/ISCanalysis/ISCanalysis.m

function varargout = ISCanalysis(varargin)

% ISCANALYSIS M-file for ISCanalysis.fig

%      ISCANALYSIS, by itself, creates a new ISCANALYSIS or raises the existing

%      singleton*.

%

%      H = ISCANALYSIS returns the handle to a new ISCANALYSIS or the handle to

%      the existing singleton*.

%

%      ISCANALYSIS('CALLBACK',hObject,eventData,handles,...) calls the local

%      function named CALLBACK in ISCANALYSIS.M with the given input arguments.

%

%      ISCANALYSIS('Property','Value',...) creates a new ISCANALYSIS or raises the

%      existing singleton*.  Starting from the left, property value pairs are

%      applied to the GUI before ISCanalysis_OpeningFunction gets called.  An

%      unrecognized property name or invalid value makes property application

%      stop.  All inputs are passed to ISCanalysis_OpeningFcn via varargin.

%

%      *See GUI Options on GUIDE's Tools menu.  Choose "GUI allows only one

%      instance to run (singleton)".

%

% See also: GUIDE, GUIDATA, GUIHANDLES



% Edit the above text to modify the response to help ISCanalysis



% Last Modified by GUIDE v2.5 01-Sep-2010 14:23:48



% Begin initialization code - DO NOT EDIT

gui_Singleton = 1;

gui_State = struct('gui_Name',       mfilename, ...

                   'gui_Singleton',  gui_Singleton, ...

                   'gui_OpeningFcn', @ISCanalysis_OpeningFcn, ...

                   'gui_OutputFcn',  @ISCanalysis_OutputFcn, ...

                   'gui_LayoutFcn',  [] , ...

                   'gui_Callback',   []);

if nargin && ischar(varargin{1})

    gui_State.gui_Callback = str2func(varargin{1});

end



if nargout

    [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});

else

    gui_mainfcn(gui_State, varargin{:});

end

% End initialization code - DO NOT EDIT





% --- Executes just before ISCanalysis is made visible.

function ISCanalysis_OpeningFcn(hObject, eventdata, handles, varargin)

% This function has no output args, see OutputFcn.

% hObject    handle to figure

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)

% varargin   command line arguments to ISCanalysis (see VARARGIN)



% Choose default command line output for ISCanalysis

handles.output = hObject;

set(gcf,'CloseRequestFcn','ISCclosereq');



handles = initISCanalysis(handles);





handles = setParamFields(handles,handles.Pub);



% Update handles structure

guidata(hObject, handles);



% UIWAIT makes ISCanalysis wait for user response (see UIRESUME)

uiwait(handles.figure1);





% --- Outputs from this function are returned to the command line.

function varargout = ISCanalysis_OutputFcn(hObject, eventdata, handles) 

% varargout  cell array for returning output args (see VARARGOUT);

% hObject    handle to figure

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Get default command line output from handles structure

%varargout{1} = handles.output;

if ~isempty(handles)

    varargout{1} = handles.output;

    delete(handles.figure1)

end



% --- Executes on button press in checkboxFreq.

function checkboxFreq_Callback(hObject, eventdata, handles)

% hObject    handle to checkboxFreq (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hint: get(hObject,'Value') returns toggle state of checkboxFreq



if get(hObject,'Value')

    set(handles.pushbuttonFreqSett,'Enable','on')

    set(handles.editBands,'Enable','on')

    set(handles.editTR,'Enable','on')

    set(handles.editFreqPerm,'Enable','on')

    handles.Pub.nrFreqBands = 3;

else

    set(handles.pushbuttonFreqSett,'Enable','off')    

    set(handles.editBands,'Enable','off')

    set(handles.editTR,'Enable','off')

    set(handles.editFreqPerm,'Enable','off')

    handles.Pub.nrFreqBands = 0;

end

set(handles.editBands,'String',handles.Pub.nrFreqBands)

guidata(hObject, handles);



% --- Executes on button press in checkboxTime.

function checkboxTime_Callback(hObject, eventdata, handles)

% hObject    handle to checkboxTime (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



if get(hObject,'Value')

    set(handles.editWinLen,'Enable','on')

    set(handles.editWinStep,'Enable','on')

else

    set(handles.editWinLen,'Enable','off')

    set(handles.editWinStep,'Enable','off')

end



handles.Pub.winOn = get(hObject,'Value');

guidata(hObject, handles);



% Hint: get(hObject,'Value') returns toggle state of checkboxTime



%set(hObject,'String', str2double(get(hObject,'String'))





function editWinLen_Callback(hObject, eventdata, handles)

% hObject    handle to editWinLen (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editWinLen as text

%        str2double(get(hObject,'String')) returns contents of editWinLen as a double

val = ceil(str2double(get(hObject,'String')));

if isnan(val) || val <= 0 || isinf(val)

   set(hObject,'String',num2str(handles.Pub.windowSize))

else

    handles.Pub.windowSize = val;

    set(hObject,'String',num2str(val))

end

guidata(hObject, handles);





% --- Executes during object creation, after setting all properties.

function editWinLen_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editWinLen (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end







function editWinStep_Callback(hObject, eventdata, handles)

% hObject    handle to editWinStep (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editWinStep as text

%        str2double(get(hObject,'String')) returns contents of editWinStep as a double

val = ceil(str2double(get(hObject,'String')));

if isnan(val) || val <= 0 || isinf(val)

   set(hObject,'String',num2str(handles.Pub.windowStep))

else

    handles.Pub.windowStep = val;

    set(hObject,'String',num2str(val))

end

guidata(hObject, handles);





% --- Executes during object creation, after setting all properties.

function editWinStep_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editWinStep (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end





% --- Executes on button press in checkboxCor.

function checkboxCor_Callback(hObject, eventdata, handles)

% hObject    handle to checkboxCor (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hint: get(hObject,'Value') returns toggle state of checkboxCor

if get(hObject,'Value')

     set(handles.pushbuttonCorSett,'Enable','on')

else

    set(handles.pushbuttonCorSett,'Enable','off')     

end

handles.Pub.corOn = get(hObject,'Value');

% handles.Pub.corOn = 1;

% set(hObject,'Value',1);

% set(handles.pushbuttonCorSett,'Enable','on')

guidata(hObject, handles);



% --- Executes on button press in checkboxKen.

function checkboxKen_Callback(hObject, eventdata, handles)

% hObject    handle to checkboxKen (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hint: get(hObject,'Value') returns toggle state of checkboxKen

handles.Pub.kenOn = get(hObject,'Value');

guidata(hObject, handles);



% --- Executes on button press in checkboxMI.

function checkboxMI_Callback(hObject, eventdata, handles)

% hObject    handle to checkboxMI (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



handles.Pub.nmiOn = get(hObject,'Value');

guidata(hObject, handles);



% Hint: get(hObject,'Value') returns toggle state of checkboxMI





% --- Executes on button press in checkboxSSI.

function checkboxSSI_Callback(hObject, eventdata, handles)

% hObject    handle to checkboxSSI (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hint: get(hObject,'Value') returns toggle state of checkboxSSI

handles.Pub.ssiOn = get(hObject,'Value');

guidata(hObject, handles);



% --- Executes on button press in pushbuttonCorSett.

function pushbuttonCorSett_Callback(hObject, eventdata, handles)

% hObject    handle to pushbuttonCorSett (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



handles.Pub = corrSettings(handles.Pub);

guidata(hObject, handles);





function editTR_Callback(hObject, eventdata, handles)

% hObject    handle to editTR (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editTR as text

%        str2double(get(hObject,'String')) returns contents of editTR as a double



val = str2double(get(hObject,'String'));

if isnan(val) || val <= 0

   set(hObject,'String',num2str(1/handles.Pub.samplingFrequency))

else

    handles.Pub.handles.Pub.samplingFrequency = 1/val;

    set(hObject,'String',num2str(val))

end



guidata(hObject, handles);





% --- Executes during object creation, after setting all properties.

function editTR_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editTR (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end



function editBands_Callback(hObject, eventdata, handles)

% hObject    handle to editBands (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editBands as text

%        str2double(get(hObject,'String')) returns contents of editBands as a double

val = ceil(str2double(get(hObject,'String')));

if isnan(val) || val < 2 || val > 15

   set(hObject,'String',num2str(handles.Pub.nrFreqBands))

else

    handles.Pub.nrFreqBands = val;

    checkLen(handles.Pub.nrFreqBands)

    set(hObject,'String',num2str(val))

end



guidata(hObject, handles);





% --- Executes during object creation, after setting all properties.

function editBands_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editBands (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end





% --- Executes on button press in pushbuttonFreqSett.

function pushbuttonFreqSett_Callback(hObject, eventdata, handles)

% hObject    handle to pushbuttonFreqSett (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



handles.Pub = freqSettings(handles.Pub);

guidata(hObject, handles);





function editSubj_Callback(hObject, eventdata, handles)

% hObject    handle to editSubj (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editSubj as text

%        str2double(get(hObject,'String')) returns contents of editSubj as a double



handles = setSubjectBox(handles);



handles = validateParams(handles,'subj');



guidata(hObject, handles);





% --- Executes during object creation, after setting all properties.

function editSubj_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editSubj (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end







function editDestin_Callback(hObject, eventdata, handles)

% hObject    handle to editDestin (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editDestin as text

%        str2double(get(hObject,'String')) returns contents of editDestin as a double



tPath = get(hObject,'String');

handles.Pub.dataDestination  = tPath;

guidata(hObject, handles);



% --- Executes during object creation, after setting all properties.

function editDestin_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editDestin (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end







function editTemplates_Callback(hObject, eventdata, handles)

% % hObject    handle to editTemplates (see GCBO)

% % eventdata  reserved - to be defined in a future version of MATLAB

% % handles    structure with handles and user data (see GUIDATA)

% 

% % Hints: get(hObject,'String') returns contents of editTemplates as text

% %        str2double(get(hObject,'String')) returns contents of editTemplates as a double

% 

% tPath = get(hObject,'String');

% handles.Pub.atlasPath  = tPath;

% handles.Pub.maskPath  = tPath;

% handles = validateParams(handles,'template');

% guidata(hObject, handles);



% --- Executes during object creation, after setting all properties.

function editTemplates_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editTemplates (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end







function editProject_Callback(hObject, eventdata, handles)

% hObject    handle to editProject (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



tPath = get(hObject,'String');

handles.Pub.dataDescription  = tPath;

guidata(hObject, handles);



% Hints: get(hObject,'String') returns contents of editProject as text

%        str2double(get(hObject,'String')) returns contents of editProject as a double





% --- Executes during object creation, after setting all properties.

function editProject_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editProject (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end





% --- Executes on selection change in popupmenuSession.

function popupmenuSession_Callback(hObject, eventdata, handles)

% hObject    handle to popupmenuSession (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: contents = get(hObject,'String') returns popupmenuSession contents as cell array

%        contents{get(hObject,'Value')} returns selected item from popupmenuSession

val = get(hObject,'Value');

if val <= size(handles.Pub.subjectSource,1)

    for h = 1:size(handles.Pub.subjectSource,2)

        D{h} = handles.Pub.subjectSource{val,h};

    end

    set(handles.editSubj,'String',D);

else

    set(handles.editSubj,'String',{});

end

guidata(hObject, handles);



% --- Executes during object creation, after setting all properties.

function popupmenuSession_CreateFcn(hObject, eventdata, handles)

% hObject    handle to popupmenuSession (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: popupmenu controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end







function editNii_Callback(hObject, eventdata, handles)

% hObject    handle to editNii (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editNii as text

%        str2double(get(hObject,'String')) returns contents of editNii as a double





% --- Executes during object creation, after setting all properties.

function editNii_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editNii (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end



% --- Executes on button press in pushbuttonRun.

function pushbuttonRun_Callback(hObject, eventdata, handles)

% hObject    handle to pushbuttonRun (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



handles.Params.PublicParams = handles.Pub;

handles.Params.PrivateParams = handles.Priv;

handles.validFlag = true;



%handles.ParamsValid

%handles.Params

%isequal(handles.ParamsValid,handles.Params)



if ~isequal(handles.ParamsValid,handles.Params)

    disp('You must succesfully validate parameters before running the analysis!')

    return

end



if handles.validFlag

    guidata(hObject, handles);

    runAnalysis(handles.Params);

end



% --- Executes on selection change in popupmenuFormat.

function popupmenuFormat_Callback(hObject, eventdata, handles)

% hObject    handle to popupmenuFormat (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: contents = get(hObject,'String') returns popupmenuFormat contents as cell array

%        contents{get(hObject,'Value')} returns selected item from popupmenuFormat

switch get(hObject,'Value')

    case 1

        handles.Pub.fileFormatSubj = 'nii';

    case 2     

        handles.Pub.fileFormatSubj = 'mat';

    otherwise

        error('Unknown file format!')

end

guidata(hObject, handles);



% --- Executes during object creation, after setting all properties.

function popupmenuFormat_CreateFcn(hObject, eventdata, handles)

% hObject    handle to popupmenuFormat (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: popupmenu controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end





function editFreqPerm_Callback(hObject, eventdata, handles)

% hObject    handle to editFreqPerm (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editFreqPerm as text

%        str2double(get(hObject,'String')) returns contents of editFreqPerm as a double



val = ceil(str2double(get(hObject,'String')));

if isnan(val) || val <= 0 || isinf(val)

   set(hObject,'String',num2str(handles.Pub.nrPermutationsZPF))

else

    handles.Pub.nrPermutationsZPF = val;

    set(hObject,'String',num2str(val))

end

guidata(hObject, handles);







% --- Executes during object creation, after setting all properties.

function editFreqPerm_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editFreqPerm (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end









% --------------------------------------------------------------------

function menuFile_Callback(hObject, eventdata, handles)

% hObject    handle to menuFile (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)





% --------------------------------------------------------------------

function menuOpen_Callback(hObject, eventdata, handles)

% hObject    handle to menuOpen (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)

[FileName,PathName] = uigetfile('*.mat','Open Parameter File');

if FileName ~= 0

    try 

        load(fullfile(PathName,FileName))

        handles.Pub = Params.PublicParams;

        handles.Priv = Params.PrivateParams;

        handles = setParamFields(handles,handles.Pub);

    catch

        disp(lasterr)

       disp('Invalid parameter file.')

       return

    end

end

guidata(hObject, handles);





% --------------------------------------------------------------------

function menuSave_Callback(hObject, eventdata, handles)

% hObject    handle to menuSave (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)

[file,path] = uiputfile('*.mat','Save Parameter File');

if file ~= 0

   Params.PublicParams = handles.Pub;

   Params.PrivateParams = handles.Priv;

   save(fullfile(path,file),'Params')

end

guidata(hObject, handles);





% --------------------------------------------------------------------

function menuExit_Callback(hObject, eventdata, handles)

% hObject    handle to menuExit (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



user_response = confCloseModal('Title','Confirm Exit');

switch lower(user_response)

    case 'no'

        % take no action

    case 'yes'

        handles.output = handles;

        guidata(hObject, handles)

        uiresume(handles.figure1)

        %        delete(handles.figure1)

end





% --- Executes on button press in pushbuttonValid.

function pushbuttonValid_Callback(hObject, eventdata, handles)

% hObject    handle to pushbuttonValid (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



Params.PublicParams = handles.Pub;

Params.PrivateParams = handles.Priv;



if isfield(handles,'ParamsValid')

    if isequal(handles.ParamsValid,Params)

        disp(' ')

        disp('Parameters already succesfully validated!')

        return

    end

end



handles = validateDataAndParams(handles);



if handles.validFlag

    guidata(hObject, handles);

end



% --- Executes on button press in checkboxTemplate.

function checkboxTemplate_Callback(hObject, eventdata, handles)

% hObject    handle to checkboxTemplate (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



if get(hObject,'Value')

    set(handles.radiobuttonTemplateMNI,'Value',1,'Enable','on')

    handles.Pub.useTemplate = 1;

    set(handles.editMask,'Enable','on','String',handles.Pub.atlasPath)

%    set(handles.editMask,'Enable','off','String','standard')

    set(handles.textMask,'Enable','on','String','Directory of standard templates','HorizontalAlignment','Left')

else

    set(handles.radiobuttonTemplateMNI,'Value',0,'Enable','off')    

    handles.Pub.useTemplate = 0;    

    set(handles.editMask,'Enable','on','String',handles.Pub.atlasPath,'HorizontalAlignment','Left')

    set(handles.textMask,'Enable','on','String','Binary mask file name (extension .nii or .mat)')

end

guidata(hObject, handles);



% --- Executes on button press in radiobuttonTemplateMNI.

function radiobuttonTemplateMNI_Callback(hObject, eventdata, handles)

% hObject    handle to radiobuttonTemplateMNI (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



set(hObject,'Value',1)



% --- Executes on button press in checkboxPhase.

function checkboxPhase_Callback(hObject, eventdata, handles)

% hObject    handle to checkboxPhase (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hint: get(hObject,'Value') returns toggle state of checkboxPhase



handles.Pub.calcPhase = get(hObject,'Value');

guidata(hObject, handles);





function editMask_Callback(hObject, eventdata, handles)

% hObject    handle to editMask (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    structure with handles and user data (see GUIDATA)



% Hints: get(hObject,'String') returns contents of editMask as text

%        str2double(get(hObject,'String')) returns contents of editMask as a double

handles.Pub.atlasPath = get(hObject,'String');

guidata(hObject, handles);



% --- Executes during object creation, after setting all properties.

function editMask_CreateFcn(hObject, eventdata, handles)

% hObject    handle to editMask (see GCBO)

% eventdata  reserved - to be defined in a future version of MATLAB

% handles    empty - handles not created until after all CreateFcns called



% Hint: edit controls usually have a white background on Windows.

%       See ISPC and COMPUTER.

if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))

    set(hObject,'BackgroundColor','white');

end