SVMCrossVal.git

@@ -1,6 +1,4 @@

 function spmv = getSPMVersion

-

-% spmv = 'SPM5';

-spmv = 'SPM2';

-

+global SVMCROSSVAL_SPMVERSION;

+spmv = SVMCROSSVAL_SPMVERSION;

 end

\ No newline at end of file

@@ -0,0 +1,4 @@

+function p = getSpmPath

+global SVMCROSSVAL_SPMDIR

+p = SVMCROSSVAL_SPMDIR;

+end

\ No newline at end of file

@@ -0,0 +1,4 @@

+function p = getTbxPath

+global SVMCROSSVAL_TOOLBOXPATH;

+p = SVMCROSSVAL_TOOLBOXPATH;

+end

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@@ -0,0 +1,4 @@

+function debug = isDebug

+global SVMCROSSVAL_DEBUG;

+debug = SVMCROSSVAL_DEBUG;

+end

\ No newline at end of file

@@ -1,10 +1,11 @@

 function output =  runFBSImageMaskMode(header,subjectdata,fbsargs)

-addpath('NIFTI_20090325');

+addpath(fullfile(getTbxPath,'NIFTI_20090325'));

-DEBUG = 0;

+SVMCROSSVAL_DEBUG = 0;

 NORM_DECODE = 0; % 1: normalize to [-1:1], 0: normalize to [0:1]

-savePath = fullfile('output',datestr(now,30));

+subjectResultDir

+savePath = fullfile(subjectResultDir,'fbs',datestr(now,30));

 mkdir(savePath);

 args = header.args;

@@ -99,7 +100,7 @@ for s = 1:nSubjects

 %              sprintf(' %g%%\t complete',p);

 %          end

     end

-    if DEBUG == 1

+    if isDebug

         figure;

         hold on;

         for i = 1:size(pst,2)

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

 %% subject loop

 function decode = som_subject_batch(header,subjectdata,somOpts)

-addpath 'somtoolbox2';

+addpath(fullfile(getTbxPath,'somtoolbox2'));

 RANDOMIZE_DATAPOINTS = somOpts.rnd;

 NAN_AS_ZERO = somOpts.nantozero;

@@ -3,7 +3,7 @@ function [sD sM] = som_train(svmlabel, svmdata, somOptions)

 som_size = somOptions.size;

 som_lattice = somOptions.lattice;

-addpath 'somtoolbox2';

+addpath(fullfile(getTbxPath,'somtoolbox2'));

 sD = som_data_struct(svmdata,'labels',num2str(svmlabel));

 sM = som_make(sD,'msize', som_size,'lattice', som_lattice, 'tracking', 1, 'init', 'lininit');

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

 %% subject loop

 function decode = som_xsubject_performance(header,subjectdata,somOpts)

-addpath 'somtoolbox2';

+addpath(fullfile(getTbxPath,'somtoolbox2'));

 nSubjects = numel(subjectdata);

 if(nSubjects < 2) 

@@ -1,5 +1,5 @@

 function decodePerformance = svm_class_performance(svmlabel,svmdata,svmopts)

-addpath 'libsvm-mat-2.88-1';

+addpath(fullfile(getTbxPath,'libsvm-mat-2.88-1'));

 svmmodel = svmtrain(svmlabel,svmdata,svmopts);

 classperformance = [];

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

 function performance = svm_single_crossval(svmlabel,svmdata,svmopts)

-addpath 'libsvm-mat-2.88-1';

+addpath(fullfile(getTbxPath,'libsvm-mat-2.88-1'));

 performance  = svmtrain(svmlabel, svmdata, svmopts);

 end

\ No newline at end of file

@@ -0,0 +1,16 @@

+function ui_createStudy()

+    frameWidth=450;

+    frameHeight=450;

+    

+    frame = figure('Visible','off','Position',[0,0,frameWidth,frameHeight]);

+    movegui(frame,'west'); % get this thing visible on smaller displays.

+    set(frame,'Name','Create Study');

+    set(frame,'NumberTitle','off');

+    set(frame,'MenuBar','none');

+%     set(frame,'Color',get(0,'defaultUicontrolBackgroundColor'));

+    set(frame,'Resize','on');

+    set(frame,'Units','normalized');

+    set(frame,'Color','y');

+

+    

+end

\ No newline at end of file

@@ -1,31 +1,5 @@

 function ui_main(varargin)

-DEFAULT.selectedSubject = [1];

-

-DEFAULT.pststart        = -5;

-DEFAULT.pstend          = 40;

-DEFAULT.baselinestart   = 0;

-DEFAULT.baselineend     = 0;

-DEFAULT.trfactor        = 0.5;

-DEFAULT.frameshiftstart = -5;

-DEFAULT.frameshiftend   = 15;

-DEFAULT.frameshiftdur   = 0;

-DEFAULT.classdefstring  = 'A,\t[9,11]\nB,\t[13,14]';

-DEFAULT.voxelstring     = 'SPL l + 3 \nSPL r + 3\n';

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

-DEFAULT.svmnfold        = '6';

-DEFAULT.svmrnd          = 1;

-DEFAULT.searchlightradius = 3;

-DEFAULT.searchlightTimeline = '';

-DEFAULT.somM = 3;

-DEFAULT.somN = 3;

-DEFAULT.somLattice = 1;

-

-

-DEFAULT.wd  = fullfile('d:','Analyze','Stimolos');

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

-% DEFAULT.wd  = fullfile('/','media','fMRI');

-

 %  Initialize and hide the GUI as it is being constructed.

     frameWidth=450;

     frameHeight=450;

@@ -42,6 +16,8 @@ DEFAULT.wd  = fullfile('d:','Analyze','Stimolos');

     task = struct;

+    DEFAULT = mcb_load_study(0,0,'study/stimolos.mat');

+    

     model1 = struct;

     model1.baseDir = DEFAULT.wd;

@@ -110,7 +86,8 @@ DEFAULT.wd  = fullfile('d:','Analyze','Stimolos');

         uimenu(savemenu,'Label','Save All','Callback',{@mcb_save,model1},'Enable','off');

         uimenu(savemenu,'Label','Load All','Callback',{@mcb_load,model1},'Enable','off');

-    uimenu(frame,'Label','change Study','Callback',{@mcb_cd,model1},'Enable','off');

+    studymenu = uimenu(frame,'Label','change Study','Enable','on');

+        fillStudyMenu(studymenu);

     cbSwitchTask(0,0,'PRE',task,model1);

@@ -119,6 +95,16 @@ DEFAULT.wd  = fullfile('d:','Analyze','Stimolos');

 end

+function fillStudyMenu(studymenu)

+    studydir = fullfile(getTbxPath,'study');

+    files = dir(studydir);

+    for fileidx = 1: numel(files)

+        if ~files(fileidx).isdir

+            uimenu(studymenu,'Label',files(fileidx).name,'Callback',{@mcb_load_study,fullfile(studydir,files(fileidx).name)});

+        end

+    end

+end

+

 function model = createFirstStepPanel(model,parent,DEFAULT)

     main_grid = cell(2,4);

@@ -470,6 +456,9 @@ function cbPlot(src,evnt,model,type)

 main(model,'plot',type);

 end

+function default = mcb_load_study(src,evnt,studyfile)

+    default = load(studyfile);

+end

 function model = mcb_cd(src,evnt,model)

 disp('CD');

@@ -1,3 +1,20 @@

 function imageList = ui_selectRoiImage(formatstring,wd)

+

+switch getSPMVersion

+    case 'SPM5'

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

+    case 'SPM2'

+        imageList = spm_vol(spm_get([1 Inf],'img',formatstring,wd,0));

+    otherwise

+        [filematrix pathmatrix]= uigetfile(...

+           {'*.nii;*.img;', 'All NIFTI/ANALYZE Files (*.hdr, *.nii, )'; ...

+            '*.*',                  'All Files (*.*)'}, ...

+        formatstring,...

+        wd,...

+        'MultiSelect', 'off'); 

+        

+        imageList = spm_vol([pathmatrix filematrix]);

 end

+end

+

+

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

 %% subject loop

 function decode = xsvm_subject_loop(header,subjectdata,svmopts)

-addpath 'libsvm-mat-2.88-1';

+addpath(fullfile(getTbxPath,'libsvm-mat-2.88-1'));

 nSubjects = numel(subjectdata);

 if(nSubjects < 2) 

@@ -2,9 +2,23 @@ function spm_SVMCrossVal(varargin)

 defineGlobals();

+global SVMCROSSVAL_SPMDIR;

+global SVMCROSSVAL_SPMVERSION;

+global SVMCROSSVAL_TOOLBOXPATH;

+global SVMCROSSVAL_DEBUG;

+% SPMDIR = 'D:\SPM\spm5human'

+SVMCROSSVAL_SPMDIR = 'D:\SPM\spm2';

+SVMCROSSVAL_SPMVERSION = 'SPM2';

+SVMCROSSVAL_TOOLBOXPATH = fullfile('C:\Dokumente und Einstellungen\Christoph\Eigene Dateien\MATLAB\spmtoolbox\SVMCrossVal\','');

+% SVMCROSSVAL_TOOLBOXPATH = fullfile(SVMCROSSVAL_SPMDIR,'toolbox');

+

 switch nargin

     case 0

-	ui_main(varargin);

+        SVMCROSSVAL_DEBUG = 0;

+        ui_main();

+    case 1

+        SVMCROSSVAL_DEBUG = varargin(1);

+        ui_main();

 otherwise

 error('spm_SVMCrossVal:main','wrong nargin');

 end