eegmp_analysis/tools/[MEG]PLS/MEGPLS_PIPELINE_v2.02b/ViewNiftiAfni.m

function varargout = ViewNiftiAfni(varargin)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Visualization HUB for viewing 3D or 4D NIFTI and AFNI files. %
% Last modified: Feb. 26, 2014                                 %
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

% Copyright (C) 2013-2014, Michael J. Cheung
%
% This file is a part of the MEG & PLS Pipeline (MEGPLS). For more 
% details, see the documentation included with the software package.
%
% MEGPLS is free software: you can redistribute it and/or modify it under
% the terms of the GNU General Public License version 2 as published by 
% the Free Software Foundation. This program is distributed in the hope 
% that it will be useful, but WITHOUT ANY WARRANTY; without even the 
% implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. 
% See the GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License along
% with this program. If not, you can download the license here: 
% <http://www.gnu.org/licenses/old-licenses/gpl-2.0>.


% Last Modified by GUIDE v2.5 28-Nov-2013 16:27:01

% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name',       mfilename, ...
                   'gui_Singleton',  gui_Singleton, ...
                   'gui_OpeningFcn', @ViewNiftiAfni_OpeningFcn, ...
                   'gui_OutputFcn',  @ViewNiftiAfni_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 ViewNiftiAfni is made visible. ---%
%------------------------------------------------------------%
function ViewNiftiAfni_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 ViewNiftiAfni (see VARARGIN)

% Choose default command line output for ViewNiftiAfni
handles.output = hObject;


% Make sure toolbox paths are added:
[PipelineDir, ~, ~] = fileparts(which('ViewNiftiAfni.m'));

addpath(genpath(PipelineDir));
rmpath([PipelineDir,'/DEFAULT_SETTINGS']);  % Make sure its calling from AnalysisID
rmpath([PipelineDir,'/TEMPORARY_FIXES']);   % Make sure its calling from FT toolbox

CheckToolboxPaths(PipelineDir);


% Initialize variables:
handles.paths.SelectedAnatFile = ...
    [PipelineDir,'/MEGPLS_TOOLBOX/Masks_Templates/template_ch2+tlrc.BRIK'];
set(handles.TextboxAnatFile, 'String', handles.paths.SelectedAnatFile);

handles.gui.NiftiAfniList      = [];
handles.paths.NiftiAfniDir     = [];
handles.paths.SelectedFuncFile = [];


% Update handles structure
guidata(hObject, handles);

% UIWAIT makes ViewNiftiAfni wait for user response (see UIRESUME)
% uiwait(handles.figure1);


%--- Outputs from this function are returned to the command line. ---%
%--------------------------------------------------------------------%
function varargout = ViewNiftiAfni_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;




%====================================%
% FUNCTIONS FOR ANATOMICAL UNDERLAY: %
%====================================%

%--- Textbox to display selected anatomical .BRIK file: ---%
%----------------------------------------------------------%
function TextboxAnatFile_Callback(hObject, eventdata, handles)
EnteredText = get(handles.TextboxAnatFile, 'String');

if ~isequal(EnteredText, handles.paths.SelectedAnatFile)
    set(handles.TextboxAnatFile, 'String', handles.paths.SelectedAnatFile);
    msgbox('Note: Use button to change anatomy file.');
end


%--- Executes on button press in ButtonAnatFile. ---%
%---------------------------------------------------%
function ButtonAnatFile_Callback(hObject, eventdata, handles)
[AnatPath, ~, ~]     = fileparts(handles.paths.SelectedAnatFile);
[BrikFile, BrikPath] = uigetfile([AnatPath,'/*+tlrc.BRIK'], ...
    'Select anatomical underlay .BRIK file.', 'MultiSelect', 'off');

if BrikFile == 0
    return;  % If user cancels
end

% Set anatomy file:
handles.paths.SelectedAnatFile = [BrikPath,BrikFile];
set(handles.TextboxAnatFile, 'String', handles.paths.SelectedAnatFile)

% Save handles:
guidata(hObject, handles);




%=============================================%
% FUNCTIONS FOR AFNI OR NIFTI FILE SELECTION: %
%=============================================%

%--- Textbox to display selected target directory: ---%
%-----------------------------------------------------%
function TextboxNiftiAfniDir_Callback(hObject, eventdata, handles)
EnteredText = get(handles.TextboxNiftiAfniDir, 'String');

if ~isequal(EnteredText, handles.paths.NiftiAfniDir)
    set(handles.TextboxNiftiAfniDir, 'String', handles.paths.NiftiAfniDir);
    msgbox('Note: Use button to change search directory.');
end


%--- Executes on selection change in ListboxNiftiAfniFiles. ---%
%---------------------------------------------------------------%
function ListboxNiftiAfniFiles_Callback(hObject, eventdata, handles)
if isempty(handles.paths.NiftiAfniDir) || isempty(handles.gui.NiftiAfniList)
    return;
end

handles = DetectSelectedFiles(handles);
guidata(hObject, handles);


%--- Executes on button press in ButtonNiftiAfniDir. ---%
%--------------------------------------------------------%
function ButtonNiftiAfniDir_Callback(hObject, eventdata, handles)
if ~isempty(handles.paths.NiftiAfniDir)
    [OneUpDir, ~, ~] = fileparts(handles.paths.NiftiAfniDir);
else
    OneUpDir = [];
end

SelectedPath = uigetdir(OneUpDir, 'Select directory for AFNI or NIFTI files:');
if SelectedPath == 0
    return;  % If user cancels
end

% Get list of AFNI & NIFTI files:
AfniFiles  = dir([SelectedPath,'/*+tlrc.BRIK']);
NiftiFiles = dir([SelectedPath,'/*.nii']);
if isempty(AfniFiles) && isempty(NiftiFiles)
    msgbox('Error: No AFNI or NIFTI files found inside directory.', 'Error:')
    return;
end

% Set current path and available files:
handles.paths.NiftiAfniDir = SelectedPath;
set(handles.TextboxNiftiAfniDir, 'String', handles.paths.NiftiAfniDir);

AfniFiles  = {AfniFiles.name}';
NiftiFiles = {NiftiFiles.name}';
handles.gui.NiftiAfniList = [AfniFiles; NiftiFiles];

handles = UpdateNiftiAfniListbox (handles);
handles = DetectSelectedFiles    (handles);

% Save handles:
guidata(hObject, handles);


%--- Acquire currently selected NIFTI / AFNI file: ---%
%-----------------------------------------------------%
function OutputHandles = DetectSelectedFiles(InputHandles)
handles = InputHandles;

% Get selected file:
SelectedIndex = get(handles.ListboxNiftiAfniFiles, 'Value');
SelectedFile  = handles.gui.NiftiAfniList{SelectedIndex};

handles.paths.SelectedFuncFile = [];
handles.paths.SelectedFuncFile = strcat([handles.paths.NiftiAfniDir,'/'], SelectedFile);

% Set output handles:
OutputHandles = handles;


%--- Update NIFTI / AFNI settings: ---%
%-------------------------------------%
function OutputHandles = UpdateNiftiAfniListbox(InputHandles)
handles = InputHandles;

% Update AFNI / NIFTI listbox:
set(handles.ListboxNiftiAfniFiles, 'String', handles.gui.NiftiAfniList);

CurrentIndex = get(handles.ListboxNiftiAfniFiles, 'Value');
MaxIndex     = length(handles.gui.NiftiAfniList);
if isempty(CurrentIndex) || CurrentIndex == 0 || CurrentIndex > MaxIndex
    set(handles.ListboxNiftiAfniFiles, 'Value', MaxIndex);
end

% Set output handles:
OutputHandles = handles;




%=========================%
% FUNCTIONS FOR PLOTTING: %
%=========================%

%--- Executes on button press in ButtonTimeLegend. ---%
%-----------------------------------------------------%
function ButtonTimeLegend_Callback(hObject, eventdata, handles)
if isempty(handles.paths.NiftiAfniDir)
    msgbox('Error: Directory for AFNI / NIFTI files not selected.', 'Error:')
    return;
end

[LegendFile, LegendPath] = uigetfile([handles.paths.NiftiAfniDir,'/*_TimeLegend.txt'], ...
    'Select TimeLegend file to load:', 'MultiSelect', 'off');

if LegendFile == 0
    return;  % If user cancels
else
    open([LegendPath,LegendFile]);
end


%--- Converts NIFTI file to temporary AFNI for viewing: ---%
%----------------------------------------------------------%
function OutputAfni = ConvertNifti2Afni(InputNifti)

% Get parameters for conversion to AFNI:
[NiiFolder, NiiName, ~] = fileparts(InputNifti);
TempAfniFile            = [NiiFolder,'/',NiiName,'+tlrc.BRIK'];

prompt = {'Associate NIFTI file with what template for AFNI conversion?';
    'Note: If file was generated by MEGPLS pipeline, choose MNI.'}
AfniSpace = questdlg(prompt, 'Template?', 'mni', 'tlrc', 'orig', 'mni');

PipeSettings.Afni4D.NaNFix   = 'yes';
PipeSettings.Afni4D.Template = AfniSpace;

% Convert selected NIFTI file to AFNI:
if exist(TempAfniFile, 'file')
    delete(TempAfniFile);
    delete([NiiFolder,'/',NiiName,'+tlrc.HEAD']);
end

CheckSavePath(TempAfniFile, 'ViewNiftiAfni');
MEGpipeline_Nifti2Afni_Guts(PipeSettings, InputNifti, TempAfniFile);

% Set output AFNI file:
OutputAfni = TempAfniFile;


%--- Executes on button press in ButtonView4DBRIK. ---%
%-----------------------------------------------------%
function ButtonView4DBRIK_Callback(hObject, eventdata, handles)
if isempty(handles.paths.SelectedAnatFile)
    msgbox('Error: Anatomical underlay not selected.', 'Error:');
    return;
end
if isempty(handles.paths.NiftiAfniDir)
    msgbox('Error: AFNI / NIFTI directory not selected.', 'Error:');
    return;
end
if isempty(handles.paths.SelectedFuncFile)
    msgbox('Error: AFNI / NIFTI file not selected.', 'Error:');
    return;
end

% Check if paths have spaces in them (AFNI paths cannot support spaces):
CheckSpaces1 = strfind(handles.paths.NiftiAfniDir, ' ');
CheckSpaces2 = strfind(handles.paths.SelectedAnatFile, ' ');
CheckSpaces3 = strfind(handles.paths.SelectedFuncFile, ' ');
if ~isempty(CheckSpaces1) || ~isempty(CheckSpaces2) || ~isempty(CheckSpaces3)
    msgbox('Error: AFNI fcns cannot read folder & file paths containing spaces.', 'Error:')
    return;
end

% Update selected files:
handles = UpdateNiftiAfniListbox (handles);
handles = DetectSelectedFiles    (handles);

% Create temp viewing directory:
TempViewFolder = [handles.paths.NiftiAfniDir,'/TEMP_VIEWER_FILES'];

if ~exist(TempViewFolder, 'dir')
    status = mkdir(TempViewFolder);
    
    if status == 0
        msgbox('Error: Failed to create viewing folder in selected directory.');
        return;
    end
end

% Get temp file paths:
[~, AnatFile, AnatExt] = fileparts(handles.paths.SelectedAnatFile);
[~, FuncFile, FuncExt] = fileparts(handles.paths.SelectedFuncFile);

TempAnatFile = [TempViewFolder,'/',AnatFile,AnatExt];
TempFuncFile = [TempViewFolder,'/',FuncFile,FuncExt];

if exist(TempAnatFile, 'file')
    delete(TempAnatFile);
    delete([TempViewFolder,'/',AnatFile,'.HEAD']);
end
if exist(TempFuncFile, 'file')
    delete(TempFuncFile);
    
    if strcmp(FuncExt, '.BRIK')
        delete([TempViewFolder,'/',FuncFile,'.HEAD']);
    end
end

% Copy func file to temp view folder & convert to AFNI if needed:
if strcmp(FuncExt, '.nii')
    copyfile(handles.paths.SelectedFuncFile, TempFuncFile, 'f');
    TempFuncFile = ConvertNifti2Afni(TempFuncFile);
    
elseif strcmp(FuncExt, '.BRIK')
    system(['3dcopy ',handles.paths.SelectedFuncFile,' ',TempFuncFile]);
    
end

% Copy anatomy file to temp view folder & resample if needed:
system(['3dcopy ',handles.paths.SelectedAnatFile,' ',TempAnatFile]);
TempAnatFile = MEGpipeline_AfniResampleAnat(TempAnatFile, TempFuncFile);

if isempty(TempAnatFile)
    msgbox('Error: Failed to resample anatomy file.', 'Error:');
    return;
end

% Check if file is 4D:
CurrentDir = pwd;
Opt.format = 'vector';

cd(TempViewFolder);
[~, CheckFunc, ~, ~] = BrikLoad(TempFuncFile, Opt);
cd(CurrentDir);

if numel(size(CheckFunc)) ~= 4
    msgbox('Error: Selected file is not 4D file. Use "View in AFNI" instead.');
    return;
end

% Run View4D_BRIK:
View4D_BRIK(TempAnatFile, TempFuncFile, [], []);


%--- Executes on button press in ButtonViewAFNI. ---%
%---------------------------------------------------%
function ButtonViewAFNI_Callback(hObject, eventdata, handles)
if isempty(handles.paths.SelectedAnatFile)
    msgbox('Error: Anatomical underlay not selected.', 'Error:');
    return;
end
if isempty(handles.paths.NiftiAfniDir)
    msgbox('Error: AFNI /NIFTI directory not selected.', 'Error:');
    return;
end
if isempty(handles.paths.SelectedFuncFile)
    msgbox('Error: AFNI / NIFTI file not selected.', 'Error:');
    return;
end

% Check if paths have spaces in them (AFNI paths cannot support spaces):
CheckSpaces1 = strfind(handles.paths.NiftiAfniDir, ' ');
CheckSpaces2 = strfind(handles.paths.SelectedAnatFile, ' ');
CheckSpaces3 = strfind(handles.paths.SelectedFuncFile, ' ');
if ~isempty(CheckSpaces1) || ~isempty(CheckSpaces2) || ~isempty(CheckSpaces3)
    msgbox('Error: AFNI fcns cannot read folder & file paths containing spaces.', 'Error:')
    return;
end

% Update selected files:
handles = UpdateNiftiAfniListbox (handles);
handles = DetectSelectedFiles    (handles);

% Create temp viewing directory:
TempViewFolder = [handles.paths.NiftiAfniDir,'/TEMP_VIEWER_FILES'];

if ~exist(TempViewFolder, 'dir')
    status = mkdir(TempViewFolder);
    
    if status == 0
        msgbox('Error: Failed to create viewing folder in selected directory.');
        return;
    end
end

% Get temp file paths:
[~, AnatFile, AnatExt] = fileparts(handles.paths.SelectedAnatFile);
[~, FuncFile, FuncExt] = fileparts(handles.paths.SelectedFuncFile);

TempAnatFile = [TempViewFolder,'/',AnatFile,AnatExt];
TempFuncFile = [TempViewFolder,'/',FuncFile,FuncExt];

if exist(TempAnatFile, 'file')
    delete(TempAnatFile);
    delete([TempViewFolder,'/',AnatFile,'.HEAD']);
end
if exist(TempFuncFile, 'file')
    delete(TempFuncFile);
    
    if strcmp(FuncExt, '.BRIK')
        delete([TempViewFolder,'/',FuncFile,'.HEAD']);
    end
end

% Copy func file to temp view folder & convert to AFNI if needed:
if strcmp(FuncExt, '.nii')
    copyfile(handles.paths.SelectedFuncFile, TempFuncFile, 'f');
    TempFuncFile = ConvertNifti2Afni(TempFuncFile);
    
elseif strcmp(FuncExt, '.BRIK')
    system(['3dcopy ',handles.paths.SelectedFuncFile,' ',TempFuncFile]);
    
end

% Copy anatomy file to temp view folder & create resample if needed:
% Note: Do not change TempAnatFile to resampled version (want high-res as default input).
system(['3dcopy ',handles.paths.SelectedAnatFile,' ',TempAnatFile]);
ResampledAnat = MEGpipeline_AfniResampleAnat(TempAnatFile, TempFuncFile);

if isempty(ResampledAnat)
    msgbox('Warning: Failed to resample anatomy file.', 'Error:');
end

% Prepare file calls to AFNI:
[~, AnatName, ~]    = fileparts(TempAnatFile);
AnatName(end-4:end) = [];  % Remove +view label

[~, FuncName, ~]    = fileparts(TempFuncFile);
FuncName(end-4:end) = [];

% Set environmental variables:
setenv('AFNI_SLAVE_FUNCTIME',    'YES');    % Locks overlay with time-index (Newer versions).
setenv('AFNI_SLAVE_BUCKETS_TOO', 'YES');    % Locks overlay with time-index (Older versions).
setenv('AFNI_SLAVE_THRTIME',     'YES');    % Locks threshold with time-index (Older versions).
setenv('AFNI_SLAVE_THROLAY',     'OLay');   % Locks threshold with time-index (Newer versions).
setenv('AFNI_LEFT_IS_LEFT',      'YES');    % Sets images to neurological view.
setenv('AFNI_THRESH_AUTO',       'NO');     % Threshold slider does not change automatically.
setenv('AFNI_THRESH_LOCK',       'VALUE');
setenv('AFNI_FLOATSCAN',         'YES');

if strcmp(getenv('AFNI_LEFT_IS_LEFT'), 'NO')
    msgbox('NOTE: "AFNI_LEFT_IS_LEFT" env. variable is now set to ''YES''.')
end

% Open AFNI command:
CmdLine = ['afni -com '''               ...
    'OPEN_WINDOW A.axialimage;'        ...
    ' OPEN_WINDOW A.sagittalimage;'     ...
    ' OPEN_WINDOW A.coronalimage;'      ...
    ' SWITCH_UNDERLAY A.',AnatName,';'  ...  % Underlay .BRIK
    ' SWITCH_OVERLAY A.',FuncName,';'   ...  % Overlay .BRIK
    ' SET_SUBBRICKS A 1 1 1;'           ...  % Sets .BRIK index to 1
    ' SET_FUNC_AUTORANGE A.+;'          ...  % Turns ON autorange
    ' REDISPLAY;'' &'];
    
CurrentDir = pwd;
cd(TempViewFolder);

system(CmdLine);
cd(CurrentDir);




%============================%
% GUIDE CREATEFCN FUNCTIONS: %
%============================%

% --- Executes during object creation, after setting all properties.
function TextboxAnatFile_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end

% --- Executes during object creation, after setting all properties.
function TextboxNiftiAfniDir_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end
% --- Executes during object creation, after setting all properties.
function ListboxNiftiAfniFiles_CreateFcn(hObject, eventdata, handles)
if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
    set(hObject,'BackgroundColor','white');
end