https://github.com/Chaogan-Yan/REST
Tip revision: 5f9de23b90b10fd5eca9e9bc1016bbde75d43ab6 authored by Chaogan-Yan on 16 June 2013, 16:06:36 UTC
Fixed a bug in temporal correlation of two groups of images in Image Calculator;The midline of VMHC results were set to zero.
Fixed a bug in temporal correlation of two groups of images in Image Calculator;The midline of VMHC results were set to zero.
Tip revision: 5f9de23
rest_gca_gui.m
function varargout = rest_gca_gui(varargin)
%Granger Causality Analysis GUI by Zang Zhen-Xiang
%-----------------------------------------------------------
% Copyright(c) 2007~2010
% State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University
% Written by Zang Zhen-Xiang
% http://www.restfmri.net
% $mail =zangzx@gmail.com
% $Version = 1.1
% $Date =20100401
%-----------------------------------------------------------
% <a href="zangzx416@gmail.com">Mail to Author</a>: Zang Zhen-Xiang
% Version=1.2;
% Release=20110226;
% Modified by GUIDE v2.5 02-Oct-2007 10:20:30
% Revised by YAN Chao-Gan 080808, in order to process multiple subjects with different covaribles in batch mode.
% Revised by YAN Chao-Gan 080903, in order to fix the bug that with no Covariables.
% Revised by YAN Chao-Gan 091104, in order to process multiple subjects with different seed time courses (.txt) in batch mode.
% Revised by YAN Chao-Gan 100130, fixed the bug in ROI-wise GCA calculation.
% Revised by YAN Chao-Gan, 101025. Will not remove linear trend in regressing out covariables step.
% Revised by ZANG Zhen-Xiang, 110504. Provides a method that could transform the residual-based F into normally distributed Z score.
% Revised by DONG Zhang-Ye and YAN Chao-Gan, 110505. Fix the GUI bug and set the default value for the Z-transformation.
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @rest_gca_gui_OpeningFcn, ...
'gui_OutputFcn', @rest_gca_gui_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 rest_gca_gui is made visible.
function rest_gca_gui_OpeningFcn(hObject, eventdata, handles, varargin)
set(handles.figGCAMain , 'Visible' , 'on');
%Matlab -Linux compatible, Initialize controls' default properties, dawnsong , 20070507
InitControlProperties(hObject, handles);
%Matlab -v6 compatible, create some frames instead of panels
InitFrames(hObject,handles);
[pathstr, name, ext] = fileparts(mfilename('fullpath'));
%the {hdr/img} directories to be processed , count of volumns(i.e. time series' point number) corresponding to the dir
handles.Cfg.DataDirs ={}; %{[pathstr '\SampleData'], 10} ;
handles.Cfg.Covariates ={};
handles.Cfg.MaskFile = 'Default'; %the user defined mask file
handles.Cfg.OutputDir =pwd; % pwd is the default dir for functional connectivity map result
handles.Cfg.ROIList =''; % ROI Definition file, a common mask, 20070830
%Covariables definition
handles.Covariables.ort_file ='';
handles.Covariables.polort =0; % YAN Chao-Gan, 101025. Will not remove linear trend in regressing out covariables step. %handles.Covariables.polort =1;
handles.Filter.BandLow =0.01; %Config about Band pass filter, dawnsong 20070429
handles.Filter.BandHigh =0.08;
handles.Filter.UseFilter ='No';
handles.Filter.Retrend ='Yes';
handles.Cfg.WantZtransformation ='Yes';
handles.Filter.SamplePeriod=2; %by default, set TR=2s
handles.Detrend.BeforeFilter ='No';% ZangYF, 20070530 decide
handles.Detrend.AfterFilter ='No';% ZangYF, 20070530 decide
handles.Log.SelfPath =pathstr; % 20070507, dawnsong, just for writing log to file for further investigation
handles.Log.Filename =GetLogFilename('','');
%Performance record, use elapsed time to describe it, 20070507
handles.Performance =0;
guidata(hObject, handles);
UpdateDisplay(handles);
movegui(handles.figGCAMain, 'center');
set(handles.figGCAMain,'Name','Granger Causality Analysis');
% Make Display correct in linux - YAN Chao-Gan 111025 Added.
if ~ispc
ZoomFactor=0.85;
ObjectNames = fieldnames(handles);
for i=1:length(ObjectNames);
eval(['IsFontSizeProp=isprop(handles.',ObjectNames{i},',''FontSize'');']);
if IsFontSizeProp
eval(['PCFontSize=get(handles.',ObjectNames{i},',''FontSize'');']);
FontSize=PCFontSize*ZoomFactor;
eval(['set(handles.',ObjectNames{i},',''FontSize'',',num2str(FontSize),');']);
end
end
end
% Choose default command line output for rest_gca_gui
handles.output = hObject;
guidata(hObject, handles);% Update handles structure
% UIWAIT makes fc_gui wait for user response (see UIRESUME)
% uiwait(handles.figGCAMain);
% --- Outputs from this function are returned to the command line.
function varargout = rest_gca_gui_OutputFcn(hObject, eventdata, handles)
% Get default command line output from handles structure
varargout{1} = handles.output;
function edtDataDirectory_Callback(hObject, eventdata, handles)
theDir =get(hObject, 'String');
SetDataDir(hObject, theDir,handles);
function edtDataDirectory_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function btnSelectDataDir_Callback(hObject, eventdata, handles)
if size(handles.Cfg.DataDirs, 1)>0
theDir =handles.Cfg.DataDirs{1,1};
else
theDir =pwd;
end
theDir =uigetdir(theDir, 'Please select the data directory to compute GCA map: ');
if ischar(theDir),
SetDataDir(hObject, theDir,handles);
end
function RecursiveAddDataDir(hObject, eventdata, handles)
if prod(size(handles.Cfg.DataDirs))>0 && size(handles.Cfg.DataDirs, 1)>0,
theDir =handles.Cfg.DataDirs{1,1};
else
theDir =pwd;
end
theDir =uigetdir(theDir, 'Please select the parent data directory of many sub-folders containing EPI data to compute GCA map: ');
if ischar(theDir),
%Make the warning dlg off! 20071201
setappdata(0, 'FC_DoingRecursiveDir', 1);
theOldColor =get(handles.listDataDirs, 'BackgroundColor');
set(handles.listDataDirs, 'BackgroundColor', [ 0.7373 0.9804 0.4784]);
try
rest_RecursiveDir(theDir, 'rest_gca_gui(''SetDataDir'',gcbo, ''%s'', guidata(gcbo) )');
catch
rest_misc( 'DisplayLastException');
end
set(handles.listDataDirs, 'BackgroundColor', theOldColor);
rmappdata(0, 'FC_DoingRecursiveDir');
end
function RecursiveAddCovariates(hObject, eventdata, handles)
if prod(size(handles.Cfg.Covariates))>0 && size(handles.Cfg.Covariates, 1)>0,
theDir =handles.Cfg.Covariates{1,1};
else
theDir =pwd;
end
theDir =uigetdir(theDir, 'Please select the directory of covariates to compute GCA map: ');
if ischar(theDir),
%Make the warning dlg off! 20071201
setappdata(0, 'FC_DoingRecursiveDir', 1);
theOldColor =get(handles.listCovariates, 'BackgroundColor');
set(handles.listDCovariates, 'BackgroundColor', [ 0.7373 0.9804 0.4784]);
try
rest_RecursiveDir(theDir, 'rest_gca_gui(''SetDataDir'',gcbo, ''%s'', guidata(gcbo) )');
catch
rest_misc( 'DisplayLastException');
end
set(handles.listDataDirs, 'BackgroundColor', theOldColor);
rmappdata(0, 'FC_DoingRecursiveDir');
end
function SetDataDir(hObject, ADir,handles)
if ~ischar(ADir), return; end
theOldWarnings =warning('off', 'all');
% if (~isequal(ADir , 0)) &&( (size(handles.Cfg.DataDirs, 1)==0)||(0==seqmatch({ADir} ,handles.Cfg.DataDirs( : , 1) ) ) )
if rest_misc('GetMatlabVersion')>=7.3,
ADir =strtrim(ADir);
end
if (~isequal(ADir , 0)) &&( (size(handles.Cfg.DataDirs, 1)==0)||(0==length(strmatch(ADir,handles.Cfg.DataDirs( : , 1),'exact' ) ) ))
handles.Cfg.DataDirs =[ {ADir , 0}; handles.Cfg.DataDirs];%update the dir
theVolumnCount =rest_CheckDataDir(handles.Cfg.DataDirs{1,1} );
if (theVolumnCount<=0),
if isappdata(0, 'FC_DoingRecursiveDir') && getappdata(0, 'FC_DoingRecursiveDir'),
else
fprintf('There is no data or non-data files in this directory:\n%s\nPlease re-select\n\n', ADir);
errordlg( sprintf('There is no data or non-data files in this directory:\n\n%s\n\nPlease re-select', handles.Cfg.DataDirs{1,1} ));
end
handles.Cfg.DataDirs(1,:)=[];
if size(handles.Cfg.DataDirs, 1)==0
handles.Cfg.DataDirs=[];
end %handles.Cfg.DataDirs = handles.Cfg.DataDirs( 2:end, :);%update the dir
else
handles.Cfg.DataDirs{1,2} =theVolumnCount;
end
guidata(hObject, handles);
UpdateDisplay(handles);
end
warning(theOldWarnings);
%% Update All the uiControls' display on the GUI
function UpdateDisplay(handles)
if size(handles.Cfg.DataDirs,1)>0
theOldIndex =get(handles.listDataDirs, 'Value');
%set(handles.listDataDirs, 'String', handles.Cfg.DataDirs(: ,1) , 'Value', 1);
set(handles.listDataDirs, 'String', GetInputDirDisplayList(handles) , 'Value', 1);
theCount =size(handles.Cfg.DataDirs,1);
if (theOldIndex>0) && (theOldIndex<= theCount)
set(handles.listDataDirs, 'Value', theOldIndex);
end
set(handles.edtDataDirectory,'String', handles.Cfg.DataDirs{1,1});
theResultFilename=get(handles.edtPrefix, 'String');
theResultFilename=[theResultFilename '_' GetDirName(handles.Cfg.DataDirs{1,1})];
%%set(handles.txtResultFilename, 'String', [theResultFilename '.{hdr/img}']);
else
set(handles.listDataDirs, 'String', '' , 'Value', 0);
%set(handles.txtResultFilename, 'String', 'Result: Prefix_DirectoryName.{hdr/img}');
end
% set(handles.pnlParametersInput,'Title', ... %show the first dir's Volumn count in the panel's title
% ['Input Parameters (Volumn count= '...
% num2str( cell2mat(handles.Cfg.DataDirs(1,2)) )...
% ' in 'handles.Cfg.DataDirs(1,1) ' )']);
set(handles.edtOutputDir ,'String', handles.Cfg.OutputDir);
if isequal(handles.Cfg.MaskFile, '')
set(handles.edtMaskfile, 'String', 'Don''t use any Mask');
else
set(handles.edtMaskfile, 'String', handles.Cfg.MaskFile);
end
%Set detrend dawnsong 20070820
if strcmpi(handles.Detrend.BeforeFilter, 'Yes')
%Update filter and detrend button's state according to Option: detrend/Filter 20070820
set(handles.btnDetrend, 'Enable', 'on');
else
%Update filter and detrend button's state according to Option: detrend/Filter 20070820
set(handles.btnDetrend, 'Enable', 'off');
end
%Set filter, dawnsong 20070430
if strcmpi(handles.Filter.UseFilter, 'Yes')
set(handles.ckboxFilter, 'Value', 1);
set(handles.ckboxRetrend, 'Enable', 'on');
set(handles.edtBandLow, 'Enable', 'on', 'String', num2str(handles.Filter.BandLow));
set(handles.edtBandHigh, 'Enable', 'on', 'String', num2str(handles.Filter.BandHigh));
set(handles.edtSamplePeriod, 'Enable', 'on', 'String', num2str(handles.Filter.SamplePeriod));
%Update filter and detrend button's state according to Option: detrend/Filter 20070820
set(handles.btnBandPass, 'Enable', 'on');
else
set(handles.ckboxFilter, 'Value', 0);
set(handles.ckboxRetrend,'Enable', 'off');
set(handles.edtBandLow, 'Enable', 'off', 'String', num2str(handles.Filter.BandLow));
set(handles.edtBandHigh, 'Enable', 'off', 'String', num2str(handles.Filter.BandHigh));
set(handles.edtSamplePeriod, 'Enable', 'off', 'String', num2str(handles.Filter.SamplePeriod));
%Update filter and detrend button's state according to Option: detrend/Filter 20070820
set(handles.btnBandPass, 'Enable', 'off');
end
% Set detrend option
set(handles.ckboxRemoveTrendBefore, 'Value', strcmpi(handles.Detrend.BeforeFilter, 'Yes'));
set(handles.ckboxRemoveTrendAfter, 'Value', strcmpi(handles.Detrend.AfterFilter, 'Yes'));
% Set Z-score transformation option
set(handles.ckboxWantZtransformation, 'Value', strcmpi(handles.Cfg.WantZtransformation, 'Yes'));
%Indicate which ROI type user has selected
if isempty(handles.Cfg.ROIList) || prod(size(handles.Cfg.ROIList)) ==0,
%User has not selected any ROI
set(handles.btnROIVoxelWise, 'ForegroundColor', 'red', 'FontWeight', 'normal');
set(handles.btnROIRegionWise, 'ForegroundColor', 'red', 'FontWeight', 'normal');
else
% [pathstr, name, ext] = fileparts(handles.Cfg.ROIFile);
% if strcmpi(ext, 'rest_roi'),
if ~iscell(handles.Cfg.ROIList) || 0 ...
% ( size(handles.Cfg.ROIList,1)==1 && ~isspace(handles.Cfg.ROIList) ),
%Single Region for Voxel Wise type ROI
set(handles.btnROIVoxelWise, 'ForegroundColor', 'red', 'FontWeight', 'bold');
set(handles.btnROIRegionWise, 'ForegroundColor', 'red', 'FontWeight', 'normal');
elseif size(handles.Cfg.ROIList,1)>=1,
%Region Wise type ROI series
set(handles.btnROIVoxelWise, 'ForegroundColor', 'red', 'FontWeight', 'normal');
set(handles.btnROIRegionWise, 'ForegroundColor', 'red', 'FontWeight', 'bold');
end
end
%Set covariables's definition
set(handles.edtCovariableFile, 'String', handles.Covariables.ort_file);
%% check the Data dir to make sure that there are only {hdr,img}
function Result=GetInputDirDisplayList(handles)
Result ={};
for x=size(handles.Cfg.DataDirs, 1):-1:1
Result =[{sprintf('%d# %s',handles.Cfg.DataDirs{x, 2},handles.Cfg.DataDirs{x, 1})} ;Result];
end
function Result=GetInputCovariatesDisplayList(handles)
Result ={};
for x=size(handles.Cfg.Covariates, 1):-1:1
Result =[{sprintf('%d# %s',handles.Cfg.Covariates{x, 2},handles.Cfg.Covariates{x, 1})} ;Result];
end
% in this dir
function [nVolumn]=CheckDataDir(ADataDir)
theFilenames = dir(ADataDir);
theHdrFiles=dir(fullfile(ADataDir,'*.hdr'));
theImgFiles=dir(fullfile(ADataDir,'*.img'));
% if (length(theFilenames)-length(theHdrFiles)-length(theImgFiles))>2
% nVolumn =-1;
% errordlg(sprintf(['There should not be any file other than *.{hdr,img} .' ...
% 'Please re-examin the DataDir\n\n%s '] ...
% , ADataDir));
% return;
% end
if ~length(theHdrFiles)==length(theImgFiles)
nVolumn =-1;
fprintf('%s, *.{hdr,img} should be pairwise. Please re-examin them.\n', ADataDir);
errordlg('*.{hdr,img} should be pairwise. Please re-examin them.');
return;
end
count = 3; nVolumn = 0;
for count = 3:size(struct2cell(theFilenames),2)
if (length(theFilenames(count).name)>4) && ...
strcmpi(theFilenames(count).name(end-3:end) , '.hdr')
if strcmpi(theFilenames(count).name(1:end-4) ... %hdr
, theFilenames(count+1).name(1:end-4) ) %img
nVolumn = nVolumn + 1;
else
%error('*.{hdr,img} should be pairwise. Please re-examin them.');
nVolumn =-1;
fprintf('%s, *.{hdr,img} should be pairwise. Please re-examin them.\n', ADataDir);
errordlg('*.{hdr,img} should be pairwise. Please re-examin them.');
break;
end
end
end
function edtMaskfile_Callback(hObject, eventdata, handles)
theMaskfile =get(hObject, 'String');
if rest_misc('GetMatlabVersion')>=7.3,
theMaskfile =strtrim(theMaskfile);
end
if exist(theMaskfile, 'file')
handles.Cfg.MaskFile =theMaskfile;
guidata(hObject, handles);
else
errordlg(sprintf('The mask file "%s" does not exist!\n Please re-check it.', theMaskfile));
end
function edtMaskfile_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function btnSelectMask_Callback(hObject, eventdata, handles)
[filename, pathname] = uigetfile({'*.img;*.nii;*.nii.gz','Brain Image Files (*.img;*.nii;*.nii.gz)';'*.*', 'All Files (*.*)';}, ...
'Pick a user''s mask');
if ~(filename==0)
handles.Cfg.MaskFile =[pathname filename];
guidata(hObject,handles);
elseif ~( exist(handles.Cfg.MaskFile, 'file')==2)
set(handles.rbtnDefaultMask, 'Value',[1]);
set(handles.rbtnUserMask, 'Value',[0]);
set(handles.edtMaskfile, 'Enable','off');
set(handles.btnSelectMask, 'Enable','off');
handles.Cfg.MaskFile ='Default';
guidata(hObject, handles);
end
UpdateDisplay(handles);
function rbtnDefaultMask_Callback(hObject, eventdata, handles)
set(handles.edtMaskfile, 'Enable','off', 'String','Use Default Mask');
set(handles.btnSelectMask, 'Enable','off');
drawnow;
handles.Cfg.MaskFile ='Default';
guidata(hObject, handles);
set(handles.rbtnDefaultMask,'Value',1);
set(handles.rbtnNullMask,'Value',0);
set(handles.rbtnUserMask,'Value',0);
function rbtnUserMask_Callback(hObject, eventdata, handles)
set(handles.edtMaskfile,'Enable','on', 'String',handles.Cfg.MaskFile);
set(handles.btnSelectMask, 'Enable','on');
set(handles.rbtnDefaultMask,'Value',0);
set(handles.rbtnNullMask,'Value',0);
set(handles.rbtnUserMask,'Value',1);
drawnow;
function rbtnNullMask_Callback(hObject, eventdata, handles)
set(handles.edtMaskfile, 'Enable','off', 'String','Don''t use any Mask');
set(handles.btnSelectMask, 'Enable','off');
drawnow;
handles.Cfg.MaskFile ='';
guidata(hObject, handles);
set(handles.rbtnDefaultMask,'Value',0);
set(handles.rbtnNullMask,'Value',1);
set(handles.rbtnUserMask,'Value',0);
function listDataDirs_Callback(hObject, eventdata, handles)
theIndex =get(hObject, 'Value');
if isempty(theIndex) || theIndex<1,
msgbox(sprintf('Nothing added.\n\nYou must add some diretories containing only paired {hdr/img} files first'), ...
'REST' ,'help');
return;
end
if strcmp(get(handles.figGCAMain, 'SelectionType'), 'open') %when double click
msgbox(sprintf('%s \t\nhas\t %d\t volumes\n\nTotal: %d Data Directories' , ...
handles.Cfg.DataDirs{theIndex, 1} , ...
handles.Cfg.DataDirs{theIndex, 2} , ...
size(handles.Cfg.DataDirs,1)), ...
'Volume count in selected dir' ,'help');
end
function listDataDirs_KeyPressFcn(hObject, eventdata, handles)
%Delete the selected item when 'Del' is pressed
key =get(handles.figGCAMain, 'currentkey');
if seqmatch({key},{'delete', 'backspace'})
DeleteSelectedDataDir(hObject, eventdata,handles);
end
function DeleteSelectedDataDir(hObject, eventdata, handles)
theIndex =get(handles.listDataDirs, 'Value');
if prod(size(handles.Cfg.DataDirs))==0 ...
|| size(handles.Cfg.DataDirs, 1)==0 ...
|| theIndex>size(handles.Cfg.DataDirs, 1),
return;
end
theDir =handles.Cfg.DataDirs{theIndex, 1};
theVolumnCount=handles.Cfg.DataDirs{theIndex, 2};
tmpMsg=sprintf('Delete\n\n "%s" \nVolumn Count :%d ?', theDir, theVolumnCount);
if strcmp(questdlg(tmpMsg, 'Delete confirmation'), 'Yes')
if theIndex>1,
set(handles.listDataDirs, 'Value', theIndex-1);
end
handles.Cfg.DataDirs(theIndex, :)=[];
if size(handles.Cfg.DataDirs, 1)==0
handles.Cfg.DataDirs={};
end
guidata(hObject, handles);
UpdateDisplay(handles);
end
function ClearDataDirectories(hObject, eventdata, handles)
if prod(size(handles.Cfg.DataDirs))==0 ...
|| size(handles.Cfg.DataDirs, 1)==0,
return;
end
tmpMsg=sprintf('Attention!\n\n\nDelete all data directories?');
if strcmpi(questdlg(tmpMsg, 'Clear confirmation'), 'Yes'),
handles.Cfg.DataDirs(:)=[];
if prod(size(handles.Cfg.DataDirs))==0,
handles.Cfg.DataDirs={};
end
guidata(hObject, handles);
UpdateDisplay(handles);
end
function listDataDirs_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edtPrefix_Callback(hObject, eventdata, handles)
%nothing need to do, because I get the prefix when I need. Look at line 229 "thePrefix =get(handles.edtPrefix, 'String');"
function edtPrefix_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edtOutputDir_Callback(hObject, eventdata, handles)
theDir =get(hObject, 'String');
SetOutputDir(hObject,handles, theDir);
function edtOutputDir_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function btnSelectOutputDir_Callback(hObject, eventdata, handles)
theDir =handles.Cfg.OutputDir;
theDir =uigetdir(theDir, 'Please select the data directory to save GCA map: ');
if ~isequal(theDir, 0)
SetOutputDir(hObject,handles, theDir);
end
function SetOutputDir(hObject, handles, ADir)
if 7==exist(ADir,'dir')
handles.Cfg.OutputDir =ADir;
guidata(hObject, handles);
UpdateDisplay(handles);
end
function Result=GetDirName(ADir)
if isempty(ADir), Result=ADir; return; end
theDir =ADir;
if strcmp(theDir(end),filesep)==1
theDir=theDir(1:end-1);
end
[tmp,Result]=fileparts(theDir);
function ckboxFilter_Callback(hObject, eventdata, handles)
if get(hObject,'Value')
handles.Filter.UseFilter ='Yes';
else
handles.Filter.UseFilter ='No';
end
guidata(hObject, handles);
UpdateDisplay(handles);
function edtBandLow_Callback(hObject, eventdata, handles)
handles.Filter.BandLow =str2double(get(hObject,'String'));
guidata(hObject, handles);
function edtBandLow_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edtBandHigh_Callback(hObject, eventdata, handles)
handles.Filter.BandHigh =str2double(get(hObject,'String'));
guidata(hObject, handles);
function edtBandHigh_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function ckboxRetrend_Callback(hObject, eventdata, handles)
if get(hObject,'Value')
handles.Filter.Retrend ='Yes';
else
handles.Filter.Retrend ='No';
end
guidata(hObject, handles);
UpdateDisplay(handles);
function edtSamplePeriod_Callback(hObject, eventdata, handles)
handles.Filter.SamplePeriod =str2double(get(hObject,'String'));
guidata(hObject, handles);
function edtSamplePeriod_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function btnBandPass_Callback(hObject, eventdata, handles)
theOldColor=get(hObject,'BackgroundColor');
set(hObject,'Enable','off', 'BackgroundColor', 'red');
drawnow;
try
%Band pass filter
if strcmpi(handles.Filter.UseFilter, 'Yes')
BandPass(hObject, handles);
msgbox('Ideal Band Pass filter Over.',...
'Filter successfully' ,'help');
else
errordlg(sprintf('You didn''t select option "Band Pass". \n\nPlease slect first.'));
end
UpdateDisplay(handles);
catch
rest_misc( 'DisplayLastException');
end
rest_waitbar;
set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
drawnow;
function InitControlProperties(hObject, handles)
%for Linux compatible 20070507 dawnsong
% --- FIGURE -------------------------------------
set(handles.figGCAMain,...
'Units', 'pixels', ...
'Position', [20 5 440 645], ...
'Name', 'fc_gui', ...
'MenuBar', 'none', ...
'NumberTitle', 'off', ...
'Color', get(0,'DefaultUicontrolBackgroundColor'));
%20071103, Add context menu to Input Data Directories to add��delete��export��import����
handles.hContextMenuDataDirs =uicontextmenu;
%Add DataDirs
set(handles.listDataDirs, 'UIContextMenu', handles.hContextMenuDataDirs);
uimenu(handles.hContextMenuDataDirs, 'Label', 'Add a directory', 'Callback', get(handles.btnSelectDataDir, 'Callback'));
uimenu(handles.hContextMenuDataDirs, 'Label', 'Remove the selected directory', 'Callback', 'rest_gca_gui(''DeleteSelectedDataDir'',gcbo,[], guidata(gcbo))');
uimenu(handles.hContextMenuDataDirs, 'Label', 'Add recursively all sub-folders of a directory', 'Callback', 'rest_gca_gui(''RecursiveAddDataDir'',gcbo,[], guidata(gcbo))');
uimenu(handles.hContextMenuDataDirs, 'Label', '=============================');
uimenu(handles.hContextMenuDataDirs, 'Label', 'Remove all data directories', 'Callback', 'rest_gca_gui(''ClearDataDirectories'',gcbo,[], guidata(gcbo))');
%Add Covariates
guidata(hObject,handles);
%% Log options to a log file for further investigation, 20070507 before Computing
function Log2File(handles)
constLineSep= '-------------------------------------------------------------------------------';
[theVer, theRelease] =rest_misc( 'GetRestVersion');
theMsgVersion = sprintf('REST Version:%s, Release %s\r\n%s\r\n', theVer, theRelease, constLineSep);
theMsgHead = sprintf('GCA computation log %s\r\n%s\r\n', rest_misc( 'GetDateTimeStr'), constLineSep);
theMsg =sprintf('%s\r\n%s\r\n\r\n%s', theMsgVersion, theMsgHead, constLineSep);
theMsg =sprintf('%s\r\nRemove Linear Trend options:\r\n%s\r\n\r\n%s',theMsg,...
LogRemoveLinearTrend(handles), constLineSep);
theMsg =sprintf('%s\r\nIdeal Band Pass filter options:\r\n%s\r\n\r\n%s',theMsg,...
LogBandPassFilter(handles), constLineSep);
theMsg =sprintf('%s\r\nGCA input parameters:\r\n%s\r\n\r\n%s', theMsg, ...
LogInputParameters(handles), constLineSep);
theMsg =sprintf('%s\r\nGCA output parameters:\r\n%s\r\n\r\n%s', theMsg, ...
LogOutputParameters(handles), constLineSep);
fid = fopen(handles.Log.Filename,'w');
if fid~=-1
fprintf(fid,'%s',theMsg);
fclose(fid);
else
errordlg(sprintf('Error to open log file:\n\n%s', handles.Log.Filename));
end
%Log the total elapsed time by once "Do all"
function LogPerformance(handles)
theMsg =sprintf('\r\n\r\nTotal elapsed time for GCA Computing: %g seconds\r\n',handles.Performance);
fid = fopen(handles.Log.Filename,'r+');
fseek(fid, 0, 'eof');
if fid~=-1
fprintf(fid,'%s',theMsg);
fclose(fid);
else
errordlg(sprintf('Error to open log file:\n\n%s', handles.Log.Filename));
end
function ResultLogString=LogRemoveLinearTrend(handles)
ResultLogString ='';
ResultLogString =sprintf('%s\tremove linear trend BEFORE filter: %s\r\n',ResultLogString, handles.Detrend.BeforeFilter);
%ResultLogString =sprintf('%s\tremove linear trend AFTER filter: %s\r\n',ResultLogString, handles.Detrend.AfterFilter);
function ResultLogString=LogBandPassFilter(handles)
ResultLogString ='';
ResultLogString =sprintf('%s\tUse Filter: %s\r\n',ResultLogString, handles.Filter.UseFilter);
ResultLogString =sprintf('%s\tBand Low: %g\r\n', ResultLogString, handles.Filter.BandLow);
ResultLogString =sprintf('%s\tBand High: %g\r\n',ResultLogString, handles.Filter.BandHigh);
ResultLogString =sprintf('%s\tSample Period(i.e. TR): %g\r\n',ResultLogString, handles.Filter.SamplePeriod);
function ResultLogString=LogInputParameters(handles)
ResultLogString ='';
constLineSep= '-------------------------------------------------------------------------------';
theDataDirString= '';
theDataDirCells =get(handles.listDataDirs, 'string');
for x=1:length(theDataDirCells)
theDataDirString =sprintf('%s\r\n\t%s', theDataDirString, theDataDirCells{x});
end
theDirType ='';
if strcmpi(handles.Detrend.BeforeFilter, 'Yes')
theDirType =sprintf(' %s after Detrend processing', theDirType);
end
if strcmpi(handles.Detrend.BeforeFilter, 'Yes') && ...
strcmpi(handles.Filter.UseFilter, 'Yes'),
theDirType =sprintf(' %s and ', theDirType);
end
if strcmpi(handles.Filter.UseFilter, 'Yes')
theDirType =sprintf(' %s after Filter processing', theDirType);
end
ResultLogString =sprintf('%s\tInput Data Directories( %s): \r\n\t%s%s\r\n\t%s\r\n',ResultLogString,...
theDirType, ...
constLineSep, ...
theDataDirString, ...
constLineSep);
ResultLogString =sprintf('%s\tMask file: %s\r\n', ResultLogString, handles.Cfg.MaskFile);
%Functional Connectivity
ResultLogString =sprintf('%s\n\n\tGCA Parameters\r\n', ResultLogString);
%ROI Definition log
if iscell(handles.Cfg.ROIList),
for x=1:size(handles.Cfg.ROIList, 1),
ResultLogString =sprintf('%s\tROI Definition: \n\t\t%s\r\n', ResultLogString, handles.Cfg.ROIList{x});
end
else
ResultLogString =sprintf('%s\tROI Definition: \n\t\t%s\r\n', ResultLogString, handles.Cfg.ROIList);
end
%Covariable log
ResultLogString =sprintf('%s\tCovariables Definition File: \n\t\t%s\r\n', ResultLogString, handles.Covariables.ort_file);
ResultLogString =sprintf('%s\tCovariables Polort (Polynomial Orthogonal Degree): \n\t\t%d\r\n', ResultLogString, handles.Covariables.polort);
function ResultLogString=LogOutputParameters(handles)
ResultLogString ='';
ResultLogString =sprintf('%s\tPrefix to the Data directories: %s\r\n',ResultLogString, get(handles.edtPrefix, 'String'));
ResultLogString =sprintf('%s\tOutput Data Directories: %s\r\n',ResultLogString, handles.Cfg.OutputDir);
%compose the log filename
function ResultLogFileName=GetLogFilename(ALogDirectory, APrefix)
if isempty(ALogDirectory)
[pathstr, name, ext] = fileparts(mfilename('fullpath'));
ALogDirectory =pathstr;
end
if ~strcmp(ALogDirectory(end), filesep)
ALogDirectory =[ALogDirectory filesep];
end
ResultLogFileName=sprintf('%s%s_%s.log', ...
ALogDirectory, ...
APrefix, ...
rest_misc( 'GetDateTimeStr'));
function btnSliceViewer_Callback(hObject, eventdata, handles)
%Display a brain image like MRIcro
theOldColor=get(hObject,'BackgroundColor');
set(hObject,'Enable','off', 'BackgroundColor', 'red');
drawnow;
try
rest_sliceviewer;
% [filename, pathname] = uigetfile({'*.img', 'ANALYZE or NIFTI files (*.img)'}, ...
% 'Pick one brain map');
% if any(filename~=0) && ischar(filename) && length(filename)>4 , % not canceled and legal
% if ~strcmpi(pathname(end), filesep)%revise pathname to remove extension
% pathname = [pathname filesep];
% end
% theBrainMap =[pathname filename];
% rest_sliceviewer('ShowImage', theBrainMap);
% end
catch
rest_misc( 'DisplayLastException');
end
set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
drawnow;
function ckboxRemoveTrendBefore_Callback(hObject, eventdata, handles)
if get(hObject,'Value')
handles.Detrend.BeforeFilter ='Yes';
else
handles.Detrend.BeforeFilter ='No';
end
guidata(hObject, handles);
UpdateDisplay(handles);
function ckboxRemoveTrendAfter_Callback(hObject, eventdata, handles)
if get(hObject,'Value')
handles.Detrend.AfterFilter ='Yes';
else
handles.Detrend.AfterFilter ='No';
end
guidata(hObject, handles);
UpdateDisplay(handles);
function btnDetrend_Callback(hObject, eventdata, handles)
try
Detrend(hObject,handles);
msgbox('Remove the Linear Trend Over.',...
'Detrend successfully' ,'help');
catch
rest_misc( 'DisplayLastException');
end
rest_waitbar;
function Detrend(hObject,handles)
for x=1:size(handles.Cfg.DataDirs, 1)
%Update display
set(handles.listDataDirs, 'Value', x);
drawnow;
if size(handles.Cfg.DataDirs, 1)>1,
rest_waitbar((x-1)/size(handles.Cfg.DataDirs, 1)+0.01, ...
handles.Cfg.DataDirs{x, 1}, ...
'Removing the Linear Trend','Parent');
end
rest_detrend(handles.Cfg.DataDirs{x, 1}, '_detrend');
%Revise the data directories
handles.Cfg.DataDirs{x, 1}=[handles.Cfg.DataDirs{x, 1} , '_detrend'];
guidata(hObject, handles); % Save Dir names
end
UpdateDisplay(handles);
function BandPass(hObject, handles)
for x=1:size(handles.Cfg.DataDirs, 1)
%Update display
set(handles.listDataDirs, 'Value', x);
drawnow;
if size(handles.Cfg.DataDirs, 1)>1,
rest_waitbar((x-1)/size(handles.Cfg.DataDirs, 1)+0.01, ...
handles.Cfg.DataDirs{x, 1}, ...
'Band Pass filter','Parent');
end
rest_bandpass(handles.Cfg.DataDirs{x, 1}, ...
handles.Filter.SamplePeriod, ...
handles.Filter.BandHigh, ...
handles.Filter.BandLow, ...
handles.Filter.Retrend, ...
handles.Cfg.MaskFile);
%build the postfix for filtering
thePostfix ='_filtered';
%Revise the data directories
handles.Cfg.DataDirs{x, 1}=[handles.Cfg.DataDirs{x, 1} , thePostfix];
guidata(hObject, handles); % Save Dir names
end
UpdateDisplay(handles);
function btnROIVoxelWise_Callback(hObject, eventdata, handles)
%msgbox( sprintf('There is two way to define a ROI:\n\n1. Define a ball with its central coordinate and radius. Such as defining a ROI ball which centered at (-2,-36,37) and had a radius 10, you could enter "(-2,-36,37), radius=10".\n\n2. Any other ROI that''s not a ball. This kind of ROI could be defined by MRIcro or other softwares and must be a ANALYZE or NIFTI hdr/img file. Then select this file as ROI definition like selecting a mask.'), ...
% 'ROI Definition method' ,'help');
set(handles.ckboxWantZtransformation,'Enable','on');
set(handles.ckboxWantZtransformation,'Value',1); % DONG 110504 set the default value for the Z-transformation
handles.Cfg.WantZtransformation='Yes';
set(handles.text16,'Enable','on');
try
if ~iscell(handles.Cfg.ROIList),
handles.Cfg.ROIList =rest_SetROI('Init', handles.Cfg.ROIList);
else
if prod(size(handles.Cfg.ROIList)),
handles.Cfg.ROIList =rest_SetROI('Init', handles.Cfg.ROIList{1});
else
handles.Cfg.ROIList =rest_SetROI('Init');
end
end
catch
rest_SetROI('Delete');
end
guidata(hObject, handles);
UpdateDisplay(handles);
function btnROIRegionWise_Callback(hObject, eventdata, handles)
if ~iscell(handles.Cfg.ROIList), handles.Cfg.ROIList={handles.Cfg.ROIList}; end
set(handles.ckboxWantZtransformation,'Enable','off');
set(handles.ckboxWantZtransformation,'Value',0);% DONG 110504 set the default value for the Z-transformation
handles.Cfg.WantZtransformation='No';
set(handles.text16,'Enable','off');
handles.Cfg.ROIList=rest_ROIList_gui(handles.Cfg.ROIList);
% if prod(size(handles.Cfg.ROIList)) && size(handles.Cfg.ROIList, 1)==1,
% handles.Cfg.ROIList =handles.Cfg.ROIList{1};
% end
guidata(hObject, handles);
UpdateDisplay(handles);
function btnComputeGCA_Callback(hObject, eventdata, handles)
if (size(handles.Cfg.DataDirs, 1)==0) %check legal parameter set first
errordlg('No Data found! Please re-config');
return;
end
if size(handles.Cfg.ROIList, 1) ==0,
errordlg('No ROI Defined! Please define ROI first');
return;
end
%Remove the blank ROI definition at the end before judging
if iscell(handles.Cfg.ROIList) && all(isspace(handles.Cfg.ROIList{1})),
handles.Cfg.ROIList(1)=[];
end
if iscell(handles.Cfg.ROIList) && size(handles.Cfg.ROIList,1)<2 ,
errordlg('Only one ROI Defined for ROI-wise GCA! Please define ROI first');
return;
end
if (exist('rest_gca_coefficient.m','file')==2) && (exist('rest_gca_residual.m','file')==2)
%write log 20070830
handles.Log.Filename =GetLogFilename(handles.Cfg.OutputDir, get(handles.edtPrefix, 'String'));
Log2File(handles);
handles.Performance =cputime; %Write down the Start time , 20070903
%start computation
theOldDir =pwd;
theOldColor=get(hObject,'BackgroundColor');
set(hObject,'Enable','off', 'BackgroundColor', 'red');
drawnow;
try
%%Remove the linear trend first, and create a new directory, then do filtering
if strcmpi(handles.Filter.UseFilter, 'Yes') && strcmpi(handles.Detrend.BeforeFilter, 'Yes'),
Detrend(hObject, handles);
%20070614, Bug fix, Update the data structure manually
handles =guidata(hObject); % I have to read it again, because I changed it for further processing
end
%%Filter all the data and create a new directory, then compute the Functional Connectivity value, dawnsong 20070429
%Band pass filter
if strcmpi(handles.Filter.UseFilter, 'Yes')
BandPass(hObject, handles);
%20070614, Bug fix, Update the data structure manually
handles =guidata(hObject); % I have to read it again, because I changed it for further processing
end
%%Remove the linear trend after filtering, and create a new directory, then do ReHo
if strcmpi(handles.Filter.UseFilter, 'Yes') && strcmpi(handles.Detrend.AfterFilter, 'Yes'),
Detrend(hObject, handles);
%20070614, Bug fix, Update the data structure manually
handles =guidata(hObject); % I have to read it again, because I changed it for further processing
end
%compute the Functional Connectivity brain
for x=1:size(handles.Cfg.DataDirs, 1)
%Update display
set(handles.listDataDirs, 'Value', x);
drawnow;
if size(handles.Cfg.DataDirs, 1)>1,
rest_waitbar((x-1)/size(handles.Cfg.DataDirs, 1)+0.01, ...
handles.Cfg.DataDirs{x, 1}, ...
'GCA Computing','Parent');
end
fprintf('\nGCA :"%s"\n', handles.Cfg.DataDirs{x, 1});
theOutputDir=get(handles.edtOutputDir, 'String');
thePrefix =get(handles.edtPrefix, 'String');
theDstFile=fullfile(theOutputDir,[thePrefix '_' ...
GetDirName(handles.Cfg.DataDirs{x, 1}) ] );
Subject_Covariables = handles.Covariables; % Revised by YAN Chao-Gan 080804, in order to process multiple subjects with different covaribles in batch mode.
if ~isempty(handles.Covariables.ort_file) % Revised by YAN Chao-Gan 080903, in order to fix the bug that with no Covariables
CovariablesList=textread(handles.Covariables.ort_file,'%s')
if strcmp(CovariablesList{1},'Covariables_List:')
Subject_Covariables.ort_file=CovariablesList{x+1};
end
end
Subject_ROIList = handles.Cfg.ROIList; % Added by YAN Chao-Gan 091104, in order to process multiple subjects with different seed time courses in batch mode.
if ~iscell(handles.Cfg.ROIList) %Revised by YAN Chao-Gan 100130, fixed the bug in ROI-wise functional connectivity calculation. %if 2==exist(handles.Cfg.ROIList)
[pathstr, name, ext] = fileparts(handles.Cfg.ROIList) ;
if strcmpi(ext,'.txt')
SeedTimeCourseList=textread(handles.Cfg.ROIList,'%s')
if strcmp(SeedTimeCourseList{1},'Seed_Time_Course_List:')
Subject_ROIList=SeedTimeCourseList{x+1};
end
end
end
Order=str2double(get(handles.edtOrder, 'String'));
CoefficientMode=get(handles.rbtnBivariatecoefficients,'value');
if get(handles.rbtnResidual,'Value')==1,
rest_gca_residual( handles.Cfg.DataDirs{x, 1}, ...
handles.Cfg.MaskFile, ...
Subject_ROIList, ...
theDstFile, ...
Subject_Covariables, ...
Order);
else
rest_gca_coefficient( handles.Cfg.DataDirs{x, 1}, ...
handles.Cfg.MaskFile, ...
Subject_ROIList, ...
theDstFile, ...
Subject_Covariables, ...
Order, ...
CoefficientMode);
end
if strcmpi(handles.Cfg.WantZtransformation, 'Yes'),
cd (theOutputDir)
Filelist = dir('GCA_*.nii'); % YAN Chao-GAN 120923.
for i=1:length(Filelist),
theOrigGCAMap = Filelist(i).name;
theMeanGCAMap = ['Z',theOrigGCAMap];
AMaskFilename = handles.Cfg.MaskFile;
ZGCAMAP = rest_gca_Std(theOrigGCAMap, theMeanGCAMap, AMaskFilename);
end
end
end
handles.Performance =cputime -handles.Performance; %Write down the End time , 20070903
LogPerformance(handles);
catch
rest_misc( 'DisplayLastException');
errordlg(sprintf('Exception occured: \n\n%s' , lasterr));
end
cd(theOldDir);
set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
drawnow;
rest_waitbar;
else
errordlg('No rest_gca_*.m ! Please re-install');
end
% function btnSelectCovariableFile_Callback(hObject, eventdata, handles)
% [filename, pathname] = uigetfile({'*.txt; *.1D', 'Covariables'' time course file (*.txt; *.1D)'; ...
% '*.txt','text file (*.txt)'; ...
% '*.1D', 'AFNI 1D file(*.1D)'}, ...
% 'Pick Covariables'' time course file');
% if ~(filename==0),
% handles.Covariables.ort_file =[pathname filename];
% guidata(hObject,handles);
% end
% UpdateDisplay(handles);
% --- Executes on button press in rbtnCoefficient.
function rbtnCoefficient_Callback(hObject, eventdata, handles)
% hObject handle to rbtnCoefficient (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
set (handles.rbtnResidual, 'value', 0);
set (handles.rbtnCoefficient, 'value',1);
set (handles.rbtnBivariatecoefficients, 'enable','on');
set (handles.rbtnMulticoefficients, 'enable','on');
% Hint: get(hObject,'Value') returns toggle state of rbtnCoefficient
% --- Executes on button press in rbtnResidual.
function rbtnResidual_Callback(hObject, eventdata, handles)
% hObject handle to rbtnResidual (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
set (handles.rbtnResidual, 'value', 1);
set (handles.rbtnCoefficient, 'value',0);
set (handles.rbtnBivariatecoefficients, 'enable','off');
set (handles.rbtnMulticoefficients, 'enable','off');
% Hint: get(hObject,'Value') returns toggle state of rbtnResidual
function edtOrder_Callback(hObject, eventdata, handles)
% hObject handle to edtOrder (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
Order = str2double(get(hObject,'String'));
guidata(hObject, handles);
% Hints: get(hObject,'String') returns contents of edtOrder as text
% str2double(get(hObject,'String')) returns contents of edtOrder as a double
% --- Executes during object creation, after setting all properties.
function edtOrder_CreateFcn(hObject, eventdata, handles)
% hObject handle to edtOrder (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 btnHelp.
function btnHelp_Callback(hObject, eventdata, handles)
% hObject handle to btnHelp (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
web('http://resting-fmri.sourceforge.net');
% --- Executes on button press in btnSliceViewer.
% --- Executes on button press in btnPowerSpectrum.
function btnPowerSpectrum_Callback(hObject, eventdata, handles)
% hObject handle to btnPowerSpectrum (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
theOldColor=get(hObject,'BackgroundColor');
set(hObject,'Enable','off', 'BackgroundColor', 'red');
drawnow;
try
rest_Powerspectrum_start; %YAN Chao-Gan, 101025. Use new program to start power spectrum.
% [filename, pathname] = uigetfile({'*.img', 'ANALYZE or NIFTI files (*.img)'}, ...
% 'Pick one functional EPI brain map in the dataset''s directory');
% if any(filename~=0) && ischar(filename), % not canceled and legal
% if ~strcmpi(pathname(end), filesep)%revise pathname to remove extension
% pathname = [pathname filesep];
% end
% theBrainMap =[pathname filename];
% theViewer =rest_sliceviewer('ShowImage', theBrainMap);
%
% %Set the Functional Connectivity figure to show corresponding voxel's time-course and its freq amplitude
% theDataSetDir =pathname;
% theVoxelPosition=rest_sliceviewer('GetPosition', theViewer);
% theSamplePeriod =handles.Filter.SamplePeriod;
% theBandRange =[handles.Filter.BandLow, handles.Filter.BandHigh];
% rest_powerspectrum('ShowFluctuation', theDataSetDir, theVoxelPosition, ...
% theSamplePeriod, theBandRange);
%
% %Update the Callback
% theCallback ='';
% cmdDataSetDir =sprintf('theDataSetDir= ''%s'';', theDataSetDir);
% cmdBrainMap =sprintf('theVoxelPosition=rest_sliceviewer(''GetPosition'', %g);', theViewer);
% cmdSamplePeriod =sprintf('theSamplePeriod= %g;', theSamplePeriod);
% cmdBandRange =sprintf('theBandRange= [%g, %g];', theBandRange(1), theBandRange(2));
% cmdUpdateWaveGraph ='rest_powerspectrum(''ShowFluctuation'', theDataSetDir, theVoxelPosition, theSamplePeriod, theBandRange);';
% theCallback =sprintf('%s\n%s\n%s\n%s\n%s\n',cmdDataSetDir, ...
% cmdBrainMap, cmdSamplePeriod, cmdBandRange, ...
% cmdUpdateWaveGraph);
% cmdClearVar ='clear theDataSetDir theVoxelPosition theSamplePeriod theBandRange;';
% rest_sliceviewer('UpdateCallback', theViewer, [theCallback cmdClearVar], 'ALFF Analysis');
%
% % Update some Message
% theMsg =sprintf('TR( s): %g\nBand( Hz): %g~%g', ...
% theSamplePeriod, theBandRange(1), theBandRange(2) );
% rest_sliceviewer('SetMessage', theViewer, theMsg);
% end
catch
rest_misc( 'DisplayLastException');
end
set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
drawnow;
rest_waitbar;
function edtCovariableFile_Callback(hObject, eventdata, handles)
% hObject handle to edtCovariableFile (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
handles.Covariables.ort_file =get(hObject, 'String');
guidata(hObject,handles);
% Hints: get(hObject,'String') returns contents of edtCovariableFile as text
% str2double(get(hObject,'String')) returns contents of edtCovariableFile as a double
% --- Executes during object creation, after setting all properties.
function edtCovariableFile_CreateFcn(hObject, eventdata, handles)
% hObject handle to edtCovariableFile (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 btnSelectCovariableFile.
function btnSelectCovariableFile_Callback(hObject, eventdata, handles)
% hObject handle to btnSelectCovariableFile (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({'*.txt; *.1D', 'Covariables'' time course file (*.txt; *.1D)'; ...
'*.txt','text file (*.txt)'; ...
'*.1D', 'AFNI 1D file(*.1D)'}, ...
'Pick Covariables'' time course file');
if ~(filename==0),
handles.Covariables.ort_file =[pathname filename];
guidata(hObject,handles);
end
UpdateDisplay(handles);
function ckboxWantZtransformation_Callback(hObject, eventdata, handles)
if get(hObject,'Value')
handles.Cfg.WantZtransformation ='Yes';
else
handles.Cfg.WantZtransformation ='No';
end
guidata(hObject, handles);
UpdateDisplay(handles);
function InitFrames(hObject,handles)
offsetY =83+50; %dawnsong, 20070504, add for the divide by the mask mean, the Y of Edit "OutPut Diectory"
%dawnsong, 20070905, add Covariable for functional connectivities
% for Matlab 6.5 compatible, draw a panel
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+65 433 1]);%bottom
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+136 433 1]);%Covariables horz line
%uicontrol(handles.figFCMain, 'Style','Frame','Position',[90 offsetY+202 343 1]);%Mask Bottom line
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+227 433 1]);%Middle, mask top line
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[95 offsetY+137 1 90]);%Middle, mask left line
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+65 1 318]); %Input left line
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[435 offsetY+65 1 318.5]);%Input right line
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+382 433 1]); %Input top line
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[280 offsetY+136 1 91]);
if ~ispc && ~ismac
set(handles.rbtnBivariatecoefficients , 'Position' , [47 24 27 2]);%Revised by sandy
set(handles.rbtnMulticoefficients , 'Position' , [47 22 27 2]);
end
if ismac
set(handles.rbtnBivariatecoefficients , 'Position' , [41 23 27 2]);%Revised by YAN Chao-Gan, 120902
set(handles.rbtnMulticoefficients , 'Position' , [41 20 27 2]);
end
uicontrol(handles.figGCAMain,'Style','Text','Position',[142 offsetY+378 180 14],...
'String','Input Parameters');
uicontrol(handles.figGCAMain,'Style','Text','Position',[160 offsetY+222 40 14],...
'String','Mask');
uicontrol(handles.figGCAMain,'Style','Text','Position',[310 offsetY+222 90 14],...
'String','ROI-wise mode');
uicontrol(handles.figGCAMain,'Style','Text','Position',[20 offsetY+222 50 14],...
'String','Set ROI', 'FontWeight', 'normal','FontSize', 10,'ForegroundColor', 'red');
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+395 433 1]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[435 offsetY+395 1 50]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+395 1 48]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+443 433 1]);
uicontrol(handles.figGCAMain,'Style','Text','Position',[142 offsetY+438 180 14],...
'String','Option: Ideal Band Pass Filter');
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+458 433 1]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[435 offsetY+458 1 50]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+458 1 50]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+508 433 1]);
uicontrol(handles.figGCAMain,'Style','Text','Position',[142 offsetY+498 180 14],...
'String','Option: Remove Linear Trend');
%I insert the area for covariables between Input and Output areas.
offsetY = offsetY -50;
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY+67 433 1]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY-8 433 1]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY-8 1 75]);
uicontrol(handles.figGCAMain, 'Style','Frame','Position',[435 offsetY-8 1 76]);
uicontrol(handles.figGCAMain,'Style','Text','Position',[142 offsetY+60 180 14],...
'String','Output Parameters');
%20070506, Add manual operation button groups like SPM
% uicontrol(handles.figGCAMain, 'Style','Frame','Position',[2 offsetY-25 433 1]);
% uicontrol(handles.figGCAMain,'Style','Text','Position',[152 offsetY-30 140 14],...
% 'String','Manual Operations');
function rbtnMulticoefficients_Callback(hObject, eventdata, handles)
% hObject handle to rbtnMulticoefficients (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
set (handles.rbtnBivariatecoefficients, 'value',0);
set (handles.rbtnMulticoefficients, 'value',1);
% Hint: get(hObject,'Value') returns toggle state of rbtnMulticoefficients
% --- Executes on button press in rbtnBivariatecoefficients.
function rbtnBivariatecoefficients_Callback(hObject, eventdata, handles)
% hObject handle to rbtnBivariatecoefficients (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
set (handles.rbtnBivariatecoefficients, 'value',1);
set (handles.rbtnMulticoefficients, 'value',0);
% Hint: get(hObject,'Value') returns toggle state of
% rbtnBivariatecoefficients
