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alff_gui.m
executable file
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alff_gui.m
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function varargout = alff_gui(varargin)
%ALFF GUI by Xiaowei Song
%-----------------------------------------------------------
% Copyright(c) 2007~2010
% State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University
% Written by Xiao-Wei Song
% http://www.restfmri.net
% $mail [email protected]
% $Version =1.3;
% $Date =20100420;
%-----------------------------------------------------------
% Mail to Authors: <a href="[email protected]">Xiaowei Song</a>; <a href="[email protected]">Chaogan Yan</a>
% Version=1.3;
% Release=20100420;
% Revised by YAN Chao-Gan 080808: also support NIFTI images.
% Revised by YAN Chao-Gan, 100420. Fixed a bug in calculating the frequency band.
% 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', @alff_gui_OpeningFcn, ...
'gui_OutputFcn', @alff_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 alff_gui is made visible.
function alff_gui_OpeningFcn(hObject, eventdata, handles, varargin)
%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.MaskFile = 'Default'; %the user defined mask file
handles.Cfg.OutputDir =pwd; % pwd is the default dir for alff map result
handles.Cfg.WantMeanAlffMap ='Yes'; %Calcute the mean alff 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, always re-trend after linear filtering after removing linear trend 20070614, bug fixes
handles.Filter.SamplePeriod=2; %by default, set TR=2s
handles.Detrend.BeforeFilter ='No';% ZangYF, 20070530 decide
handles.Detrend.AfterFilter ='No';% ZangYF, 20070530 decide
handles.ALFF.BandLow =0.01; % Band Info for ALFF computing
handles.ALFF.BandHigh =0.08; % Band Info for ALFF computing
handles.ALFF.SamplePeriod =2; % Band Info for ALFF computing
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.figAlffMain, 'center');
set(handles.figAlffMain,'Name','Amplitude of Low Frequency Fluctuation');
% 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 alff_gui
handles.output = hObject;
guidata(hObject, handles);% Update handles structure
% UIWAIT makes alff_gui wait for user response (see UIRESUME)
% uiwait(handles.figAlffMain);
% --- Outputs from this function are returned to the command line.
function varargout = alff_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 alff 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 ALFF map: ');
if ischar(theDir),%Make the warning dlg off! 20071201
setappdata(0, 'ALFF_DoingRecursiveDir', 1);
theOldColor =get(handles.listDataDirs, 'BackgroundColor');
set(handles.listDataDirs, 'BackgroundColor', [ 0.7373 0.9804 0.4784]);
try
rest_RecursiveDir(theDir, 'alff_gui(''SetDataDir'',gcbo, ''%s'', guidata(gcbo) )');
catch
rest_misc( 'DisplayLastException');
end
set(handles.listDataDirs, 'BackgroundColor', theOldColor);
rmappdata(0, 'ALFF_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
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, 'ALFF_DoingRecursiveDir') && getappdata(0, 'ALFF_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', '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 mean calculation, dawnsong 20070504
set(handles.ckboxDivideMean, 'Value', strcmpi(handles.Cfg.WantMeanAlffMap, 'Yes'));
% Set detrend option
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
for x=1:size(handles.Cfg.DataDirs,1)
%Result =[{sprintf('%d# %s',handles.Cfg.DataDirs{x, 2},handles.Cfg.DataDirs{x, 1})} ;Result];
%Change by Sandy for select order of Dir 201207
Result =[Result;...
{sprintf('%d# %s',handles.Cfg.DataDirs{x, 2},handles.Cfg.DataDirs{x, 1})}];
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 btnComputeAlff_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('alff.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');
set(handles.listDataDirs, 'Value', 1);%Added by Sandy
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 alff 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 alff brain
%Add by Sandy Wang 20120326 for parallel computing
PF_edtOutputDir=get(handles.edtOutputDir, 'String');
PF_edtPrefix =get(handles.edtPrefix, 'String');
PF_DataDirs=handles.Cfg.DataDirs(:,1);
PF_ALFF_SamplePeriod=handles.ALFF.SamplePeriod;
PF_ALFF_BandHigh=handles.ALFF.BandHigh;
PF_ALFF_BandLow=handles.ALFF.BandLow;
PF_MaskFile=handles.Cfg.MaskFile;
PF_WantMeanAlffMap=handles.Cfg.WantMeanAlffMap;
%for x=1:size(handles.Cfg.DataDirs, 1)
tic;
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}, ...
% 'ALFF Computing','Parent');
%end
%fprintf('\nALFF :"%s"\n', handles.Cfg.DataDirs{x, 1});
fprintf('\nALFF :"%s"\n', PF_DataDirs{x});
%theOutputDir=get(handles.edtOutputDir, 'String');
%Add by Sandy Wang 20120326
%thePrefix =get(handles.edtPrefix, 'String');
theOutputDir=PF_edtOutputDir;
thePrefix=PF_edtPrefix;
theDstFile=fullfile(theOutputDir,[thePrefix,'_',GetDirName(PF_DataDirs{x})]);
%GetDirName(handles.Cfg.DataDirs{x, 1}) ] );
%add by Sandy Wang 20120326
alff( PF_DataDirs{x},...%handles.Cfg.DataDirs{x, 1}, ... add by Sandy Wang 20120326
PF_ALFF_SamplePeriod,...%handles.ALFF.SamplePeriod, ...
PF_ALFF_BandHigh,...%handles.ALFF.BandHigh, ...
PF_ALFF_BandLow,...%handles.ALFF.BandLow, ...
PF_MaskFile,...%handles.Cfg.MaskFile, ...
theDstFile);
%20070504, divide alff brain by the mean within the mask
%if strcmpi(handles.Cfg.WantMeanAlffMap, 'Yes')
%change by Sandy Wang 20120326
if strcmpi(PF_WantMeanAlffMap, 'Yes')
theOrigAlffMap=theDstFile;
theMeanAlffMap=fullfile(theOutputDir,['m',thePrefix,'_',...
GetDirName(PF_DataDirs{x})]);
%GetDirName(handles.Cfg.DataDirs{x, 1}) ] ); 20120326
%theMaskFile =handles.Cfg.MaskFile;
theMaskFile=PF_MaskFile;
rest_DivideMeanWithinMask(theOrigAlffMap, theMeanAlffMap, theMaskFile);
end
end
toc;
set(handles.listDataDirs, 'Value', size(PF_DataDirs, 1));
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 alff.m ! Please re-install');
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.figAlffMain, '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.figAlffMain, '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 compute alff 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 ckboxDivideMean_Callback(hObject, eventdata, handles)
if get(hObject,'Value')
handles.Cfg.WantMeanAlffMap ='Yes';
else
handles.Cfg.WantMeanAlffMap ='No';
end
guidata(hObject, handles);
UpdateDisplay(handles);
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 alff 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 filename to remove extension
pathname = [pathname filesep];
end
theOrigAlffMap =[pathname filename];
theMeanAlffMap =[pathname 'm' filename];
theMaskFile =handles.Cfg.MaskFile;
rest_DivideMeanWithinMask(theOrigAlffMap, theMeanAlffMap, theMaskFile);
msgbox(sprintf('Alff brain "%s.{hdr/img}" \ndivide its mean within mask successfully.\t\n\nSave to "%s.{hdr/img}"\n' , ...
theOrigAlffMap, theMeanAlffMap), ...
'Divide mean within mask successfully' ,'help');
end
catch
rest_misc( 'DisplayLastException');
end
set(hObject,'Enable','on', 'BackgroundColor', theOldColor);
drawnow;
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')
tic;
BandPass(hObject, handles);
handles =guidata(hObject);
toc;
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 InitFrames(hObject,handles)
offsetY =83; %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.figAlffMain, 'Style','Frame','Position',[2 offsetY+152 433 1]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+202 433 1]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[90 offsetY+291 343 1]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[90 offsetY+202 1 90]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+152 1 280]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[435 offsetY+152 1 280]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+432 433 1]);
uicontrol(handles.figAlffMain,'Style','Text','Position',[152 offsetY+430 100 14],...
'String','Input Parameters');
uicontrol(handles.figAlffMain,'Style','Text','Position',[208 offsetY+288 40 14],...
'String','Mask');
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+94 433 1]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY-8 433 1]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY-8 1 102]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[435 offsetY-8 1 102]);
uicontrol(handles.figAlffMain,'Style','Text','Position',[152 offsetY+88 160 14],...
'String','Output Parameters (ALFF map)');
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+450 433 1]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[435 offsetY+450 1 50]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+450 1 50]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+500 433 1]);
uicontrol(handles.figAlffMain,'Style','Text','Position',[142 offsetY+495 180 14],...
'String','Option: Ideal Band Pass Filter');
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+515 433 1]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[435 offsetY+515 1 50]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+515 1 50]);
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY+565 433 1]);
uicontrol(handles.figAlffMain,'Style','Text','Position',[142 offsetY+555 180 14],...
'String','Option: Remove Linear Trend');
%20070506, Add manual operation button groups like SPM
uicontrol(handles.figAlffMain, 'Style','Frame','Position',[2 offsetY-25 433 1]);
uicontrol(handles.figAlffMain,'Style','Text','Position',[152 offsetY-30 140 14],...
'String','Manual Operations');
function InitControlProperties(hObject, handles)
%for Linux compatible 20070507 dawnsong
% --- FIGURE -------------------------------------
set(handles.figAlffMain,...
'Units', 'pixels', ...
'Position', [20 5 440 650], ...
'Name', 'alff_gui', ...
'MenuBar', 'none', ...
'NumberTitle', 'off', ...
'Color', get(0,'DefaultUicontrolBackgroundColor'));
% --- STATIC TEXTS -------------------------------------
set(handles.txtAlff, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [16 186 91 40], ...
'FontSize', 24, ...
'FontWeight', 'bold', ...
'String', 'ALFF');
theFontSize =8;
if isunix, theFontSize =10; end
set(handles.txtAlffLongName, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [10 300 65 76], ...
'FontSize', theFontSize, ...
'FontWeight', 'normal', ...
'Enable', 'off', ...
'String', sprintf('Amplitude\nof Low\nFrequency\nFluctuation\nComputation'));
set(handles.txtOutputDir, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [8 109 80 21], ...
'FontSize', theFontSize, ...
'String', 'Directory:');
set(handles.txtInputDir, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [7 386 80 21], ...
'String', 'Data Directory:');
set(handles.txtPrefix, ...
'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.txtBandSep, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [146 526 25 51], ...
'FontSize', 28, ...
'String', '~');
set(handles.txtTR, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [230 540 40 16], ...
'String', 'TR: (s)');
set(handles.txtAlffBand, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [20 245 50 16], ...
'String', 'Band( Hz)');
set(handles.txtAlffBandSep, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [144 230 25 51], ...
'FontSize', 28, ...
'String', '~');
set(handles.txtAlffTR, ...
'Style', 'text', ...
'Units', 'pixels', ...
'Position', [230 245 40 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', [396 384 30 25], ...
'FontSize', 18, ...
'String', '...', ...
'CData', zeros(1,0));
set(handles.btnSelectMask, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [396 290 30 25], ...
'FontSize', 18, ...
'String', '...', ...
'Enable', 'off', ...
'CData', zeros(1,0));
set(handles.btnComputeAlff, ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [320 186 107 33], ...
'FontSize', 12, ...
'FontWeight', 'bold', ...
'String', 'Do all');
set(handles.btnDetrend , ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [337 603 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', [337 540 90 25], ...
'FontSize', 10, ...
'Enable', 'off', ... %Update filter and detrend button's state according to Option: detrend/Filter 20070820
'String', 'Filter');
set(handles.btnAlffBandDetail , ...
'Style', 'pushbutton', ...
'Units', 'pixels', ...
'Position', [337 244 90 25], ...
'FontSize', 10, ...
'String', 'Band Hint');
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.rbtnDefaultMask, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [110 347 158 16], ...
'String', 'Default mask');
set(handles.rbtnUserMask, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [110 321 148 16], ...
'String', 'User-defined mask');
set(handles.rbtnNullMask, ...
'Style', 'radiobutton', ...
'Units', 'pixels', ...
'Position', [277 348 82 16], ...
'String', 'No mask');
% --- CHECKBOXES -------------------------------------
set(handles.ckboxFilter, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [14 540 80 22], ...
'String', 'Band (Hz)');
set(handles.ckboxDivideMean, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [12 82 430 19], ...
'String', 'Divide ALFF brain by the mean within the mask (mPrefix_DirectoryName.{hdr/img})');
set(handles.ckboxRetrend, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [366 540 60 22], ...
'Enable', 'Off', ...
'String', 'Retrend');
set(handles.ckboxRemoveTrendBefore, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [13 605 140 21],...
'String', 'detrend'); %'String', 'detrend BEFORE Filter');
set(handles.ckboxRemoveTrendAfter, ...
'Style', 'checkbox', ...
'Units', 'pixels', ...
'Position', [171 605 140 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', [94 386 300 22], ...
'BackgroundColor', [1 1 1], ...
'String', '');
set(handles.edtMaskfile, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [94 290 300 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', 'ALFFMap');
set(handles.edtBandLow, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [94 541 50 22], ...
'BackgroundColor', [1 1 1], ...
'String', '0.01', ...
'Enable', 'off');
set(handles.edtBandHigh, ...
'Style', 'edit', ...
'Units', 'pixels', ...
'Position', [171 541 50 22], ...
'BackgroundColor', [1 1 1], ...
'String', '0.08', ...
'Enable', 'off');
set(handles.edtSamplePeriod, ...