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cat12.m
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cat12.m
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function varargout = cat12(varargin)
% ______________________________________________________________________
% CAT12 Toolbox wrapper to start CAT with different user modes or
% default files. Changing the user mode requires restarting of CAT and
% SPM. The expert user mode allows to control further parameters and
% semi-evaluated functions, whereas the developer mode contain parameter
% for internal tests and unsafe functions.
%
% cat12(action)
%
% CAT user modes:
% action = ['default','expert','developer']
%
% CAT default files for other species (in development):
% action = ['oldwoldmonkeys'|'greaterapes'|'macaque'|'baboon'| ...
% 'chimpanzee']
%
% CAT start with own default files:
% action = 'select'
% action = 'mypath/cat_defaults_mydefaults'
%
% CAT12 M-file for cat12.fig
% CAT12, by itself, creates a new CAT12 or raises the existing
% singleton*.
%
% H = CAT12 returns the handle to a new CAT12 or the handle to
% the existing singleton*.
%
% CAT12('CALLBACK',hObject,eventData,handles,...) calls the local
% function named CALLBACK in CAT12.M with the given input arguments.
%
% CAT12('Property','Value',...) creates a new CAT12 or raises the
% existing singleton*. Starting from the left, property value pairs are
% applied to the GUI before DEM_demo_OpeningFunction gets called. An
% unrecognized property name or invalid value makes property application
% stop. All inputs are passed to cat12_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
% Turn off gifti data warning in gifti/subsref (line 45)
% Warning: A value of class "int32" was indexed with no subscripts specified.
% Currently the result of this operation is the indexed value itself,
% but in a future release, it will be an error.
% ______________________________________________________________________
%
% Christian Gaser, Robert Dahnke
% Structural Brain Mapping Group (https://neuro-jena.github.io)
% Departments of Neurology and Psychiatry
% Jena University Hospital
% ______________________________________________________________________
% $Id$
%#ok<*NASGU,*INUSD,*DEFNU>
global sz sc FS catversion expert cat_bg
warning('off','MATLAB:subscripting:noSubscriptsSpecified');
if nargin==0
spm_cat12;
return;
elseif nargin==1 && ~strcmp(varargin{1},'fig')
spm_cat12(varargin{1});
return;
elseif nargin==2 && ~strcmp(varargin{1},'fig')
spm_cat12(varargin{1},varargin{2});
return;
end
% do some initializations if called for the first time
if nargin <= 1
expert = cat_get_defaults('extopts.expertgui');
WSM = spm('WinSize','M');
sc = max(1,(WSM(4)/550));
sz = sc*[391 550]; % window size
[catversion.rel, catversion.ver, catversion.dat] = cat_version;
% check for update and send Matlab version with 10s delay
if strcmpi(spm_check_version,'octave')
call_server;
else
try
start(timer('StartDelay',10,'TimerFcn',@call_server));
catch
call_server;
end
end
cat_bg = imread(fullfile(fileparts(mfilename('fullpath')),'doc','images','cat_bg.jpg'));
% get default font size
FS = cat_get_defaults('extopts.fontsize');
if isempty(FS)
FS = get(0,'defaultuicontrolFontSize');
end
FS = max(9, FS);
end
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @cat12_OpeningFcn, ...
'gui_OutputFcn', @cat12_OutputFcn, ...
'gui_LayoutFcn', @cat12_LayoutFcn, ...
'gui_Callback', []);
if nargin && ~strcmp(varargin{1},'fig') && 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 cat12 is made visible.
function cat12_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 cat12 (see VARARGIN)
% Choose default command line output for cat12
handles.output = hObject;
% Update handles structure
guidata(hObject, handles);
% enable/disable different menus if TFCE is installed or not
if exist('spm_TFCE')
set(handles.popupTFCEToolbox,'String',{center('TFCE'),'Call TFCE Toolbox'});
else
set(handles.popupTFCEToolbox,'String',{center('TFCE'),'Install TFCE Toolbox'});
end
% --- Outputs from this function are returned to the command line.
function varargout = cat12_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)
global sz sc FS expert cat_bg
spm_clf('Interactive');
% Get default command line output from handles structure
varargout{1} = handles.output;
species = cat_get_defaults('extopts.species');
switch expert
case 1, set(handles.CAT,'color', [0.85 0.85 0.85]);
case 2, set(handles.CAT,'color', [0.93 0.93 0.93]);
end
% This creates the 'background' image
handles.ma = axes('parent',handles.CAT,'units','pixels','position',[1 1 sz]);
imagesc(cat_bg,'parent',handles.ma);
axis('off');
text(sz(1)/20,sc*80,'Computational Anatomy Toolbox','Color',[1 1 1],'Fontsize',FS+5,'Fontweight','bold');
switch species
case 'human', speciesdisp = '';
case 'ape_greater', speciesdisp = ' (greater apes)';
case 'ape_lesser', speciesdisp = ' (lesser apes)';
case 'monkey_oldworld', speciesdisp = ' (oldworld monkeys)';
case 'monkey_newworld', speciesdisp = ' (newworld monkeys)';
case 'chimpanzee', speciesdisp = ' (chimpanzee)';
case 'baboon', speciesdisp = ' (baboons)';
case 'macaque', speciesdisp = ' (macaques)';
case 'dog', speciesdisp = ' (dogs)';
case 'canine', speciesdisp = ' (canine)';
otherwise, speciesdisp = '';
end
switch expert
case 1, text(sz(1)/20,sc*105,['Expert Mode' speciesdisp],'Color',[0.1 0.7 1.0],'Fontsize',FS+3,'Fontweight','bold');
case 2, text(sz(1)/20,sc*105,['Developer Mode' speciesdisp],'Color',[1.0 0.0 0.0],'Fontsize',FS+3,'Fontweight','bold');
end
guidata(hObject, handles);
% --- Executes during object creation, after setting all properties.
function CAT_CreateFcn(hObject, eventdata, handles)
% hObject handle to CAT (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles empty - handles not created until after all CreateFcns called
%-------------------------------------------------------------------
% --- Executes on button press in pushSegment.
function pushSegment_Callback(hObject, eventdata, handles)
spm_jobman('interactive','','spm.tools.cat.estwrite');
% --- Executes on button press in pushSegmentLong.
function pushSegmentLong_Callback(hObject, eventdata, handles)
spm_jobman('interactive','','spm.tools.cat.long');
% --- Executes on button press in pushResampleSmooth.
function pushResampleSmooth_Callback(hObject, eventdata, handles)
spm_jobman('interactive','','spm.tools.cat.stools.surfresamp');
% --- Executes on button press in pushDisplaySurfaces.
function pushDisplaySurfaces_Callback(hObject, eventdata, handles)
cat_surf_display;
% --- Executes on button press in pushQuickStartGuide.
function pushQuickStartGuide_Callback(hObject, eventdata, handles)
web(fullfile(fileparts(which('cat12')),'doc','index.html#quick'));
% --- Executes on button press in pushMode.
function pushMode_Callback(hObject, eventdata, handles)
global expert
if expert
spm_cat12;
else
spm_cat12('expert');
end
% --- Executes on button press in pushBasicModels.
function pushBasicModels_Callback(hObject, eventdata, handles)
spm_jobman('interactive','','spm.tools.cat.factorial_design');
% --- Executes on button press in pushEstimateSurfaceModels.
function pushEstimateSurfaceModels_Callback(hObject, eventdata, handles)
cat_stat_spm;
% --- Executes on button press in pushROIAnalysis.
function pushROIAnalysis_Callback(hObject, eventdata, handles)
cat_stat_analyze_ROIs;
% --- Executes on button press in pushGetTIV.
function pushGetTIV_Callback(hObject, eventdata, handles)
spm_jobman('interactive','','spm.tools.cat.tools.calcvol');
% --- Executes on selection change in popupTFCEToolbox.
function popupTFCEToolbox_Callback(hObject, eventdata, handles)
% Hints: contents = cellstr(get(hObject,'String')) returns popupTFCEToolbox contents as cell array
% contents{get(hObject,'Value')} returns selected item from popupTFCEToolbox
if get(hObject,'Value') == 2
if exist('spm_TFCE')
% call TFCE toolbox
spm_jobman('interactive','','spm.tools.tfce_estimate');
spm_TFCE;
else % install TFCE toolbox
cat_install_tfce(1);
end
end
%-------------------------------------------------------------------
% --- Creates and returns a handle to the GUI figure.
function h0 = cat12_LayoutFcn(policy)
persistent hsingleton;
global sz sc FS x2w expert catversion cat_bg
appdata = [];
appdata.GUIDEOptions = struct(...
'active_h', [], ...
'taginfo', struct(...
'figure', 2, ...
'uipanel', 38, ...
'text', 13, ...
'axes', 7, ...
'pushbutton', 175, ...
'popupmenu', 18, ...
'togglebutton', 2, ...
'activex', 2), ...
'override', 1, ...
'release', 13, ...
'resize', 'simple', ...
'accessibility', 'callback', ...
'mfile', 1, ...
'callbacks', 1, ...
'singleton', 1, ...
'syscolorfig', 0, ...
'blocking', 0);
appdata.lastValidTag = 'CAT';
appdata.GUIDELayoutEditor = [];
appdata.initTags = struct(...
'handle', [], ...
'tag', 'CAT');
%PF = spm_platform('fonts'); %-Font names (for this platform)
Fgraph = spm_figure('GetWin','Graphics');
WSG = get(Fgraph,'Position');
% close existing cat12 window
Tag = 'CAT';
F = findall(allchild(0),'Flat','Tag',Tag);
if ~isempty(F), close(F); end
%-------------------------------------------------------------------
% gui positions
x2 = sc*[27 201]; % x-pos two columns
bh = 26; % button height
x2w = sc*163; % width button/popupmenu for two columns
th = sc*(FS+5); % text field height
tw = sc*333; % text field width
yo = sc*30; % y-offset of button field from bottom
yd = sc*30; % y-distance between buttons
to = sc*[-10 0 20 0];% offset for correcting text fields
bo = [to(1) -0.15*yd*sc to(3) -0.4*yd*sc]; % offset for correcting background box
tg = [tw*1.5,tw*1.5]; % resolution adaptation for menu panels
if ismac
if cat_io_matlabversion>20110
po = [-3 -2 7 0]; % offset for correcting popup menus
else
po = [-1 -3 3 0]; % offset for correcting popup menus
end
else
po = [0 0 0 0];
end
%-------------------------------------------------------------------
h0 = figure(...
'PaperUnits','inches',...
'Units','pixels',...
'Position',[WSG(1)+WSG(3)+5 WSG(2)+WSG(4)-sz(2)+25 sz(1) sz(2)],...
'Visible',get(0,'defaultfigureVisible'),...
'Color',[0.8 0.8 0.8],...
'Colormap',gray(64),...
'DockControls','off',...
'CloseRequestFcn',get(0,'defaultfigureCloseRequestFcn'),...
'ResizeFcn',blanks(0),...
'IntegerHandle','off',...
'MenuBar','none',...
'ToolBar',get(0,'defaultfigureToolBar'),...
'Pointer',get(0,'defaultfigurePointer'),...
'PointerShapeHotSpot',get(0,'defaultfigurePointerShapeHotSpot'),...
'Name','cat12',...
'NumberTitle','off',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag',Tag,...
'UserData',[],...
'WindowStyle',get(0,'defaultfigureWindowStyle'),...
'Resize','off',...
'PaperPosition',get(0,'defaultfigurePaperPosition'),...
'PaperSize',[8.5 11],...
'PaperType','usletter',...
'InvertHardcopy',get(0,'defaultfigureInvertHardcopy'),...
'PaperOrientation',get(0,'defaultfigurePaperOrientation'),...
'HandleVisibility','callback');
%-------------------------------------------------------------------
% Preprocessing
%-------------------------------------------------------------------
h01 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','',...
'Style','pushbutton',...
'enable','inactive',...
'cdata',cat_interp_menuimgs(cat_bg,tg),...
'Position',[x2(1) yo+(9*yd) tw 5*yd]+bo,...
'Callback',blanks(0),...
'TooltipString',blanks(0),...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','textPreprocessing',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
h02 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Preprocessing',...
'FontWeight','bold',...
'Style','pushbutton',...
'enable','inactive',...
'ForegroundColor',[0.9 0.9 0.9],...
'cdata',cat_interp_menuimgs(imread(fullfile(fileparts(mfilename('fullpath')),'doc','images','cat_hd02blue2.png')),tg),...
'Position',[x2(1) yo+(13*yd) tw th]+to,...
'Callback',blanks(0),...
'TooltipString',blanks(0),...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','textPreprocessing',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'pushSegment_Callback';
h03 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Segment',...
'Position',[x2(1) yo+(12*yd) x2w bh],...
'TooltipString','Segment Cross-Sectional Data',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushSegment',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'),...
'Style','pushbutton','Callback',@(hObject,eventdata)cat12('pushSegment_Callback',hObject,eventdata,guidata(hObject)));
appdata = [];
appdata.lastValidTag = 'pushSegmentLong_Callback';
h04 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Segment Longitudinal',...
'Position',[x2(2) yo+(12*yd) x2w bh],...
'TooltipString','Segment Longitudinal Data',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushSegmentLong',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'),...
'Style','pushbutton','Callback',@(hObject,eventdata)cat12('pushSegmentLong_Callback',hObject,eventdata,guidata(hObject)));
appdata = [];
appdata.lastValidTag = 'popupROITools_Callback';
h05 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Value',1,...
'Position',[x2(2) yo+(11*yd) x2w bh]+po,...
'TooltipString','Extract ROI Data Using Atlases or Estimate Mean Volumes',...
'String',{ center('ROI Tools');...
'Extract ROI-based Surface Values';...
'Estimate Mean Value Inside ROI for External Analysis';...
'Summarise 3D/4D Data Within a ROI' },...
'UserData',{...
'spm_jobman(''interactive'','''',''spm.tools.cat.stools.surf2roi'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.calcroi'');' ...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.ROIsum'');' },...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupROITools',...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupVolumeTools_Callback';
str_vol = {center('Volume Tools'),...
'Denoising Filter (SANLM)',...
'Apply Deformations (Many Subjects)',...
'Apply Deformations (Many Images)',...
'Save (resampled) Volume Data as mat-File',...
'Calculate Differences Between Volumes',...
'Longitudinal Registration',...
'Calculate Volume Average'};
userdata_vol = {...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.sanlm'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.defs2'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.defs'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.data2mat'');'...
'cat_stat_diff;'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.series'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.avg_img'');'...
};
% add some expert entries
if expert
str_vol = [str_vol, ...
{'Reduce Bounding Box (Data Trimming)'}];
userdata_vol = [userdata_vol, ...
{'spm_jobman(''interactive'','''',''spm.tools.cat.tools.datatrimming'')'}];
end
h06 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Position',[x2(1) yo+(11*yd) x2w bh]+po,...
'TooltipString','Additional Volume Tools',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupVolumeTools',...
'String',str_vol,...
'UserData',userdata_vol,...
'Value',1,...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupSurfaceMeasures_Callback';
h07 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Value',1,...
'Position',[x2(1) yo+(10*yd) x2w bh]+po,...
'TooltipString','Additional Surface Tools',...
'String',{ center('Surface Tools');...
'Extract Additional Surface Parameters ';...
'Map Volume (Native Space) to Individual Surface';...
'Map Normalized Volume (Template Space) to Template Surface';...
'Map Surface Atlas to Individual Surface';...
'Save Surface Data as mat-File';...
'Nonlinear Co-Register and Map Volume (Native Space) to Individual Surface' },...
'UserData',{...
'spm_jobman(''interactive'','''',''spm.tools.cat.stools.surfextract'')'...
'spm_jobman(''interactive'','''',''spm.tools.cat.stools.vol2surf'')'...
'spm_jobman(''interactive'','''',''spm.tools.cat.stools.vol2surftemp'')'...
'cat_surf_map_atlas;'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.data2mat'')'...
'spm_jobman(''interactive'',''cat_surf_coregvol2surf.m'')'},...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupSurfaceMeasures',...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupSurfaceCalulator_Callback';
h08 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Position',[x2(2) yo+(10*yd) x2w bh]+po,...
'TooltipString','Surface Calulator (i.e. Imcalc for Surfaces)',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupSurfaceCalulator',...
'Value',1,...
'String',{ center('Surface Calculator');...
'Surface Calculator ';...
'Surface Calculator (Subject-wise)';...
'Calculate Differences Between Surfaces'; },...
'UserData',{...
'spm_jobman(''interactive'','''',''spm.tools.cat.stools.surfcalc'')'...
'spm_jobman(''interactive'','''',''spm.tools.cat.stools.surfcalcsub'')'...
'cat_stat_diff;'},...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'pushResampleSmooth_Callback';
h09 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Resamp. & Smooth Surf.',...
'Style','pushbutton',...
'Position',[x2(1) yo+(9*yd) x2w bh],...
'Callback',@(hObject,eventdata)cat12('pushResampleSmooth_Callback',hObject,eventdata,guidata(hObject)),...
'TooltipString','Resample and Smooth Surface Data',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushResampleSmooth',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'pushDisplaySurfaces_Callback';
h10 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Display Surfaces',...
'Style','pushbutton',...
'Position',[x2(2) yo+(9*yd) x2w bh],...
'Callback',@(hObject,eventdata)cat12('pushDisplaySurfaces_Callback',hObject,eventdata,guidata(hObject)),...
'TooltipString','Display Surfaces',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushDisplaySurfaces',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
%-------------------------------------------------------------------
% Statistical Analysis
%-------------------------------------------------------------------
h11 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','',...
'Style','pushbutton',...
'enable','inactive',...
'cdata',cat_interp_menuimgs(cat_bg,tg),...
'Position',[x2(1) yo+(5*yd) tw 4*yd]+bo,...
'Callback',blanks(0),...
'TooltipString',blanks(0),...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','textPreprocessing',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
h12 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Statistical Analysis',...
'FontWeight','bold',...
'Style','pushbutton',...
'enable','inactive',...
'ForegroundColor',[0.9 0.9 0.9],...
'cdata',cat_interp_menuimgs(imread(fullfile(fileparts(mfilename('fullpath')),'doc','images','cat_hd02red.png')),tg),...
'Position',[x2(1) yo+(8*yd) tw th]+to,...
'Callback',blanks(0),...
'TooltipString',blanks(0),...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','textStatisticalAnalysis',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupDataQuality_Callback';
h13 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Value',1,...
'Position',[x2(1) yo+(7*yd) x2w bh]+po,...
'TooltipString','Check Data Quality or SPM Design',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupDataQuality',...
'String',{ center('Data Quality');...
'Check Sample Homogeneity';...
'Check Sample Homogeneity for long. Data';...
... 'Check Sample Homogeneity for Very Large Samples Using Mean z-Score';...
'Get Weighted Overall Image Quality';...
'Check SPM Design';...
'Single Slice Display' },...
'UserData',{...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.check_homogeneity'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.check_cov'');'...
... 'spm_jobman(''interactive'','''',''spm.tools.cat.tools.quality_measures'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.iqr'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.check_SPM'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.showslice'');' },...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupTFCEToolbox_Callback';
h14 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback',@(hObject,eventdata)cat12('popupTFCEToolbox_Callback',hObject,eventdata,guidata(hObject)),...
'Style','popupmenu',...
'Value',1,...
'Position',[x2(2) yo+(7*yd) x2w bh]+po,...
'TooltipString','Call Threshold-Free Cluster Enhancement (TFCE) Toolbox',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupTFCEToolbox',...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'pushBasicModels_Callback';
h15 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Basic Models',...
'Style','pushbutton',...
'Position',[x2(1) yo+(6*yd) x2w bh],...
'Callback',@(hObject,eventdata)cat12('pushBasicModels_Callback',hObject,eventdata,guidata(hObject)),...
'TooltipString','Basic Statistical Models (2nd-Level)',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushBasicModels',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'pushEstimateSurfaceModels_Callback';
h16 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Estimate (Surface) Models)',...
'Style','pushbutton',...
'Position',[x2(2) yo+(6*yd) x2w bh],...
'Callback',@(hObject,eventdata)cat12('pushEstimateSurfaceModels_Callback',hObject,eventdata,guidata(hObject)),...
'TooltipString','Model Estimation for Surface Data',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushEstimateSurfaceModels',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'pushROIAnalysis_Callback';
h17 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','ROI Analysis',...
'Style','pushbutton',...
'Position',[x2(1) yo+(5*yd) x2w bh],...
'Callback',@(hObject,eventdata)cat12('pushROIAnalysis_Callback',hObject,eventdata,guidata(hObject)),...
'TooltipString','Analyze ROIs Using Existing SPM Design',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushROIAnalysis',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'pushGetTIV_Callback';
h18 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Get TIV',...
'Style','pushbutton',...
'Position',[x2(2) yo+(5*yd) x2w bh],...
'Callback',@(hObject,eventdata)cat12('pushGetTIV_Callback',hObject,eventdata,guidata(hObject)),...
'TooltipString','Estimate Total Intracranial Volume (TIV)',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushGetTIV',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
%-------------------------------------------------------------------
% Result Presentation
%-------------------------------------------------------------------
h20 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','',...
'Style','pushbutton',...
'enable','inactive',...
'cdata',cat_interp_menuimgs(cat_bg,tg),...
'Position',[x2(1) yo+(3*yd) tw 2*yd]+bo,...
'Callback',blanks(0),...
'TooltipString',blanks(0),...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','textPreprocessing',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
h21 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Result Presentation',...
'FontWeight','bold',...
'Style','pushbutton',...
'enable','inactive',...
'ForegroundColor',[0.9 0.9 0.9],...
'cdata',cat_interp_menuimgs(imread(fullfile(fileparts(mfilename('fullpath')),'doc','images','cat_hd02green.png')),tg),...
'Position',[x2(1) yo+(4*yd) tw th]+to,...
'Callback',blanks(0),...
'TooltipString',blanks(0),...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','textPresentation',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupTransform_Callback';
h22 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Value',1,...
'Position',[x2(1) yo+(3*yd) x2w bh]+po,...
'TooltipString','Threshold and Transform SPM-Maps to (Log-Scaled) p-Maps or Correlation Maps',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupTransform',...
'String',{ center('Transf. SPM Maps');...
'T-Volume-Maps';...
'F-Volume-Maps';...
'T-Surface-Maps';...
'F-Surface-Maps' },...
'UserData',{...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.T2x'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.F2x'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.T2x_surf'');'...
'spm_jobman(''interactive'','''',''spm.tools.cat.tools.F2x_surf'');' },...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupViewResults_Callback';
h23 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Value',1,...
'Position',[x2(2) yo+(3*yd) x2w bh]+po,...
'TooltipString','Display Results as Overlay on Slices or Surfaces',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupViewResults',...
'String',{ center('View Results');...
'Call Results';...
'Slice Overlay (for Volumes)';...
'Surface Overlay (for Surfaces and GM-Volumes)' },...
'UserData',{...
'[hReg xSPM SPM] = cat_spm_results_ui(''Setup'');'...
'cat_vol_slice_overlay'...
'y = cat_surf_results;' },...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
%-------------------------------------------------------------------
% Tools
%-------------------------------------------------------------------
h30 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','',...
'Style','pushbutton',...
'enable','inactive',...
'cdata',cat_interp_menuimgs(cat_bg,tg),...
'Position',[x2(1) yo+(0*yd) tw 3*yd]+bo,...
'Callback',blanks(0),...
'TooltipString',blanks(0),...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','textPreprocessing',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
h31 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Tools',...
'FontWeight','bold',...
'Style','pushbutton',...
'enable','inactive',...
'ForegroundColor',[0.9 0.9 0.9],...
'cdata',cat_interp_menuimgs(imread(fullfile(fileparts(mfilename('fullpath')),'doc','images','cat_hd02purple.png')),tg),...
'Position',[x2(1) yo+(2*yd) tw th]+to,...
'Callback',blanks(0),...
'TooltipString',blanks(0),...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','textTools',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupHelp_Callback';
h32 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Value',1,...
'Position',[x2(1) yo+(1*yd) x2w bh]+po,...
'TooltipString','Help Functions',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupHelp',...
'String',{ center('Help');...
'Interactive Manual'; ...
'Website' },...
'UserData',{...
'web(fullfile(fileparts(which(''cat12'')),''doc'',''index.html''));' ...
'web(''https://neuro-jena.github.io'');' },...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'popupUtils_Callback';
h33 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'Callback','spm(''PopUpCB'',gcbo)',...
'Style','popupmenu',...
'Value',1,...
'Position',[x2(2) yo+(1*yd) x2w bh]+po,...
'TooltipString','Check for Updates and Add-Ons',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','popupUtils',...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
% disable some not available menu entries
if isdeployed
set(h33,...
'String',{ center('Add-Ons');...
'Install CAT Atlases to SPM' },...
'UserData',{...
'cat_install_atlases' })
else
set(h33,...
'String',{ center('Updates/Add-Ons');...
'Check for Updates';...
'Install CAT Atlases to SPM' },...
'UserData',{...
'cat_update(1);'...
'cat_install_atlases' })
end
appdata = [];
appdata.lastValidTag = 'pushQuickStartGuide_Callback';
h34 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Quick Start Guide',...
'Style','pushbutton',...
'Position',[x2(1) yo x2w bh],...
'Callback',@(hObject,eventdata)cat12('pushQuickStartGuide_Callback',hObject,eventdata,guidata(hObject)),...
'TooltipString','Call Quick Start Guide',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushQuickStartGuide',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
appdata = [];
appdata.lastValidTag = 'pushMode_Callback';
h35 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
'String','Switch to Expert Mode',...
'Style','pushbutton',...
'Position',[x2(2) yo x2w bh],...
'Callback',@(hObject,eventdata)cat12('pushMode_Callback',hObject,eventdata,guidata(hObject)),...
'TooltipString','Switch Between Standard and Expert Mode',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata} ,...
'Tag','pushMode',...
'UserData',[],...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
if expert == 1
set(h35,'String','Switch to Standard Mode');
% for standalone installations beginners mode is not allowed
if isdeployed
set(h35, 'Enable', 'off');
end
end
%-------------------------------------------------------------------
% set bottom box
h40 = uicontrol(...
'Parent',h0,...
'Units','pixels',...
... 'BackgroundColor',[0.9400 0.9400 0.9400],...
'ForegroundColor',[0.5 0.5 0.5],...
'ListboxTop',0,...
'HorizontalAlignment','center',...
'Position',[x2(1) 7 tw th]+to,...
'String','Copyright (c) Structural Brain Mapping Group',...
'Style','pushbutton',...
'enable','inactive',...
'Tag','text080',...
'CreateFcn', {@local_CreateFcn, blanks(0), appdata},...
'FontSize',FS,...
'FontName',get(0,'defaultuicontrolFontName'));
h0pos = get(h0,'Position');
h40pos = get(h40,'Position');
I2 = cat_interp_menuimgs(cat_bg,h0pos(3:4));
% cutting the image
I2( round(h0pos(4) - h40pos(2) + 1) : end ,:,:) = [];
I2( 1 : round(h0pos(4) - h40pos(2) - h40pos(4) -1) ,:,:) = [];
I2(:, round(h40pos(3) + h40pos(1) + 1) : end ,:) = [];
I2(:, round(1 : h40pos(1) - 1) ,:) = [];
set(h40,'cdata',I2);
hsingleton = h0;
%-------------------------------------------------------------------
function I2 = cat_interp_menuimgs(I,sx)
[X2,Y2] = meshgrid(1:size(I,2)/sx(1):size(I,2),1:size(I,1)/sx(2):size(I,1)); clear I2;
I(end+1,:,:) = I(end,:,:); I(:,end+1,:) = I(:,end,:);
for i=1:3, I2(:,:,i) = cat_vol_ctype(interp2(double(I(:,:,i)),X2,Y2)); end %#ok<AGROW>
%-------------------------------------------------------------------
function out = center(in)
global FS x2w
if ismac && cat_io_matlabversion<20092
out = in;
else
out = sprintf('%s%s',repmat(' ',1,round((1.4*x2w/FS-length(in)))),in);