/
spm.m
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spm.m
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function varargout=spm(varargin)
% SPM: Statistical Parametric Mapping (startup function)
%_______________________________________________________________________
% ___ ____ __ __
% / __)( _ \( \/ )
% \__ \ )___/ ) ( Statistical Parametric Mapping
% (___/(__) (_/\/\_) SPM - http://www.fil.ion.ucl.ac.uk/spm
%_______________________________________________________________________
%
% SPM (Statistical Parametric Mapping) is a package for the analysis
% functional brain mapping experiments. It is the in-house package of
% the Wellcome Department of Cognitive Neurology, and is available to
% the scientific community as copyright freeware under the terms of the
% GNU General Public Licence.
%
% Theoretical, computational and other details of the package are
% available in SPM's "Help" facility. This can be launched from the
% main SPM Menu window using the "Help" button, or directly from the
% command line using the command `spm_help`.
%
% Details of this release are availiable via the "About SPM" help topic
% (file spm.man), accessible from the SPM splash screen. (Or type
% `spm_help spm.man` in the MatLab command window)
%
% This spm function initialises the default parameters, and displays a
% splash screen with buttons leading to the PET(SPECT) & fMRI
% modalities Alternatively, `spm('pet')` and `spm('fmri')`
% (equivalently `spm pet` and `spm mri`) lead directly to the respective
% modality interfaces.
%
% Once the modality is chosen, (and it can be toggled mid-session) the
% SPM user interface is displayed. This provides a constant visual
% environment in which data analysis is implemented. The layout has
% been designed to be simple and at the same time show all the
% facilities that are available. The interface consists of three
% windows: A menu window with pushbuttons for the SPM routines (each
% button has a 'CallBack' string which launches the appropriate
% function/script); A blank panel used for interaction with the user;
% And a graphics figure with various editing and print facilities (see
% spm_figure.m). (These windows are 'Tag'ged 'Menu', 'Interactive', and
% 'Graphics' respectively, and should be referred to by their tags
% rather than their figure numbers.)
%
% Further interaction with the user is (mainly) via questioning in the
% 'Interactive' window (managed by spm_input), and file selection
% (managed by spm_get). See the help on spm_input.m and spm_get.m for
% details on using these functions.
%
% If a "message of the day" file named spm_motd.man exists in the SPM
% directory (alongside spm.m) then it is displayed in the Graphics
% window on startup.
%
% Arguments to this routine (spm.m) lead to various setup facilities,
% mainly of use to SPM power users and programmers. See programmers
% FORMAT & help in the main body of spm.m
%
%_______________________________________________________________________
% SPM is developed by members and collaborators of the
% Wellcome Department of Cognitive Neurology
%-SCCS ID and authorship of this program...
%-----------------------------------------------------------------------
% @(#)spm.m 2.87 Andrew Holmes 03/02/28
%=======================================================================
% - FORMAT specifications for embedded CallBack functions
%=======================================================================
%( This is a multi function function, the first argument is an action )
%( string, specifying the particular action function to take. Recall )
%( MatLab's command-function duality: `spm Welcome` is equivalent to )
%( `spm('Welcome')`. )
%
% FORMAT spm
% Defaults to spm('Welcome')
%
% FORMAT spm('Welcome')
% Clears command window, deletes all figures, prints welcome banner and
% splash screen, sets window defaults.
%
% FORMAT spm('AsciiWelcome')
% Prints ASCII welcome banner in MatLab command window.
%
% FORMAT spm('PET') spm('FMRI')
% Closes all windows and draws new Menu, Interactive, and Graphics
% windows for an SPM session. The buttons in the Menu window launch the
% main analysis routines.
%
% FORMAT Fmenu = spm('CreateMenuWin',Vis)
% Creates SPM menu window, 'Tag'ged 'Menu'
% F - handle of figure created
% Vis - Visibility, 'on' or 'off'
%
% Finter = FORMAT spm('CreateIntWin',Vis)
% Creates an SPM Interactive window, 'Tag'ged 'Interactive'
% F - handle of figure created
% Vis - Visibility, 'on' or 'off'
%
% FORMAT spm('ChMod',Modality)
% Changes modality of SPM: Currently SPM supports PET & MRI modalities,
% each of which have a slightly different Menu window and different
% defaults. This function switches to the specified modality, setting
% defaults and displaying the relevant buttons.
%
% FORMAT spm('defaults',Modality)
% Sets default global variables for the specified modality.
%
% FORMAT [Modality,ModNum]=spm('CheckModality',Modality)
% Checks the specified modality against those supported, returns
% upper(Modality) and the Modality number, it's position in the list of
% supported Modalities.
%
% FORMAT WS=spm('WinScale')
% Returns ratios of current display dimensions to that of a 1152 x 900
% Sun display. WS=[Xratio,Yratio,Xratio,Yratio]. Used for scaling other
% GUI elements.
% (Function duplicated in spm_figure.m, repeated to reduce inter-dependencies.)
%
% FORMAT [FS,sf] = spm('FontSize',FS)
% FORMAT [FS,sf] = spm('FontSizes',FS)
% Returns fontsizes FS scaled for the current display.
% FORMAT sf = spm('FontScale')
% Returns font scaling factor
% FS - (vector of) Font sizes to scale [default [1:36]]
% sf - font scaling factor (FS(out) = floor(FS(in)*sf)
%
% Rect = spm('WinSize',Win,raw)
% Returns sizes and positions for SPM windows.
% Win - 'Menu', 'Interactive', 'Graphics', or '0'
% - Window whose position is required. Only first character is
% examined. '0' returns size of root workspace.
% raw - If specified, then positions are for a 1152 x 900 Sun display.
% Otherwise the positions are scaled for the current display.
%
% FORMAT SPMdir=spm('Dir',Mfile)
% Returns the directory containing the version of spm in use,
% identified as the first in MATLABPATH containing the Mfile spm (this
% file) (or Mfile if specified).
%
% FORMAT [v,c]=spm('Ver',Mfile,ReDo,Cache,Con)
% Returns the current version (v) & copyright notice, extracted from
% the top line of the Contents.m file in the directory containing the
% currently used file Mfile (defaults on omission or empty to 'spm').
%
%-The version and copyright information are saved in a global
% variable called [upper(spm_str_manip(Mfile,'rt')),'_VER'], as a
% structure with fields 'v' and 'c'. This enables repeat use without
% recomputation.
%
%-If Con [default (missing or empty) 1] is false, then the version
% information is extracted from Mfile itself, rather than the
% Contents.m file in the same directory. When using a Contents.m file,
% the first line is read. For other files, the second line (the H1 help
% line) is used. This is for consistency with MatLab's ver and help
% commands respectively. (This functionality enables toolboxes to be
% identified by a function rather than a Contents.m file, allowing
% installation in a directory which already has a Contents.m file.)
%
%-If Cache [default (missing or empty) 1] is true, then the version and
% copyright information cached in the global variable
% [upper(Mfile),'_VER'], as a structure with fields 'v' and 'c'. This
% enables repeat use without recomputation.
%
%-If ReDo [default (missing or empty) 0] is true, then the version and
% copyright information are recomputed (regardless of any stored global
% data).
%
% FORMAT xTB = spm('TBs')
% Identifies installed SPM toolboxes: SPM toolboxes are defined as the
% contents of sub-directories of fullfile(spm('Dir'),'toolbox') - the
% SPM toolbox installation directory. For SPM to pick a toolbox up,
% there must be a single mfile in the directory whose name ends with
% the toolbox directory name. (I.e. A toolbox called "test" would be in
% the "test" subdirectory of spm('Dir'), with a single file named
% *test.m.) This M-file is regarded as the launch file for the
% toolbox.
% xTB - structure array containing toolbox definitions
% xTB.name - name of toolbox (taken as toolbox directory name)
% xTB.prog - launch program for toolbox
% xTB.dir - toolbox directory
%
% FORMAT spm('TBlaunch',xTB,i)
% Launch a toolbox, prepending TBdir to path if necessary
% xTB - toolbox definition structure (i.e. from spm('TBs')
% xTB.name - name of toolbox
% xTB.prog - name of program to launch toolbox
% xTB.dir - toolbox directory (prepended to path if not on path)
%
% FORMAT [c,cName] = spm('Colour')
% Returns the RGB triple and a description for the current en-vogue SPM
% colour, the background colour for the Menu and Help windows.
%
% FORMAT [v1,v2,...] = spm('GetGlobal',name1,name2,...)
% Returns values of global variables (without declaring them global)
% name1, name2,... - name strings of desired globals
% a1, a2,... - corresponding values of global variables with given names
% ([] is returned as value if global variable doesn't exist)
%
% FORMAT CmdLine = spm('CmdLine',CmdLine)
% Command line SPM usage?
% CmdLine (input) - CmdLine preference
% [defaults (missing or empty) to global defaults.cmdline,]
% [if it exists, or 0 (GUI) otherwise. ]
% CmdLine (output) - true if global CmdLine if true,
% or if on a terminal with no support for graphics windows.
%
% FORMAT v = spm('MLver')
% Returns MatLab version, truncated to major & minor revision numbers
%
% FORMAT spm('SetCmdWinLabel',WinStripe,IconLabel)
% Sets the names on the headers and icons of Sun command tools.
% WinStripe defaults to a summary line identifying the user, host and
% MatLab version; IconLabel to 'MatLab'.
%
% FORMAT spm('PopUpCB',h)
% Callback handler for PopUp UI menus with multiple callbacks as cellstr UserData
%
% FORMAT str = spm('GetUser',fmt)
% Returns current users login name, extracted from the hosting environment
% fmt - format string: If USER is defined then sprintf(fmt,USER) is returned
%
% FORMAT spm('Beep')
% plays the keyboard beep!
%
% FORMAT spm('time')
% Returns the current time and date as hh:mm dd/mm/yyyy
%
% FORMAT spm('Pointer',Pointer)
% Changes pointer on all SPM (HandleVisible) windows to type Pointer
% Pointer defaults to 'Arrow'. Robust to absence of windows
%
% FORMAT h = spm('alert',Message,Title,CmdLine,wait)
% FORMAT h = spm('alert"',Message,Title,CmdLine,wait)
% FORMAT h = spm('alert*',Message,Title,CmdLine,wait)
% FORMAT h = spm('alert!',Message,Title,CmdLine,wait)
% Displays an alert, either in a GUI msgbox, or as text in the command window.
% ( 'alert"' uses the 'help' msgbox icon, 'alert*' the )
% ( 'error' icon, 'alert!' the 'warn' icon )
% Message - string (or cellstr) containing message to print
% Title - title string for alert
% CmdLine - CmdLine preference [default spm('CmdLine')]
% - If CmdLine is complex, then a CmdLine alert is always used,
% possibly in addition to a msgbox (the latter according
% to spm('CmdLine').)
% wait - if true, waits until user dismisses GUI / confirms text alert
% [default 0] (if doing both GUI & text, waits on GUI alert)
% h - handle of msgbox created, empty if CmdLine used
%
% FORMAT SPMid = spm('FnBanner', Fn,FnV)
% Prints a function start banner, for version FnV of function Fn, & datestamps
% FORMAT SPMid = spm('SFnBanner',Fn,FnV)
% Prints a sub-function start banner
% FORMAT SPMid = spm('SSFnBanner',Fn,FnV)
% Prints a sub-sub-function start banner
% Fn - Function name (string)
% FnV - Function version (string)
% SPMid - ID string: [SPMver: Fn (FnV)]
%
% FORMAT [Finter,Fgraph,CmdLine] = spm('FnUIsetup',Iname,bGX,CmdLine)
% Robust UIsetup procedure for functions:
% Returns handles of 'Interactive' and 'Graphics' figures.
% Creates 'Interactive' figure if ~CmdLine, creates 'Graphics' figure if bGX.
% Iname - Name for 'Interactive' window
% bGX - Need a Graphics window? [default 1]
% CmdLine - CommandLine usage? [default spm('CmdLine')]
% Finter - handle of 'Interactive' figure
% Fgraph - handle of 'Graphics' figure
% CmdLine - CommandLine usage?
%
% FORMAT F = spm('FigName',Iname,F,CmdLine)
% Set name of figure F to "SPMver (User): Iname" if ~CmdLine
% Robust to absence of figure.
% Iname - Name for figure
% F (input) - Handle (or 'Tag') of figure to name [default 'Interactive']
% CmdLine - CommandLine usage? [default spm('CmdLine')]
% F (output) - Handle of figure named
%
% FORMAT spm('GUI_FileDelete')
% CallBack for GUI for file deletion, using spm_get and confirmation dialogs
%
% FORMAT Fs = spm('Show')
% Opens all SPM figure windows (with HandleVisibility) using `figure`.
% Maintains current figure.
% Fs - vector containing all HandleVisible figures (i.e. get(0,'Children'))
%
% FORMAT spm('Clear',Finter, Fgraph)
% Clears and resets SPM-GUI, clears and timestamps MatLab command window
% Finter - handle or 'Tag' of 'Interactive' figure [default 'Interactive']
% Fgraph - handle or 'Tag' of 'Graphics' figure [default 'Graphics']
%
% FORMAT spm('Help',varargin)
% Merely a gateway to spm_help(varargin) - so you can type "spm help"
%
%_______________________________________________________________________
%-Parameters
%-----------------------------------------------------------------------
Modalities = str2mat('PET','FMRI');
%-Format arguments
%-----------------------------------------------------------------------
if nargin == 0, Action='Welcome'; else, Action = varargin{1}; end
%=======================================================================
switch lower(Action), case 'welcome' %-Welcome splash screen
%=======================================================================
spm_defaults;
if isfield(defaults,'modality'), spm(defaults.modality); return; end;
%-Open startup window, set window defaults
%-----------------------------------------------------------------------
S = get(0,'ScreenSize');
if all(S==1), error('Can''t open any graphics windows...'), end
[SPMver,SPMc] = spm('Ver','',1);
PF = spm_platform('fonts');
F = figure('IntegerHandle','off',...
'Name',sprintf('%s%s',spm('ver'),spm('GetUser',' (%s)')),...
'NumberTitle','off',...
'Tag','Welcome',...
'Position',[S(3)/2-300,S(4)/2-140,500,280],...
'Resize','off',...
'Pointer','Watch',...
'Color',[1 1 1]*.8,...
'MenuBar','none',...
'DefaultUicontrolFontName',PF.helvetica,...
'HandleVisibility','off',...
'Visible','off');
%-Text
%-----------------------------------------------------------------------
hA = axes('Parent',F,'Position',[0 0 100/500 280/280],'Visible','Off');
text(0.5,0.5,'SPM',...
'Parent',hA,...
'FontName',PF.times,'FontSize',96,...
'FontAngle','Italic','FontWeight','Bold',...
'Rotation',90,...
'VerticalAlignment','Middle','HorizontalAlignment','Center',...
'Color',[1 1 1]*.6);
uicontrol(F,'Style','Text','Position',[110 245 390 030],...
'String','Statistical Parametric Mapping',...
'FontName',PF.times,'FontSize',18,'FontAngle','Italic',...
'FontWeight','Bold',...
'ForegroundColor',[1 1 1]*.6,'BackgroundColor',[1 1 1]*.8);
uicontrol(F,'Style','Frame','Position',[110 130 380 115]);
uicontrol(F,'Style','Frame','Position',[110 015 380 087]);
uicontrol(F,'Style','Text','String',SPMver,...
'ToolTipString','by the FIL methods group',...
'Position',[112 200 376 030],...
'FontName',PF.times,'FontSize',18,'FontWeight','Bold',...
'ForegroundColor','b')
uicontrol(F,'Style','Text','Position',[112 175 376 020],...
'String','developed by members and collaborators of',...
'ToolTipString','',...
'FontName',PF.times,'FontSize',10,'FontAngle','Italic')
uicontrol(F,'Style','Text','Position',[112 160 376 020],...
'String','The Wellcome Department of Imaging Neuroscience',...
'ToolTipString','',...
'FontName',PF.times,'FontSize',12,'FontWeight','Bold')
uicontrol(F,'Style','Text', 'Position',[112 140 376 020],...
'String','Institute of Neurology, University College London',...
'ToolTipString','',...
'FontName',PF.times,'FontSize',12)
uicontrol(F,'Style','Text','String',SPMc,'ToolTipString',SPMc,...
'ForegroundColor',[1 1 1]*.6,'BackgroundColor',[1 1 1]*.8,...
'FontName',PF.times,'FontSize',10,...
'HorizontalAlignment','center',...
'Position',[110 003 380 010])
%-Objects with Callbacks - PET, fMRI, About SPM, SPMweb
%-----------------------------------------------------------------------
set(F,'DefaultUicontrolFontSize',12,'DefaultUicontrolInterruptible','on')
uicontrol(F,'String','PET and SPECT',...
'ToolTipString',...
'launch SPM-GUI in PET/SPECT modality (or type "spm pet" in MatLab)',...
'Position',[140 061 150 030],...
'CallBack','delete(gcbf),clear all,spm(''PET'')',...
'ForegroundColor',[0 1 1])
uicontrol(F,'String','fMRI time-series',...
'ToolTipString',...
'launch SPM-GUI in fMRI modality (or type "spm fmri" in MatLab)',...
'Position',[310 061 150 030],...
'CallBack','delete(gcbf),clear all,spm(''FMRI'')',...
'ForegroundColor',[0 1 1])
uicontrol(F,'String','About SPM',...
'ToolTipString','launch SPMhelp browser - about SPM',...
'Position',[140 025 100 030],...
'CallBack','spm_help(''spm.man'')',...
'ForegroundColor','g')
uicontrol(F,'String','SPMweb',...
'FontWeight','Bold','FontName',PF.courier,...
'ToolTipString',...
'launch web browser - http://www.fil.ion.ucl.ac.uk/spm',...
'Position',[250 025 100 030],...
'CallBack',['set(gcbf,''Pointer'',''Watch''),',...
'web(''http://www.fil.ion.ucl.ac.uk/spm'');',...
'set(gcbf,''Pointer'',''Arrow'')'],...
'ForegroundColor','k')
uicontrol(F,'String','Quit',...
'ToolTipString','close this splash screen',...
'Position',[360 025 100 030],...
'CallBack','delete(gcbf)',...
'Interruptible','off',...
'ForegroundColor','r')
set(F,'Pointer','Arrow','Visible','on')
%=======================================================================
case 'asciiwelcome' %-ASCII SPM banner welcome
%=======================================================================
disp( ' ___ ____ __ __ ')
disp( '/ __)( _ \( \/ ) ')
disp( '\__ \ )___/ ) ( Statistical Parametric Mapping ')
disp(['(___/(__) (_/\/\_) ',spm('Ver'),' - http://www.fil.ion.ucl.ac.uk/spm'])
fprintf('\n')
%=======================================================================
case {'pet','fmri'} %-Initialise SPM in PET or fMRI modality
%=======================================================================
% spm(Modality)
%-Turn on warning messages for debugging - disabled as syntax for Matlab 6.5 has changed
%warning always, warning backtrace
%-Initialisation and workspace canonicalisation
%-----------------------------------------------------------------------
clc, spm('SetCmdWinLabel')
spm('AsciiWelcome'), fprintf('\n\nInitialising SPM')
Modality = upper(Action); fprintf('.')
delete(get(0,'Children')), fprintf('.')
%-Draw SPM windows
%-----------------------------------------------------------------------
Fmenu = spm('CreateMenuWin','off'); fprintf('.')
Finter = spm('CreateIntWin','off'); fprintf('.')
spm_figure('WaterMark',Finter,spm('Ver'),'',45), fprintf('.')
Fgraph = spm_figure('Create','Graphics','Graphics','off'); fprintf('.')
Fmotd = fullfile(spm('Dir'),'spm_motd.man');
if exist(Fmotd), spm_help('!Disp',Fmotd,'',Fgraph,spm('Ver')); end
fprintf('.')
%-Load startup global defaults
%-----------------------------------------------------------------------
spm_defaults, fprintf('.')
%-Setup for current modality
%-----------------------------------------------------------------------
spm('ChMod',Modality), fprintf('.')
%-Reveal windows
%-----------------------------------------------------------------------
set([Fmenu,Finter,Fgraph],'Visible','on')
fprintf('done\n\n')
%-Print present working directory
%-----------------------------------------------------------------------
fprintf('SPM present working directory:\n\t%s\n',pwd)
%=======================================================================
case 'createmenuwin' %-Draw SPM menu window
%=======================================================================
% Fmenu = spm('CreateMenuWin',Vis)
if nargin<2, Vis='on'; else, Vis=varargin{2}; end
%-Close any existing 'Menu' 'Tag'ged windows
delete(spm_figure('FindWin','Menu'))
%-Get size and scalings and create Menu window
%-----------------------------------------------------------------------
WS = spm('WinScale'); %-Window scaling factors
FS = spm('FontSizes'); %-Scaled font sizes
PF = spm_platform('fonts'); %-Font names (for this platform)
Rect = spm('WinSize','Menu','raw').*WS; %-Menu window rectangle
[SPMver,SPMc] = spm('Ver','',1,1);
Fmenu = figure('IntegerHandle','off',...
'Name',sprintf('%s%s',spm('ver'),spm('GetUser',' (%s)')),...
'NumberTitle','off',...
'Tag','Menu',...
'Position',Rect,...
'Resize','off',...
'Color',[1 1 1]*.8,...
'UserData',struct('SPMver',SPMver,'SPMc',SPMc),...
'MenuBar','none',...
'DefaultTextFontName',PF.helvetica,...
'DefaultTextFontSize',FS(10),...
'DefaultUicontrolFontName',PF.helvetica,...
'DefaultUicontrolFontSize',FS(12),...
'DefaultUicontrolInterruptible','on',...
'Renderer','zbuffer',...
'Visible','off');
%-Frames and text
%-----------------------------------------------------------------------
uicontrol(Fmenu,'Style','Frame','BackgroundColor',spm('Colour'),...
'Position',[010 145 380 295].*WS)
uicontrol(Fmenu,'Style','Frame',...
'Position',[020 340 360 90].*WS)
uicontrol(Fmenu,'Style','Text',...
'String','Spatial pre-processing',...
'Position',[025 410 350 020].*WS,...
'ForegroundColor','w',...
'FontAngle','Italic',...
'FontSize',FS(10),...
'HorizontalAlignment','Left')
uicontrol(Fmenu,'Style','Frame',...
'Position',[020 245 360 90].*WS)
uicontrol(Fmenu,'Style','Text',...
'String','Model specification & parameter estimation',...
'Position',[025 315 350 020].*WS,...
'ForegroundColor','w',...
'FontAngle','Italic',...
'FontSize',FS(10),...
'HorizontalAlignment','Left')
uicontrol(Fmenu,'Style','Frame',...
'Position',[020 200 360 40].*WS)
uicontrol(Fmenu,'Style','Text',...
'String','Inference',...
'Position',[025 220 350 020].*WS,...
'ForegroundColor','w',...
'FontAngle','Italic',...
'FontSize',FS(10),...
'HorizontalAlignment','Left')
uicontrol(Fmenu,'Style','Frame',...
'Position',[020 155 360 40].*WS)
uicontrol(Fmenu,'Style','Text',...
'String','SPM for PET/SPECT',...
'ToolTipString','modality & defaults set for PET/SPECT',...
'ForegroundColor',[1 1 1]*.6,...
'BackgroundColor',[1 1 1]*.8,...
'FontAngle','Italic',...
'HorizontalAlignment','center',...
'Position',[020 122 360 020].*WS,...
'Tag','PET',...
'Visible','off')
uicontrol(Fmenu,'Style','Text',...
'String','SPM for functional MRI',...
'ToolTipString','modality & defaults set for fMRI',...
'ForegroundColor',[1 1 1]*.6,...
'BackgroundColor',[1 1 1]*.8,...
'FontAngle','Italic',...
'HorizontalAlignment','center',...
'Position',[020 122 360 020].*WS,...
'Tag','FMRI',...
'Visible','off')
% Utilities frames and text
%-----------------------------------------------------------------------
uicontrol(Fmenu,'Style','Frame',...
'BackgroundColor',spm('Colour'),...
'Position',[010 010 380 112].*WS)
uicontrol(Fmenu,'Style','Text','String',SPMc,...
'ToolTipString',SPMc,...
'ForegroundColor',[1 1 1]*.6,...
'BackgroundColor',[1 1 1]*.8,...
'FontName',PF.times,...
'FontSize',FS(10),...
'HorizontalAlignment','center',...
'Position',[020 002 360 008].*WS)
%-Objects with Callbacks - main spm_*_ui.m routines
%=======================================================================
%-Spatial
%-----------------------------------------------------------------------
uicontrol(Fmenu,'Style','popup',...
'String','Realign|Realign & Unwarp',...
'Position',[035 380 100 030].*WS,...
'FontSize',FS(10),...
'ToolTipString','realignment',...
'UserData','spm_realign_ui',...
'CallBack','spm_realign_ui;',...
'Tag','FMRI','Visible','off');
uicontrol(Fmenu,'String','Realign',...
'Position',[040 380 080 030].*WS,...
'FontSize',FS(10),...
'ToolTipString','realignment',...
'UserData','spm_realign_ui',...
'CallBack','spm_realign_ui;',...
'Tag','PET','Visible','off');
uicontrol(Fmenu,'String','Normalize',...
'Position',[150 370 100 030].*WS,...
'FontSize',FS(10),...
'ToolTipString','spatial normalization',...
'CallBack','spm_normalise_ui;',...
'Tag','PET',...
'UserData','spm_normalise_ui',...
'Visible','off');
uicontrol(Fmenu,'String','Normalize',...
'Position',[150 345 100 030].*WS,...
'FontSize',FS(10),...
'ToolTipString','spatial normalisation',...
'CallBack','spm_normalise_ui;',...
'UserData','spm_normalise_ui',...
'Tag','FMRI', 'Visible','off');
uicontrol(Fmenu,'String','Slice timing',...
'Position',[150 380 100 030].*WS,...
'FontSize',FS(10),'ToolTipString',...
'correct slice acquisition times',...
'CallBack','spm_slice_timing;',...
'UserData','spm_slice_timing',...
'Tag','FMRI',...
'Visible','off');;
uicontrol(Fmenu,'String','Smooth',...
'Position',[280 380 080 030].*WS,...
'ToolTipString','spatial smoothing with Gaussian kernel',...
'FontSize',FS(10),...
'UserData','spm_smooth_ui',...
'CallBack','spm_smooth_ui;');
uicontrol(Fmenu,'String','Coregister',...
'Position',[040 345 080 030].*WS,...
'ToolTipString','co-register images from disparate modalities',...
'FontSize',FS(10),...
'UserData','spm_coreg_ui',...
'CallBack','spm_coreg_ui;');
uicontrol(Fmenu,'String','Segment',...
'Position',[280 345 080 030].*WS,...
'ToolTipString','segment',...
'FontSize',FS(10),...
'UserData','spm_segment_ui',...
'CallBack','spm_segment_ui;');
%-Statistical
%-----------------------------------------------------------------------
uicontrol(Fmenu,'String','Basic models',...
'Position',[035 285 110 030].*WS,...
'FontSize',FS(10),...
'ToolTipString','basic statistical models',...
'UserData','spm_spm_ui',...
'CallBack','SPM = spm_spm_ui(''cfg'',spm_spm_ui(''DesDefs_Stats''));');
uicontrol(Fmenu,'String','PET',...
'Position',[150 285 95 030].*WS,...
'FontSize',FS(10),...
'ToolTipString','GLM setup for PET',...
'CallBack','SPM = spm_spm_ui(''cfg'',spm_spm_ui(''DesDefs_PET''));',...
'Visible','off',...
'Tag','PET',...
'UserData','spm_spm_ui',...
'Enable','on');
uicontrol(Fmenu,'String','fMRI',...
'Position',[150 285 95 030].*WS,...
'ToolTipString',['GLM setup for fMRI time series'],...
'FontSize',FS(10),...
'CallBack','SPM = spm_fmri_spm_ui;',...
'Visible','off',...
'UserData','spm_fmri_spm_ui',...
'Tag','FMRI');
uicontrol(Fmenu,'String','Review design',...
'Position',[250 285 110 030].*WS,...
'FontSize',FS(10),...
'ToolTipString','review a specified model',...
'UserData','spm_DesRep',...
'CallBack','spm pointer watch, spm_DesRep; spm pointer arrow');
uicontrol(Fmenu,'String','Estimate',...
'Position',[035 250 160 030].*WS,...
'ToolTipString','estimate (WLS) the parameters of a specified model',...
'FontSize',FS(10),...
'UserData','spm_spm',...
'CallBack','SPM = spm_spm;');
uicontrol(Fmenu,'String','-> Bayesian',...
'Position',[200 250 160 030].*WS,...
'ToolTipString','Bayesian or conditional estimators',...
'FontSize',FS(10),...
'UserData','spm_spm_Bayes',...
'CallBack','spm_spm_Bayes',...
'ForeGroundColor',[1 1 1]/2);
uicontrol(Fmenu,'String','Results',...
'Position',[130 205 130 030].*WS,...
'ToolTipString','Inference and regional responses etc.',...
'FontSize',FS(10),...
'UserData','spm_results_ui',...
'CallBack','[hReg,xSPM,SPM] = spm_results_ui;');
uicontrol(Fmenu,'String','Dynamic Causal Modelling',...
'Position',[60 160 280 030].*WS,...
'ToolTipString','Specify and estimate a dynamic causal model',...
'FontSize',FS(10),...
'Visible','off',...
'Tag','FMRI',...
'UserData','spm_dcm_ui',...
'CallBack','spm_dcm_ui',...
'ForeGroundColor',[1 1 1]/2);
%-Utility buttons (first line)
%-----------------------------------------------------------------------
uicontrol(Fmenu,'String','Display',...
'Position',[020 088 082 024].*WS,...
'ToolTipString','orthogonal sections',...
'FontSize',FS(9),...
'UserData','spm_image',...
'CallBack','spm_image')
uicontrol(Fmenu,'String','Check Reg',...
'Position',[112 088 083 024].*WS,...
'ToolTipString','check image registration',...
'FontSize',FS(9),...
'UserData','spm_check_registration',...
'CallBack','spm_check_registration;')
uicontrol(Fmenu,'Style','PopUp',...
'String','Render...|Display|Xtract Brain',...
'Position',[205 088 083 024].*WS,...
'ToolTipString','rendering utilities...',...
'FontSize',FS(9),...
'CallBack','spm(''PopUpCB'',gcbo)',...
'UserData',{ 'spm_render;',...
'spm_surf;' })
uicontrol(Fmenu,'Style','PopUp',...
'String',Modalities,...
'ToolTipString','change modality PET<->fMRI',...
'Tag','Modality',...
'Position',[298 088 082 024].*WS,...
'CallBack',[...
'if isempty(get(gco,''UserData'')) | ',...
'get(gco,''Value'')~=get(gco,''UserData''),',...
'spm(''ChMod'',get(gco,''Value'')),',...
'end'],...
'UserData','SPM_Modality',...
'Interruptible','off')
%-Utility buttons (second line)
%-----------------------------------------------------------------------
%-Toolbox pulldown
xTB = spm('TBs');
if isempty(xTB)
uicontrol(Fmenu,'String','Toolboxes...',...
'Position',[020 054 082 024].*WS,...
'ToolTipString','Additional Toolboxes',...
'FontSize',FS(9),...
'UserData','MenuWin_Toolboxes_PullDown',...
'CallBack','','Enable','off')
else
uicontrol(Fmenu,'Style','PopUp',...
'String',{'Toolboxes...',xTB.name},...
'ToolTipString','Additional Toolboxes',...
'Position',[020 054 082 024].*WS,...
'FontSize',FS(9),...
'CallBack',...
['spm(''TBlaunch'',get(gcbo,''UserData''),get(gcbo,''Value'')-1), ',...
'set(gcbo,''Value'',1)'],...
'UserData', xTB)
end
uicontrol(Fmenu,...
'String','PPIs',...
'Position',[112 054 083 024].*WS,...
'ToolTipString',...
'Forms PPI regressors for fMRI using hemodynamic deconvolution',...
'FontSize',FS(9),...
'UserData','spm_peb_ppi',...
'CallBack','spm_peb_ppi')
uicontrol(Fmenu,'String','ImCalc',...
'Position',[205 054 083 024].*WS,...
'ToolTipString','image calculator',...
'FontSize',FS(9),...
'UserData','spm_imcalc_ui',...
'CallBack','spm_imcalc_ui;')
uicontrol(Fmenu,'String','Bias cor',...
'Position',[298 054 082 024].*WS,...
'ToolTipString','Bias correction',...
'FontSize',FS(9),...
'UserData','spm_bias_ui',...
'CallBack','spm_bias_ui;')
%-Utility buttons (third line)
%-----------------------------------------------------------------------
uicontrol(Fmenu,'String','Help',...
'Position',[020 020 082 024].*WS,...
'ToolTipString','launch SPMhelp browser',...
'CallBack','spm_help;',...
'UserData','spm_help',...
'ForeGroundColor','g')
uicontrol(Fmenu,'Style','PopUp',...
'String','Utils...|CD|PWD|delete files|Show SPM|Run mFile|SPMweb',...
'ToolTipString','misc SPM utilities',...
'Position',[112 020 083 024].*WS,...
'FontSize',FS(9),...
'CallBack','spm(''PopUpCB'',gcbo)',...
'UserData',{ [...
'spm(''FnBanner'',''CD'');',...
'cd(spm_get(-1,''*'',''Select new working directory'',pwd)),',...
'spm(''alert"'',',...
'{''New working directory:'',['' '',pwd]},',...
'''CD'',sqrt(-1));'],...
['spm(''alert"'',',...
'{''Present working directory:'',['' '',pwd]},',...
'''PWD'',0);'],...
'spm(''GUI_FileDelete'')',...
'spm(''Show'');',...
'run(spm_get(1,''*.m'',''Select mFile to run''))',...
'web(''http://www.fil.ion.ucl.ac.uk/spm'')' } )
uicontrol(Fmenu,'String','Defaults',...
'Position',[205 020 083 024].*WS,...
'ToolTipString','adjust default SPM behaviour for this session',...
'FontSize',FS(9),...
'CallBack','spm_defaults_edit;')
uicontrol(Fmenu,'String','Quit',...
'Position',[298 020 082 024].*WS,...
'ToolTipString','exit SPM',...
'ForeGroundColor','r',...
'Interruptible','off',...
'UserData','QuitSPM',...
'CallBack','spm(''Quit''), clear all')
%-----------------------------------------------------------------------
set(Fmenu,'CloseRequestFcn','spm(''Quit'')')
set(Fmenu,'Visible',Vis)
varargout = {Fmenu};
%=======================================================================
case 'createintwin' %-Create SPM interactive window
%=======================================================================
% Finter = spm('CreateIntWin',Vis)
if nargin<2, Vis='on'; else, Vis=varargin{2}; end
%-Close any existing 'Interactive' 'Tag'ged windows
delete(spm_figure('FindWin','Interactive'))
FS = spm('FontSizes'); %-Scaled font sizes
PF = spm_platform('fonts'); %-Font names (for this platform)
Rect = spm('WinSize','Interactive'); %-Interactive window rectangle
%-Create SPM Interactive window
Finter = figure('IntegerHandle','off',...
'Tag','Interactive',...
'Name','','NumberTitle','off',...
'Position',Rect,...
'Resize','off',...
'Color',[1 1 1]*.7,...
'MenuBar','none',...
'DefaultTextFontName',PF.helvetica,...
'DefaultTextFontSize',FS(10),...
'DefaultAxesFontName',PF.helvetica,...
'DefaultUicontrolBackgroundColor',[1 1 1]*.7,...
'DefaultUicontrolFontName',PF.helvetica,...
'DefaultUicontrolFontSize',FS(10),...
'DefaultUicontrolInterruptible','on',...
'Renderer', 'zbuffer',...
'Visible',Vis);
varargout = {Finter};
%=======================================================================
case 'chmod' %-Change SPM modality PET<->fMRI
%=======================================================================
% spm('ChMod',Modality)
%-Sort out arguments
%-----------------------------------------------------------------------
if nargin<2, Modality = ''; else, Modality = varargin{2}; end
[Modality,ModNum] = spm('CheckModality',Modality);
if strcmp(Modality,'PET'), OModality = 'FMRI'; else, OModality='PET'; end
%-Sort out global defaults
%-----------------------------------------------------------------------
spm('defaults',Modality)
%-Sort out visability of appropriate controls on Menu window
%-----------------------------------------------------------------------
Fmenu = spm_figure('FindWin','Menu');
if isempty(Fmenu), error('SPM Menu window not found'), end
set(findobj(Fmenu,'Tag',OModality),'Visible','off')
set(findobj(Fmenu,'Tag', Modality),'Visible','on')
set(findobj(Fmenu,'Tag','Modality'),'Value',ModNum,'UserData',ModNum)
%=======================================================================
case 'defaults' %-Set SPM defaults (as global variables)
%=======================================================================
% spm('defaults',Modality)
global defaults
if isempty(defaults), spm_defaults, end;
%-Sort out arguments
%-----------------------------------------------------------------------
if nargin<2, Modality=''; else, Modality=varargin{2}; end
Modality = spm('CheckModality',Modality);
defaults.modality = Modality;
defaults.SWD = spm('Dir'); % SPM directory
defaults.TWD = spm_platform('tempdir'); % Temp directory
%-Set Modality specific default (global variables)
%-----------------------------------------------------------------------
global UFp
if strcmp(lower(defaults.modality),'pet')
UFp = defaults.stats.pet.ufp; % Upper tail F-prob
elseif strcmp(lower(defaults.modality),'fmri')
UFp = defaults.stats.fmri.ufp; % Upper tail F-prob
elseif strcmp(lower(defaults.modality),'unknown')
else
error('Illegal Modality')
end
%=======================================================================
case 'quit' %-Quit SPM and clean up
%=======================================================================
% spm('Quit')
%-----------------------------------------------------------------------
delete(get(0,'Children'))
clc
fprintf('Bye...\n\n')
%=======================================================================
case 'checkmodality' %-Check & canonicalise modality string
%=======================================================================
% [Modality,ModNum] = spm('CheckModality',Modality)
%-----------------------------------------------------------------------
if nargin<2, Modality=''; else, Modality=upper(varargin{2}); end
if isempty(Modality)
global defaults
if isfield(defaults,'modality'); Modality = defaults.modality;
else, Modality = 'UNKNOWN'; end
end
if isstr(Modality)
ModNum = find(all(Modalities(:,1:length(Modality))'==...
Modality'*ones(1,size(Modalities,1))));
else
if ~any(Modality==[1:size(Modalities,1)])
Modality = 'ERROR';
ModNum = [];
else
ModNum = Modality;
Modality = deblank(Modalities(ModNum,:));
end
end
if isempty(ModNum), error('Unknown Modality'), end
varargout = {upper(Modality),ModNum};
%=======================================================================
case {'winscale','getwinscale'} %-Window scale factors (to fit display)
%=======================================================================
% WS = spm('WinScale')
if strcmp(lower(Action),'getwinscale')
warning('spm(''GetWinScale'' GrandFathered, use ''WinScale''')
end
S0 = get(0,'ScreenSize');
if all(S0==1), error('Can''t open any graphics windows...'), end
varargout = {[S0(3)/1152 (S0(4)-50)/900 S0(3)/1152 (S0(4)-50)/900]};
%=======================================================================
case {'fontsize','fontsizes','fontscale'} %-Font scaling