,ze)~=eventList(zr,ze-1))

+                    n_col=n_col+1;

+                    tmp_index=[];

+                    tmp_index=find(pstevnt{zr}(:)==eventList(zr,ze));

+                    % Calculate Average PST for each COL within ROW

+                    pst4col(n_col,:)=nanmean(pst{zr}(tmp_index,:));

+                    % COL BIAS: Calculate Difference between COL Ave and Overall Row Ave

+                    pst_delta(n_col,:)=pst4col(n_col,:)-pst4row(zr,:);

+                    % Remove COL BIAS from single PSTs

+                    for z=1:length(tmp_index)

+                        pst{zr}(tmp_index(z),:)=pst{zr}(tmp_index(z),:)-pst_delta(n_col,:);

+                    end;

+                end;

+            end;

+        end;

+    end;

+    %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%    

+                

+            

+            

+    

+    

+    

+    

     %%%%%%%%%%% new 090109 Axel: "Normalization" for SVM

-    norm4SVM='none'; %Normalization method for SVM

+    norm4SVM='mean'; %Normalization method for SVM

     disp(['normalization: ' norm4SVM]);   

     % none - no normalization

     % mean - mean normalization (meanPSTH max at .5, baseline at -.5]