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_GRFCorrection_gui.m
function varargout = rest_GRFCorrection_gui(varargin)
% varargout = rest_GRFCorrection_gui(varargin)
% Perform Gaussian Random Field theory multiple comparison correction
% -------------------------------------------------------------------
% GUI by Sandy Wang and ZANG Zhen-Xiang
% State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University
% Center for Cognition and Brain Disorders and The Affiliated Hospital,Hangzhou Normal University
% --------------------------------------------------------------------
% GRF_Function (rest_GRF_Threshold) by YAN Chao-Gan.
% The Nathan Kline Institute for Psychiatric Research, 140 Old Orangeburg Road, Orangeburg, NY 10962, USA
% Child Mind Institute, 445 Park Avenue, New York, NY 10022, USA
% The Phyllis Green and Randolph Cowen Institute for Pediatric
% Neuroscience, New York University Child Study Center, New York, NY 10016, USA
% --------------------------------------------------------------------
% http://www.restfmri.net
% Mail to Authors: <a href="ycg.yan@gmail.com">YAN Chao-Gan</a>; <a href="zangzx416@sina.com">ZANG Zhen-Xiang</a>;
% Version=1.0; Released: 120501
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @rest_GRFCorrection_gui_OpeningFcn, ...
'gui_OutputFcn', @rest_GRFCorrection_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 sandy_GRF_Correction is made visible.
function rest_GRFCorrection_gui_OpeningFcn(hObject, eventdata, handles, varargin)
% This function has no output args, see OutputFcn.
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% varargin command line arguments to sandy_GRF_Correction (see VARARGIN)
% Choose default command line output for sandy_GRF_Correction
handles.output = hObject;
set(handles.output_entry , 'String' , pwd);
% Update handles structure
guidata(hObject, handles);
% UIWAIT makes sandy_GRF_Correction wait for user response (see UIRESUME)
% uiwait(handles.fig_GRF_multi);
% --- Outputs from this function are returned to the command line.
function varargout = rest_GRFCorrection_gui_OutputFcn(hObject, eventdata, handles)
% varargout cell array for returning output args (see VARARGOUT);
% hObject handle to figure
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Get default command line output from handles structure
varargout{1} = handles.output;
% --- Executes on selection change in input_listbox.
function input_listbox_Callback(hObject, eventdata, handles)
% hObject handle to input_listbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: contents = cellstr(get(hObject,'String')) returns input_listbox contents as cell array
% contents{get(hObject,'Value')} returns selected item from input_listbox
% --- Executes during object creation, after setting all properties.
function input_listbox_CreateFcn(hObject, eventdata, handles)
% hObject handle to input_listbox (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: listbox 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 input_pushbutton.
function input_pushbutton_Callback(hObject, eventdata, handles)
% hObject handle to input_pushbutton (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[input_filename , input_pathname]=uigetfile({'*.img;*.nii;*.nii.gz','Brain Image Files (*.img;*.nii;*.nii.gz)';'*.*', 'All Files (*.*)';}, ...
'Pick statistical maps' , 'MultiSelect' , 'On');
if (ischar(input_filename) || iscell(input_filename)) && ischar(input_pathname)
present_list=get(handles.input_listbox , 'String');
if iscell(input_filename)
for i=1:size(input_filename , 2)
if isempty(present_list)
present_list={[input_pathname , input_filename{i}]};
else
present_list=...
[present_list , {[input_pathname , input_filename{i}]}];
end
end
else
if isempty(present_list)
present_list={[input_pathname , input_filename]};
else
present_list=[present_list , {[input_pathname , input_filename]}];
end
end
set(handles.input_listbox , 'String' , present_list);
set(handles.input_listbox , 'Value' , size(present_list ,2));
end
function mask_entry_Callback(hObject, eventdata, handles)
% hObject handle to mask_entry (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of mask_entry as text
% str2double(get(hObject,'String')) returns contents of mask_entry as a double
% --- Executes during object creation, after setting all properties.
function mask_entry_CreateFcn(hObject, eventdata, handles)
% hObject handle to mask_entry (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 mask_pushbutton.
function mask_pushbutton_Callback(hObject, eventdata, handles)
% hObject handle to mask_pushbutton (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
[RESTPath , Filename , extn]=fileparts(which('rest.m'));
RESTMask=[RESTPath , filesep , 'mask'];
current_directory=pwd;
cd(RESTMask);
[mask_filename , mask_pathname]=uigetfile({'*.img;*.nii;*.nii.gz','Brain Image Files (*.img;*.nii;*.nii.gz)';'*.*', 'All Files (*.*)';}, ...
'Pick one mask file');
cd(current_directory);
mask_entry=[mask_pathname,mask_filename];
if ischar(mask_entry)
set(handles.mask_entry , 'String' , mask_entry);
end
function voxel_entry_Callback(hObject, eventdata, handles)
% hObject handle to voxel_entry (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of voxel_entry as text
% str2double(get(hObject,'String')) returns contents of voxel_entry as a double
% --- Executes during object creation, after setting all properties.
function voxel_entry_CreateFcn(hObject, eventdata, handles)
% hObject handle to voxel_entry (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function cluster_entry_Callback(hObject, eventdata, handles)
% hObject handle to voxel_entry (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of voxel_entry as text
% str2double(get(hObject,'String')) returns contents of voxel_entry as a double
% --- Executes during object creation, after setting all properties.
function cluster_entry_CreateFcn(hObject, eventdata, handles)
% hObject handle to voxel_entry (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
% Hint: edit controls usually have a white background on Windows.
% See ISPC and COMPUTER.
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
set(hObject,'BackgroundColor','white');
end
function output_entry_Callback(hObject, eventdata, handles)
% hObject handle to output_entry (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
% Hints: get(hObject,'String') returns contents of output_entry as text
% str2double(get(hObject,'String')) returns contents of output_entry as a double
% --- Executes during object creation, after setting all properties.
function output_entry_CreateFcn(hObject, eventdata, handles)
% hObject handle to output_entry (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 output_pushbutton.
function output_pushbutton_Callback(hObject, eventdata, handles)
% hObject handle to output_pushbutton (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
output_dir=uigetdir('Please pick a directory');
set(handles.output_entry , 'String' , output_dir);
% --- Executes on button press in run_pushbutton.
function run_pushbutton_Callback(hObject, eventdata, handles)
% hObject handle to run_pushbutton (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
check_tag=0;
if isempty(get(handles.input_listbox , 'String'))
check_warning(handles.input_listbox);
check_tag=1;
end
if isempty(get(handles.voxel_entry , 'String'))
check_warning(handles.voxel_entry);
check_tag=1;
end
if isempty(get(handles.voxel_entry , 'String'))
check_warning(handles.voxel_entry);
check_tag=1;
end
if check_tag==1
return;
end
is_two_tag=get(handles.two_tail , 'Value');
mask_file=get(handles.mask_entry , 'String');
voxel_p=str2num(get(handles.voxel_entry , 'String'));
cluster_p=str2num(get(handles.cluster_entry , 'String'));
input=get(handles.input_listbox , 'String');
output_path=get(handles.output_entry , 'String');
try
set(handles.input_listbox , 'Value' , 1);
for i=1:size(input ,2)
[Data VoxelSize Header]=rest_readfile(input{i});
[input_path , input_name , input_ext]=fileparts(input{i});
if isfield(Header,'descrip')
headinfo=Header.descrip;
testDf2=0;
if ~isempty(strfind(headinfo,'{T_['))% dong 100331 begin
testFlag='T';
Tstart=strfind(headinfo,'{T_[')+length('{T_[');
Tend=strfind(headinfo,']}')-1;
testDf = str2num(headinfo(Tstart:Tend));
elseif ~isempty(strfind(headinfo,'{F_['))
testFlag='F';
Tstart=strfind(headinfo,'{F_[')+length('{F_[');
Tend=strfind(headinfo,']}')-1;
F_Df = str2num(headinfo(Tstart:Tend));
testDf=F_Df(1,1);
testDf2=F_Df(1,2);
elseif ~isempty(strfind(headinfo,'{R_['))
testFlag='R';
Tstart=strfind(headinfo,'{R_[')+length('{R_[');
Tend=strfind(headinfo,']}')-1;
testDf = str2num(headinfo(Tstart:Tend));
elseif ~isempty(strfind(headinfo,'{Z_['))
testFlag='Z';
Tstart=strfind(headinfo,'{Z_[')+length('{Z_[');
Tend=strfind(headinfo,']}')-1;
testDf = str2num(headinfo(Tstart:Tend));
end
end
rest_GRF_Threshold(input{i},... %rest_GRF_Threshold(Data,...
voxel_p,...
is_two_tag,...
cluster_p,...
[output_path , filesep , input_name],...
mask_file,...
testFlag,...
testDf,...
testDf2,...
VoxelSize,...
Header); %rest_GRF_Threshold by YAN Chao-Gan
end
catch
rest_misc( 'DisplayLastException');
end
function check_warning(UIcontrol)
set(UIcontrol , 'BackgroundColor' , 'Red');
pause(0.1);
set(UIcontrol , 'BackgroundColor' , 'White');
pause(0.1);
set(UIcontrol , 'BackgroundColor' , 'Red');
pause(0.1);
set(UIcontrol , 'BackgroundColor' , 'White');
pause(0.1);
set(UIcontrol , 'BackgroundColor' , 'Red');
pause(0.1);
set(UIcontrol , 'BackgroundColor' , 'White');
pause(0.1);
function two_tail_Callback(hObject, eventdata, handles)
% --- Executes when selected object is changed in tail_panel.
function tail_panel_SelectionChangeFcn(hObject, eventdata, handles)
% hObject handle to the selected object in tail_panel
% eventdata structure with the following fields (see UIBUTTONGROUP)
% EventName: string 'SelectionChanged' (read only)
% OldValue: handle of the previously selected object or empty if none was selected
% NewValue: handle of the currently selected object
% handles structure with handles and user data (see GUIDATA)
is_two_tag=get(handles.two_tail , 'Value');
if is_two_tag
uiwait(msgbox('The "two-tailed" option is doing as following (e.g., if set VoxelPThreshold = 0.01 and cluster level p<0.05): 1) Get Group A > Group B, set Z>2.576 (two-tailed p <0.01) and cluster level p<0.025 2) Get Group A < Group B, set a Z<-2.576 (two-tailed p <0.01) and cluster level p<0.025. 3) Add 1 and 2 together, which could ensure the total p<0.05.','Two-tailed'));
end