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ivlsm.m
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ivlsm.m
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function varargout = ivlsm(varargin)
% VLSM MATLAB code for vlsm.fig
% iVLSM, by itself, creates a new VLSM or raises the existing
% singleton*.
%
% H = iVLSM returns the handle to a new VLSM or the handle to
% the existing singleton*.
%
% iVLSM('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in VLSM.M with the given input arguments.
%
% iVLSM('Property','Value',...) creates a new VLSM or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before vlsm_OpeningFcn gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to vlsm_OpeningFcn via varargin.
%
% *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
% instance to run (singleton)".
%
% See also: GUIDE, GUIDATA, GUIHANDLES
% Edit the above text to modify the response to help vlsm
% Last Modified by GUIDE v2.5 17-Mar-2017 10:09:16
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @ivlsm_OpeningFcn, ...
'gui_OutputFcn', @ivlsm_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 vlsm is made visible.
function ivlsm_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 vlsm (see VARARGIN)
% Choose default command line output for vlsm
handles.output = hObject;
% Update handles structure
warning('off','all');
guidata(hObject, handles);
vlsm_defaults(handles);
% Addpath toolbox
global VLSM
PathName = fileparts(which('ivlsm'));
VLSM.iVLSMpath = PathName;
addpath(genpath(PathName));
% UIWAIT makes vlsm wait for user response (see UIRESUME)
% uiwait(handles.figure1);
% --- Outputs from this function are returned to the command line.
function varargout = ivlsm_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;
function edit_subjlist_Callback(hObject, eventdata, handles)
global VLSM
filepath = get(hObject,'String');
VLSM.filepath = filepath;
set(handles.edit_subjlist,'String',fullfile(PathName,FileName));
% --- Executes on button press in pushbutton_subjlist.
function pushbutton_subjlist_Callback(hObject, eventdata, handles)
global VLSM
[FileName, PathName] = uigetfile({'*.xls;*.xlsx','Excel files (*.xls,*.xlsx)'});
[~,~,xls] = xlsread(fullfile(PathName,FileName));
hdr = xls(1,:);
dat = xls(2:end,:);
group=[];
for i=1:length(hdr),
if strcmpi(hdr{i},'subjname'),
subjname = dat(:,i);
elseif strcmpi(hdr{i}, VLSM.groupVar),
group = cell2mat(dat(:,i));
end
end
VLSM.subjinfo.hdr = hdr;
VLSM.subjinfo.dat = dat;
VLSM.nsubj = length(subjname);
VLSM.ngrp = length(unique(group));
VLSM.subjname = subjname;
VLSM.group = group;
VLSM.inputFile = fullfile(PathName,FileName);
text_nsubj = sprintf('Number of Subjects: %d', VLSM.nsubj);
if isempty(group),
text_ngrp = sprintf('Number of Groups: no group info');
else
text_ngrp = sprintf('Number of Groups: %d', VLSM.ngrp);
end
set(handles.edit_subjlist,'String',fullfile(PathName,FileName));
set(handles.text_nsubj,'String',text_nsubj);
set(handles.text_ngrp,'String',text_ngrp);
function edit_datapath_Callback(hObject, eventdata, handles)
global VLSM
DATApath = get(hObject,'String');
VLSM.DATApath = DATApath{1};
set(handles.edit_datapath,'String',VLSM.DATApath);
% --- Executes on button press in pushbutton_datapath.
function pushbutton_datapath_Callback(hObject, eventdata, handles)
global VLSM
DATApath = uigetdir;
VLSM.DATApath = DATApath;
set(handles.edit_datapath,'String',DATApath);
%--------------------------------------------------------------------------
% Variables for Step2: T1 (Structural Image)
%--------------------------------------------------------------------------
function edit_T1prefix_Callback(hObject, eventdata, handles)
global VLSM
VLSM.T1prefix = get(hObject,'String');
function edit_T1folder_Callback(hObject, eventdata, handles)
global VLSM
VLSM.T1folder = get(hObject,'String');
%--------------------------------------------------------------------------
% Variables for Step3: ROI (Lesion Image)
%--------------------------------------------------------------------------
function edit_ROIprefix_Callback(hObject, eventdata, handles)
global VLSM
VLSM.ROIprefix = get(hObject,'String');
function edit_ROIfolder_Callback(hObject, eventdata, handles)
global VLSM
VLSM.ROIfolder = get(hObject,'String');
%--------------------------------------------------------------------------
% Parameters for Normalization
%--------------------------------------------------------------------------
function checkbox_segment_Callback(hObject, eventdata, handles)
global VLSM;
doSeg = get(hObject,'Value');
VLSM.doSeg = doSeg;
function pushbutton_normalization_Callback(hObject, eventdata, handles)
vlsm_normalization(handles);
%--------------------------------------------------------------------------
% Parameters for Overlapping and Crosstab analysis
%--------------------------------------------------------------------------
function popupmenu_groupStat_Callback(hObject, eventdata, handles)
global VLSM;
index_input_data = get(hObject,'Value');
if index_input_data == 1,
% Overlap map
VLSM.statMethods = 'overlap';
disp('Analysis methods: Create overlay map');
elseif index_input_data == 2,
% Pearson's Chi-squared test
VLSM.statMethods = 'chi2test';
disp('Analysis methods: Pearson Chi2 Test');
else
% Logistic regression (covariates are available)
VLSM.statMethods = 'logistic';
disp('Analysis methods: Logistic Regression');
end
function edit_groupVar_Callback(hObject, eventdata, handles)
global VLSM;
groupVar = get(hObject,'String');
hdr = VLSM.subjinfo.hdr;
dat = VLSM.subjinfo.dat;
group = [];
for i=1:length(hdr),
if strcmpi(hdr{i}, groupVar),
group = cell2mat(dat(:,i));
end
end
VLSM.group = group;
VLSM.groupVar = groupVar;
VLSM.ngrp = length(unique(group));
if isempty(group),
text_ngrp = sprintf('Number of Groups: no group info');
else
text_ngrp = sprintf('Number of Groups: %d', VLSM.ngrp);
end
set(handles.text_ngrp,'String',text_ngrp);
function edit_covariates_Callback(hObject, eventdata, handles)
global VLSM;
% hObject handle to edit_covariates (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
if isempty(VLSM.inputFile),
disp('Select Subject List in Step1 ...');
return
end
covariateNames = strsplit(get(hObject,'String'),'\s*,\s*',...
'DelimiterType','RegularExpression');
nsubj = VLSM.nsubj;
hdr = VLSM.subjinfo.hdr;
dat = VLSM.subjinfo.dat;
nCovariates = 0;
if isempty(covariateNames{1}),
covariateVars = [];
covariateNames = '';
else
covariateVars = zeros(nsubj,0);
for i=1:length(covariateNames),
for j=1:length(hdr),
if strcmpi(covariateNames{i},hdr{j}),
covariateVars(:,i) = cell2mat(dat(:,j));
nCovariates = nCovariates+1;
end
end
end
end
VLSM.nCovariates = nCovariates;
VLSM.covariate.values = covariateVars;
if nCovariates>1,
VLSM.covariate.names = strjoin(covariateNames,'_');
else
VLSM.covariate.names = covariateNames;
end
%--------------------------------------------------------------------------
% Parameters for VLSM Analysis
%--------------------------------------------------------------------------
function edit_medvars_Callback(hObject, eventdata, handles)
global VLSM
vars = get(hObject,'String');
medvars = splitstrings(vars,',');
VLSM.medvars = medvars;
function edit_nMinSubj_Callback(hObject, eventdata, handles)
global VLSM
nMinSubj = str2double(get(hObject,'String'));
VLSM.nMinSubj = nMinSubj;
function popupmenu_StatMethods_Callback(hObject, eventdata, handles)
global VLSM;
index_input_data = get(hObject,'Value');
if index_input_data == 1,
% Mann-whitey U-test
VLSM.statMethods = 'mw';
elseif index_input_data == 2,
% independent t-test
VLSM.statMethods = 'ttest';
else
VLSM.statMethods = '';
end
%--------------------------------------------------------------------------
% Overlay Buttons
%--------------------------------------------------------------------------
function pushbutton_runGroup_Callback(hObject, eventdata, handles)
global VLSM
if strcmpi(VLSM.statMethods,'overlap'),
set(handles.text_status,'String', 'Creating overlay map...'); pause(0.5);
vlsm_overlay(handles);
elseif strcmpi(VLSM.statMethods,'chi2test'),
set(handles.text_status,'String', 'Performing Pearson Chi2 Test...'); pause(0.5);
vlsm_chi2tests(handles);
elseif strcmpi(VLSM.statMethods,'logistic'),
set(handles.text_status,'String', 'Performing logistic regression...'); pause(0.5);
vlsm_logistic(handles);
else
disp('Analysis methods - selection error');
end
%--------------------------------------------------------------------------
% Correlation Analysis Buttons
%--------------------------------------------------------------------------
function pushbutton_vlsm_Callback(hObject, eventdata, handles)
global VLSM;
if isempty(VLSM.statMethods),
errordlg('Specify Statistical Methods', 'Run Error');
return
end
set(handles.text_status,'String', 'Performing lesion-symptom mapping...'); pause(0.5);
vlsm_mapping(handles);
% --- Executes on button press in pushbutton_extractROIvalue.
function pushbutton_extractROIvalue_Callback(hObject, eventdata, handles)
extract
% --- Executes on button press in pushbutton_createROIs.
function pushbutton_createROIs_Callback(hObject, eventdata, handles)
create_ROI_mask
% --- Executes on button press in pushbutton_filpImages.
function pushbutton_filpImages_Callback(hObject, eventdata, handles)
imageFlip
% --- Executes on button press in pushbutton_thresholding.
function pushbutton_thresholding_Callback(hObject, eventdata, handles)
% hObject handle to pushbutton_thresholding (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)