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_cohe_gui.m
function varargout = rest_cohe_gui(varargin)
% GUI for Regional Homogeneity based on Coherence
%-----------------------------------------------------------
% Copyright(c) 2007~2010
% State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University
% Based on SONG Xiao-Wei's ReHo GUI
% For methodology, please see: Liu D, Yan C, Ren J, Yao L, Kiviniemi VJ and Zang Y (2010) Using coherence to measure regional homogeneity of resting-state fMRI signal. Front. Syst. Neurosci. 4:24. doi: 10.3389/fnsys.2010.00024
% http://www.restfmri.net
% Mail to Authors: <a href="charlesliu116@gmail.com">LIU Dong-Qiang</a>; <a href="dongzy08@gmail.com">DONG Zhang-Ye</a>; <a href="ycg.yan@gmail.com">YAN Chao-Gan</a>
% Version=1.0;
% Release=20101025;
% Last Revised by Sandy Wang, 120719. Added parfor.
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @rest_cohe_gui_OpeningFcn, ...
'gui_OutputFcn', @rest_cohe_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_cohe_gui is made visible.
function rest_cohe_gui_OpeningFcn(hObject, eventdata, handles, varargin)
%Matlab -Linux compatible, Initialize controls' default properties, dawnsong , 20070507
%Matlab -v6 compatible, create some frames instead of panels
InitControlProperties(hObject, handles);
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.MaskFile = 'Default'; %the user defined mask file
handles.Cfg.ClusterCount =27 ; % the cluster type, 27 or 19 or 7
handles.Cfg.OutputDir =pwd; % pwd is the default dir for Cohe map result
handles.Cfg.WantMeanCoheMap ='Yes'; %Calcute the mean Cohe map default
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'; % by default, do re-trend after linear filtering after removing linear trend and disable changing this value, 20070530 ZangYF decide
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;
handles.Cfg.Auto =1;
guidata(hObject, handles);
UpdateDisplay(handles);
movegui(handles.figCoheMain, 'center');
% set(handles.figCoheMain,'Name','Coherence Based on Region');
% 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_cohe_gui
handles.output = hObject;
guidata(hObject, handles);% Update handles structure
% UIWAIT makes rest_cohe_gui wait for user response (see UIRESUME)
% uiwait(handles.figCoheMain);
% --- Outputs from this function are returned to the command line.
function varargout = rest_cohe_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');
restGui_SetDataDir(hObject,theDir, handles);
function edtDataDirectory_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
% --- Executes on button press in btnSelectDataDir.
function btnSelectDataDir_Callback(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 data directory to compute Cohe-ReHo map: ');
if ischar(theDir),
restGui_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 Cohe-ReHo map: ');
if ischar(theDir),
%Make the warning dlg off! 20071201
setappdata(0, 'Cohe_DoingRecursiveDir', 1);
theOldColor =get(handles.listDataDirs, 'BackgroundColor');
set(handles.listDataDirs, 'BackgroundColor', [ 0.7373 0.9804 0.4784]);
try
rest_RecursiveDir(theDir, 'rest_cohe_gui(''restGui_SetDataDir'',gcbo, ''%s'', guidata(gcbo) )');
catch
rest_misc( 'DisplayLastException');
end
set(handles.listDataDirs, 'BackgroundColor', theOldColor);
rmappdata(0, 'Cohe_DoingRecursiveDir');
end
function restGui_SetDataDir(hObject,ADir, handles)
theOldWarnings =warning('off', 'all');
if ~isequal(ADir , 0) && rest_misc('GetMatlabVersion')>=7.3,
ADir =strtrim(ADir);
end
% if (~isequal(ADir , 0)) &&( (size(handles.Cfg.DataDirs, 1)==0)||(0==seqmatch({ADir} ,handles.Cfg.DataDirs( : , 1) ) ) ) ,20070519
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
handles.Cfg.DataDirs =[handles.Cfg.DataDirs ; {ADir,0}];
%theVolumnCount =rest_CheckDataDir(handles.Cfg.DataDirs{1,1} );
DirList_Count=size(handles.Cfg.DataDirs,1);%Added by Sandy
theVolumnCount =...
rest_CheckDataDir(handles.Cfg.DataDirs{DirList_Count,1});
if (theVolumnCount<=0),
if isappdata(0, 'Cohe_DoingRecursiveDir') && getappdata(0, 'Cohe_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
%Fix a bug when no data in directory Sandy
handles.Cfg.DataDirs(DirList_Count,:)=[];
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{DirList_Count,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);
theCount =size(handles.Cfg.DataDirs,1);
%set(handles.listDataDirs, 'String', GetInputDirDisplayList(handles) , 'Value', 1);
set(handles.listDataDirs, 'String', GetInputDirDisplayList(handles) , 'Value', theCount);
%Removed by Sandy
%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', 'off');
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 mean calculation, dawnsong 20070504
set(handles.ckboxDivideMean, 'Value', strcmpi(handles.Cfg.WantMeanCoheMap, 'Yes'));
set(handles.ckboxRemoveTrendBefore, 'Value', strcmpi(handles.Detrend.BeforeFilter, 'Yes'));
set(handles.ckboxRemoveTrendAfter, 'Value', strcmpi(handles.Detrend.AfterFilter, 'Yes'));
%% 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
% 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.', ADataDir);
errordlg('*.{hdr,img} should be pairwise. Please re-examin them.');
break;
end
end
end
%% --- Executes on button press in btnComputeCohe.
function btnComputeCohe_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 (exist('rest_Cohe_ReHo_Brain.m','file')==2)
%write log 20070507
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 change it for further processing
end
pause(0.01);
%%Filter all the data and create a new directory, then compute the ReHo 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 change it for further processing
end
pause(0.01);
%%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 change it for further processing
end
pause(0.01);
%compute the ReHo brain
if size(handles.Cfg.DataDirs, 1)>1,
rest_waitbar(0,'Cohe-ReHo Batch Compution, wait ...','Cohe-ReHo','Parent');
end
pause(0.01);
%add by Sandy Wang for parallel computing 20120404
PF_DataDirs=handles.Cfg.DataDirs(:,1);
PF_edtOutputDir=get(handles.edtOutputDir,'String');
PF_edtPrefix=get(handles.edtPrefix,'String');
PF_ClusterCount=handles.Cfg.ClusterCount;
PF_MaskFile=handles.Cfg.MaskFile;
PF_SamplePeriod=handles.Filter.SamplePeriod;
PF_edtLBC=str2num(get(handles.edtLBC,'String'));
PF_edtHBC=str2num(get(handles.edtHBC,'String'));
PF_Auto=handles.Cfg.Auto;
PF_TimeP=str2num(get(handles.edtTimeP, 'String'));
PF_Overlap=str2num(get(handles.edtOverlap, 'String'));
PF_WantMeanCoheMap=handles.Cfg.WantMeanCoheMap;
parfor 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}, ...
% 'Cohe-ReHo Computing','Parent');
%end
%cd(handles.Cfg.DataDirs{x, 1});%Change current dir to the data dir
%fprintf('\nCohe :"%s"\n', handles.Cfg.DataDirs{x, 1});
fprintf('\nCohe :"%s"\n', PF_DataDirs{x});
%theOutputDir=get(handles.edtOutputDir, 'String');
%thePrefix =get(handles.edtPrefix, 'String');
theOutputDir=PF_edtOutputDir;
thePrefix =PF_edtPrefix;
%theDstFile=fullfile(theOutputDir,[thePrefix '_' ...
% GetDirName(handles.Cfg.DataDirs{x, 1}) ] );
theDstFile=fullfile(theOutputDir,[thePrefix '_' ...
GetDirName(PF_DataDirs{x}) ] );
%LowB =str2num(get(handles.edtLBC, 'String'));
%HighB =str2num(get(handles.edtHBC, 'String'));
%LowB =PF_edtLBC;
%HighB =PF_edtHBC;
%Auto=handles.Cfg.Auto;
%TimeP=str2num(get(handles.edtTimeP, 'String'));
%Overlap=str2num(get(handles.edtOverlap, 'String'));
rest_Cohe_ReHo_Brain(PF_DataDirs{x}, ...
PF_ClusterCount, ...
PF_MaskFile, ...
theDstFile, ...
PF_SamplePeriod, ...
PF_edtHBC, ...
PF_edtLBC,PF_Auto,PF_TimeP,PF_Overlap); % Revised by YAN Chao-Gan, 090420. Designate the input file path and output file path for the revised reho.m
%20070504, divide ReHo brain by the mean within the mask
%if strcmpi(handles.Cfg.WantMeanCoheMap, 'Yes')
if strcmpi(PF_WantMeanCoheMap, 'Yes')
theOrigCoheMap =theDstFile;
theMeanCoheMap =fullfile(theOutputDir,['m' thePrefix '_' ...
GetDirName(PF_DataDirs{x}) ] );
%GetDirName(handles.Cfg.DataDirs{x, 1}) ] );
% theMaskFile =handles.Cfg.MaskFile;
theMaskFile =PF_MaskFile;
rest_DivideMeanWithinMask(theOrigCoheMap, theMeanCoheMap, theMaskFile);
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
rest_waitbar;
cd(theOldDir);
set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
drawnow;
else
errordlg('No rest_Cohe_ReHo_Brain.m ! Please re-install');
end
%%
function edtMaskfile_Callback(hObject, eventdata, handles)
theMaskfile =get(hObject, 'String');
if ~isequal(theMaskfile , 0) && 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
% --- Executes during object creation, after setting all properties.
function edtMaskfile_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
%% --- Executes on button press in btnSelectMask.
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);
%% --- Select Default mask
function rbtnDefaultMask_Callback(hObject, eventdata, handles)
set(handles.btnSelectMask, 'Enable','off');
handles.Cfg.MaskFile ='Default';
guidata(hObject, handles);
set(handles.rbtnDefaultMask,'Value',1);
set(handles.rbtnNullMask,'Value',0);
set(handles.rbtnUserMask,'Value',0);
% --- Executes on button press in rbtnNullMask.
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);
%% --- Select user defined mask
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;
% --- Executes on button press in rbtn27voxels.
function rbtn27voxels_Callback(hObject, eventdata, handles)
handles.Cfg.ClusterCount =27;
guidata(hObject, handles);
set(handles.rbtn7voxels,'Value',0);
set(handles.rbtn19voxels,'Value',0);
set(handles.rbtn27voxels,'Value',1);
% --- Executes on button press in rbtn19voxels.
function rbtn19voxels_Callback(hObject, eventdata, handles)
handles.Cfg.ClusterCount =19;
guidata(hObject, handles);
set(handles.rbtn7voxels,'Value',0);
set(handles.rbtn19voxels,'Value',1);
set(handles.rbtn27voxels,'Value',0);
% --- Executes on button press in rbtn7voxels.
function rbtn7voxels_Callback(hObject, eventdata, handles)
handles.Cfg.ClusterCount =7;
guidata(hObject, handles);
set(handles.rbtn7voxels,'Value',1);
set(handles.rbtn19voxels,'Value',0);
set(handles.rbtn27voxels,'Value',0);
%% Double-click to show the volumn count of the selected dir
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.figCoheMain, '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.figCoheMain, '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');"
UpdateDisplay(handles);
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 compute Cohe-ReHo 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);
%Matlab -v6 compatible, create some frames instead of panels
% --- Executes on button press in ckboxFilter.
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
%Divide ReHo brain by the mean within the mask, output: mRehoMap.{hdr/img}
function ckboxDivideMean_Callback(hObject, eventdata, handles)
if get(hObject,'Value')
handles.Cfg.WantMeanCoheMap ='Yes';
else
handles.Cfg.WantMeanCoheMap ='No';
end
guidata(hObject, handles);
UpdateDisplay(handles);
% ---Manaul Operations, Divide one rehomap by its global mean
function btnDivideMean_Callback(hObject, eventdata, handles)
theOldColor=get(hObject,'BackgroundColor');
set(hObject,'Enable','off', 'BackgroundColor', 'red');
drawnow;
try
[filename, pathname] = uigetfile({'*.img;*.nii;*.nii.gz','Brain Image Files (*.img;*.nii;*.nii.gz)';'*.*', 'All Files (*.*)';}, ...
'Pick one Cohe-ReHo map');
if (filename~=0)% not canceled
if strcmpi(filename(end-3:end), '.img')%revise filename to remove extension
filename = filename(1:end-4);
end
if ~strcmpi(pathname(end), filesep)%revise dir name to remove the last \ or /
pathname = [pathname filesep];
end
theOrigCoheMap =[pathname filename];
theMeanCoheMap =[pathname 'm' filename];
theMaskFile =handles.Cfg.MaskFile;
rest_DivideMeanWithinMask(theOrigCoheMap, theMeanCoheMap, theMaskFile);
msgbox(sprintf('Cohe-ReHo brain "%s.{hdr/img}" \ndivide its mean within mask successfully.\t\n\nSave to "%s.{hdr/img}"\n' , ...
theOrigCoheMap, theMeanCoheMap), ...
'Divide mean within mask successfully' ,'help');
end
catch
rest_misc( 'DisplayLastException');
end
set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
drawnow;
% manually band pass filter
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;
%%Create GUI
%%Create Frames/Lines
function InitFrames(hObject,handles);
offsetY =130; %dawnsong, 20070504, add for the divide by the mask mean, the Y of Edit "OutPut Diectory"
% for Matlab 6.5 compatible, draw a panel
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+151 433 1]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+241 433 1]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[90 offsetY+152 1 90]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+152 1 233]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[435 offsetY+152 1 233]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+385 433 1]);
uicontrol(handles.figCoheMain,'Style','Text','Position',[152 offsetY+380 140 14],...
'String','Input Parameters');
uicontrol(handles.figCoheMain,'Style','Text','Position',[8 offsetY+238 40 14],...
'String','Cluster');
uicontrol(handles.figCoheMain,'Style','Text','Position',[208 offsetY+238 40 14],...
'String','Mask');
offsetY=offsetY-50;
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+94 433 1]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY-8 433 1]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY-8 1 102]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[435 offsetY-8 1 102]);
uicontrol(handles.figCoheMain,'Style','Text','Position',[152 offsetY+88 180 14],...
'String','Output Parameters (Cohe-ReHo map)');
offsetY=offsetY+50;
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+400 433 1]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[435 offsetY+400 1 50]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+400 1 50]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+450 433 1]);
uicontrol(handles.figCoheMain,'Style','Text','Position',[142 offsetY+445 180 14],...
'String','Option: Ideal Band Pass Filter');
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+465 433 1]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[435 offsetY+465 1 50]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+465 1 50]);
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY+515 433 1]);
uicontrol(handles.figCoheMain,'Style','Text','Position',[142 offsetY+505 180 14],...
'String','Option: Remove Linear Trend');
offsetY=offsetY-50;
%20070506, Add manual operation button groups like SPM
uicontrol(handles.figCoheMain, 'Style','Frame','Position',[2 offsetY-25 433 1]);
uicontrol(handles.figCoheMain,'Style','Text','Position',[152 offsetY-30 140 14],...
'String','Manual Operations');
function InitControlProperties(hObject, handles)
%for Linux compatible 20070507 dawnsong
% --- FIGURE -------------------------------------
offset=50;
set(handles.figCoheMain,...
'Units', 'pixels', ...
'Position', [10 5 440 600+offset], ...
'Name', 'Regional Homogeneity based on Coherence', ...
'MenuBar', 'none', ...
'NumberTitle', 'off', ...
'Color', get(0,'DefaultUicontrolBackgroundColor'));
% --- STATIC TEXTS -------------------------------------
set(handles.text2, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [16 186+offset 175 40], ...
'FontSize', 24, ...
'FontWeight', 'bold', ...
'ToolTipString','Regional Homogeneity based on Coherence', ...
'String', 'Cohe-ReHo');
set(handles.text4, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [8 109 80 21], ...
'String', 'Directory:');
set(handles.txtInputDir, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [7 336+offset 80 21], ...
'String', 'Data Directory:');
set(handles.text5, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [9 140 80 21], ...
'String', 'Prefix:');
set(handles.txtResultFilename, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [227 148 200 16], ...
'HorizontalAlignment','left' , ...
'String', 'Result: Prefix_DirectoryName.{hdr/img}');
set(handles.text7, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [144 476+offset 25 51], ...
'FontSize', 28, ...
'String', '~');
set(handles.text8, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [230 491+offset 45 16], ...
'String', 'TR: (s)');
% --- PUSHBUTTONS -------------------------------------
set(handles.btnSelectOutputDir, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [396 107 30 25], ...
'FontSize', 18, ...
'String', '...');
set(handles.btnSelectDataDir, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [396 334+offset 30 25], ...
'FontSize', 18, ...
'String', '...', ...
'CData', zeros(1,0));
set(handles.btnSelectMask, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [396 240+offset 30 25], ...
'FontSize', 18, ...
'String', '...', ...
'Enable', 'off', ...
'CData', zeros(1,0));
set(handles.btnComputeCohe, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [319 238 105 30], ...
'FontSize', 12, ...
'FontWeight', 'bold', ...
'String', 'Do all');
set(handles.btnDetrend , ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [337 553+offset 90 25], ...
'FontSize', 10, ...
'Enable', 'off', ... %Update filter and detrend button's state according to Option: detrend/Filter 20070820
'String', 'Detrend');
set(handles.btnBandPass , ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [337 490+offset 90 25], ...
'FontSize', 10, ...
'Enable', 'off', ... %Update filter and detrend button's state according to Option: detrend/Filter 20070820
'String', 'Filter');
set(handles.btnHelp, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [10 10 90 33], ...
'FontSize', 10, ...
'String', 'Help');
set(handles.btnDivideMean, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [110 10 90 33], ...
'FontSize', 10, ...
'String', 'Divide Mean');
set(handles.btnSliceViewer, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [210 10 90 33], ...
'FontSize', 10, ...
'String', 'Slice Viewer');
set(handles.btnWaveGraph, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [314 10 110 33], ...
'FontSize', 10, ...
'String', 'Power Spectrum');
% --- RADIO BUTTONS -------------------------------------
set(handles.rbtn7voxels, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [10 298+offset 70 16], ...
'String', '7 voxels');
set(handles.rbtn19voxels, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [10 273+offset 70 16], ...
'String', '19 voxels');
set(handles.rbtn27voxels, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [10 248+offset 70 16], ...
'String', '27 voxels');
set(handles.rbtnDefaultMask, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [110 297+offset 158 16], ...
'String', 'Default mask');
set(handles.rbtnUserMask, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [110 271+offset 148 16], ...
'String', 'User-defined mask');
set(handles.rbtnNullMask, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [277 298+offset 82 16], ...
'String', 'No mask');
% --- CHECKBOXES -------------------------------------
set(handles.ckboxFilter, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [14 491+offset 80 22], ...
'String', 'Band (Hz)');
set(handles.ckboxRetrend, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Visible', 'off', ...
'Position', [366 490+offset 60 22], ...
'String', 'Retrend');
set(handles.ckboxDivideMean, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [12 82 430 19], ...
'String', 'Divide ReHo brain by the mean within the mask (mPrefix_DirectoryName.{hdr/img})');
set(handles.ckboxRemoveTrendBefore, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [13 555+offset 140 21],...
'String', 'detrend'); %'String', 'detrend BEFORE Filter');
set(handles.ckboxRemoveTrendAfter, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [171 555+offset 140 21],...
'Visible', 'off', ...
'String', 'detrend AFTER Filter');
% --- EDIT TEXTS -------------------------------------
set(handles.edtOutputDir, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [94 109 300 23], ...
'BackgroundColor', [1 1 1], ...
'String', 'Edit Text');
set(handles.edtDataDirectory, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [94 336+offset 300 22], ...
'BackgroundColor', [1 1 1], ...
'String', '');
set(handles.edtMaskfile, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [94 240+offset 300 23], ...
'BackgroundColor', [1 1 1], ...
'String', 'Edit Text', ...
'Enable', 'off');
set(handles.edtPrefix, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [94 142 115 22], ...
'BackgroundColor', [1 1 1], ...
'String', 'CoheReHoMap');
set(handles.edtBandLow, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [94 491+offset 50 22], ...
'BackgroundColor', [1 1 1], ...
'String', '0.01', ...
'Enable', 'off');
set(handles.edtBandHigh, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [171 491+offset 50 22], ...
'BackgroundColor', [1 1 1], ...
'String', '0.08', ...
'Enable', 'off');
set(handles.edtSamplePeriod, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [276 491+offset 50 22], ...
'BackgroundColor', [1 1 1], ...
'String', '2', ...
'Enable', 'off');
% --- LISTBOXES -------------------------------------
set(handles.listDataDirs, ...
'Style', 'listbox', ...
'Units', 'pixels', ...
'Position', [14 363+offset 413 98], ...
'BackgroundColor', [1 1 1], ...
'String', '');
%20071103, Add context menu to Input Data Directories to add��delete��export��import����
handles.hContextMenu =uicontextmenu;
set(handles.listDataDirs, 'UIContextMenu', handles.hContextMenu);
uimenu(handles.hContextMenu, 'Label', 'Add a directory', 'Callback', get(handles.btnSelectDataDir, 'Callback'));
uimenu(handles.hContextMenu, 'Label', 'Remove selected directory', 'Callback', 'rest_cohe_gui(''DeleteSelectedDataDir'',gcbo,[], guidata(gcbo))');
uimenu(handles.hContextMenu, 'Label', 'Add recursively all sub-folders of a directory', 'Callback', 'rest_cohe_gui(''RecursiveAddDataDir'',gcbo,[], guidata(gcbo))');
uimenu(handles.hContextMenu, 'Label', '=============================');
uimenu(handles.hContextMenu, 'Label', 'Remove all data directories', 'Callback', 'rest_cohe_gui(''ClearDataDirectories'',gcbo,[], guidata(gcbo))');
% Save handles structure
guidata(hObject,handles);
%% Log options to a log file for further investigation, 20070507
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('Cohe-ReHo 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\nCohe input parameters:\r\n%s\r\n\r\n%s', theMsg, ...
LogCoheInputParameters(handles), constLineSep);
theMsg =sprintf('%s\r\nCohe output parameters:\r\n%s\r\n\r\n%s', theMsg, ...
LogCoheOutputParameters(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 Regional Coherence 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=LogCoheInputParameters(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);
ResultLogString =sprintf('%s\tCluster Count: %g\r\n',ResultLogString, handles.Cfg.ClusterCount);
function ResultLogString=LogCoheOutputParameters(handles)
ResultLogString ='';
ResultLogString =sprintf('%s\tPrefix to the Data directories: %s\r\n',ResultLogString, get(handles.edtPrefix, 'String'));
ResultLogString =sprintf('\tOutput Prefix: %s\r\n', get(handles.edtPrefix, 'String'));
ResultLogString =sprintf('%s\tOutput Data Directories: %s\r\n',ResultLogString, handles.Cfg.OutputDir);
ResultLogString =sprintf('%s\tWant mean Cohe-ReHo map computation: %s \r\n',ResultLogString, handles.Cfg.WantMeanCoheMap);
%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_%sCohe.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 add \ or /
% 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 btnWaveGraph_Callback(hObject, eventdata, handles)
%Display a brain image like MRIcro, and show specific voxel's time course and its freq domain's fluctuation
theOldColor=get(hObject,'BackgroundColor');
set(hObject,'Enable','off', 'BackgroundColor', 'red');
drawnow;
try
% if strcmpi(handles.Filter.UseFilter, 'Yes'),
% else
% msgbox(sprintf('You didn''t select option "Band Pass" before show Wave Graph. \n\nYou may enable it first and then you can set Band parameter and TR.'));
% end
[filename, pathname] = uigetfile({'*.img;*.nii;*.nii.gz','Brain Image Files (*.img;*.nii;*.nii.gz)';'*.*', 'All Files (*.*)';}, ...
'Pick one functional EPI brain map in the dataset''s directory');
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];
theViewer =rest_sliceviewer('ShowImage', theBrainMap);
%Set the ALFF 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;', handles.Filter.SamplePeriod);
cmdBandRange =sprintf('theBandRange= [%g, %g];', handles.Filter.BandLow, handles.Filter.BandHigh);
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 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);
% --- Executes on button press in btnDetrend.
function btnDetrend_Callback(hObject, eventdata, handles)
theOldColor=get(hObject,'BackgroundColor');
set(hObject,'Enable','off', 'BackgroundColor', 'red');
drawnow;
try
Detrend(hObject,handles);
msgbox('Remove the Linear Trend Over.',...
'Detrend successfully' ,'help');
catch
rest_misc( 'DisplayLastException');
end
rest_waitbar;
set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
drawnow;
function Detrend(hObject,handles)
PF_DataDirs=handles.Cfg.DataDirs(:,1);
tic;
parfor x=1:size(PF_DataDirs, 1)
%Update display
%set(handles.listDataDirs, 'Value', x);
%drawnow;
%Changed by Sandy Wang for parallel computing 20120518
%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(PF_DataDirs{x}, '_detrend');
end
for x=1:size(PF_DataDirs, 1)
%Revise the data directories
handles.Cfg.DataDirs{x, 1}=[handles.Cfg.DataDirs{x, 1} , '_detrend'];
end
guidata(hObject, handles); % Save Dir names
toc;
set(handles.listDataDirs, 'Value', size(PF_DataDirs, 1));
UpdateDisplay(handles);
function BandPass(hObject, handles)
%add by Sandy Wang 20120430 for parallel computation
PF_DataDirs=handles.Cfg.DataDirs(:,1);
PF_BandHigh=handles.Filter.BandHigh;
PF_SamplePeriod=handles.Filter.SamplePeriod;
PF_BandLow=handles.Filter.BandLow;
PF_Retrend=handles.Filter.Retrend;
PF_MaskFile=handles.Cfg.MaskFile;
%for x=1:size(handles.Cfg.DataDirs, 1)
parfor x=1:size(PF_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_(handles.Cfg.DataDirs{x, 1}, ...
% handles.Filter.SamplePeriod, ...
% handles.Filter.BandHigh, ...
% handles.Filter.BandLow, ...
% handles.Filter.Retrend, ...
% handles.Cfg.MaskFile);
rest_bandpass(PF_DataDirs{x}, ...
PF_SamplePeriod, ...
PF_BandHigh, ...
PF_BandLow, ...
PF_Retrend, ...
PF_MaskFile);
end
for x=1:size(handles.Cfg.DataDirs, 1)
%build the postfix for filtering
thePostfix ='_filtered';
%Revise the data directories
handles.Cfg.DataDirs{x, 1}=[handles.Cfg.DataDirs{x, 1} , thePostfix];
end
guidata(hObject, handles);% Save Dir names
set(handles.listDataDirs, 'Value', size(PF_DataDirs, 1));
UpdateDisplay(handles);
function btnHelp_Callback(hObject, eventdata, handles)
web('http://resting-fmri.sourceforge.net');
%web (sprintf('%s/man/English/ReHo/index.html', rest_misc( 'WhereIsREST')), '-helpbrowser');
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edtLBC_Callback(hObject, eventdata, handles)
function edtLBC_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edtHBC_Callback(hObject, eventdata, handles)
function edtHBC_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function rtnAuto_Callback(hObject, eventdata, handles)
handles.Cfg.Auto =1;
guidata(hObject, handles);
set(handles.rtnManual,'Value',0);
set(handles.rtnAuto,'Value',1);
set(handles.edtTimeP,'Visible','off');
set(handles.txtTimeP,'Visible','off');
set(handles.edtOverlap,'Visible','off');
set(handles.txtOverlap,'Visible','off');
% --- Executes on button press in rtnManual.
function rtnManual_Callback(hObject, eventdata, handles)
handles.Cfg.Auto =0;
guidata(hObject, handles);
set(handles.rtnManual,'Value',1);
set(handles.rtnAuto,'Value',0);
set(handles.edtTimeP,'Visible','on');
set(handles.txtTimeP,'Visible','on');
set(handles.edtOverlap,'Visible','on');
set(handles.txtOverlap,'Visible','on');
function edtTimeP_Callback(hObject, eventdata, handles)
function edtTimeP_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function edtOverlap_Callback(hObject, eventdata, handles)
function edtOverlap_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
