2023_Blaschke_Stroke_tDCS_rsfMRI/scripts/toolbox/spm12/spm_defaults.m

function spm_defaults
% Set the defaults which are used by SPM
%__________________________________________________________________________
%
% If you want to customise some defaults for your installation, do not
% modify this file directly, but create a file named spm_my_defaults.m
% instead, accessible from MATLAB search path; e.g., it can be saved in
% MATLAB Startup Folder: userhome/Documents/MATLAB.
%
% Example: create the following file to change the image file extension:
% ----------- file /home/karl/Documents/MATLAB/spm_my_defaults.m -----------
% global defaults
% defaults.images.format = 'img';
%--------------------------------------------------------------------------
%
% spm_defaults should not be called directly in any script or function
% (apart from SPM internals).
% To load the defaults, use spm('Defaults',modality).
% To get/set the defaults, use spm_get_defaults.
%
%                 ** This file should not be edited **
%__________________________________________________________________________
% Copyright (C) 1994-2018 Wellcome Trust Centre for Neuroimaging

% SPM
% $Id: spm_defaults.m 7296 2018-04-18 10:36:49Z guillaume $


global defaults

% Command Line Usage default
%==========================================================================
defaults.cmdline  = 0;

% User Interface defaults
%==========================================================================
defaults.ui.monitor = NaN;
defaults.ui.colour  = [0.58 0.77 0.57];
defaults.ui.fs      = 14;  % unused
defaults.ui.print   = 'ps';
defaults.renderer   = 'opengl';

% File format specific
%==========================================================================
% Note that defaults.analyze.flip is no longer used.  Specifying the
% left/right handedness of the voxel indices is now done entirely by
% spm_flip_analyze_images.m
defaults.images.format  = 'nii'; % options: 'img', 'nii'
defaults.mat.format     = '-v6'; % options: '-mat', '-v6', '-v7.0', '-v7.3'

% Toolboxes defaults
%==========================================================================
defaults.tbx.dir = { fullfile(spm('Dir'),'toolbox') };

% DICOM Import defaults
%==========================================================================
defaults.dicom.root = 'flat'; % Folder hierarchy

% fMRI design defaults
%==========================================================================
defaults.stats.fmri.t   = 16;
defaults.stats.fmri.t0  = 8;
defaults.stats.fmri.hpf = 128;
defaults.stats.fmri.cvi = 'AR(1)';
defaults.stats.fmri.hrf = [6 16 1 1 6 0 32];

% Mask defaults
%==========================================================================
defaults.mask.thresh    = 0.8;

% Stats defaults
%==========================================================================
defaults.stats.maxmem      = 2^29;
defaults.stats.maxres      = 64;
defaults.stats.resmem      = false;
defaults.stats.fmri.ufp    = 0.001;  % Upper tail F-probability
defaults.stats.pet.ufp     = 0.05;
defaults.stats.eeg.ufp     = 0.05;
defaults.stats.topoFDR     = 1;
defaults.stats.rft.nonstat = 0;
defaults.stats.results.volume.distmin =  8;
defaults.stats.results.volume.nbmax   =  3;
defaults.stats.results.svc.distmin    =  4;
defaults.stats.results.svc.nbmax      = 16;
defaults.stats.results.mipmat         = {fullfile(spm('dir'),'MIP.mat')};

% Filename prefix defaults
%==========================================================================
defaults.slicetiming.prefix           = 'a';
defaults.realign.write.prefix         = 'r';
defaults.coreg.write.prefix           = 'r';
defaults.unwarp.write.prefix          = 'u';
defaults.normalise.write.prefix       = 'w';
defaults.deformations.modulate.prefix = 'm';
defaults.smooth.prefix                = 's';
defaults.imcalc.prefix                = 'i';

% Realignment defaults
%==========================================================================
defaults.realign.estimate.quality = 0.9;
defaults.realign.estimate.interp  = 2;
defaults.realign.estimate.wrap    = [0 0 0];
defaults.realign.estimate.sep     = 4;
defaults.realign.estimate.fwhm    = 5;
defaults.realign.estimate.rtm     = 1;
defaults.realign.write.mask       = 1;
defaults.realign.write.interp     = 4;
defaults.realign.write.wrap       = [0 0 0];
defaults.realign.write.which      = [2 1];

% Unwarp defaults
%==========================================================================
defaults.unwarp.estimate.rtm      = 0;
defaults.unwarp.estimate.fwhm     = 4;
defaults.unwarp.estimate.basfcn   = [12 12];
defaults.unwarp.estimate.regorder = 1;
defaults.unwarp.estimate.regwgt   = 1e5;
defaults.unwarp.estimate.foe      = [4 5];
defaults.unwarp.estimate.soe      = [];
defaults.unwarp.estimate.rem      = 1;
defaults.unwarp.estimate.jm       = 0;
defaults.unwarp.estimate.noi      = 5;
defaults.unwarp.estimate.expround = 'Average';
%
% Unwarp uses defaults.realign.write defaults for writing.
%

% Coregistration defaults
%==========================================================================
defaults.coreg.estimate.cost_fun = 'nmi';
defaults.coreg.estimate.sep      = [4 2];
defaults.coreg.estimate.tol      = [0.02 0.02 0.02 0.001 0.001 0.001 0.01 0.01 0.01 0.001 0.001 0.001];
defaults.coreg.estimate.fwhm     = [7 7];
defaults.coreg.write.interp      = 4;
defaults.coreg.write.wrap        = [0 0 0];
defaults.coreg.write.mask        = 0;

% Spatial Normalisation defaults
%==========================================================================
defaults.normalise.write.preserve   = 0;
defaults.normalise.write.bb         = [[-78 -112 -70];[78 76 85]];
defaults.normalise.write.vox        = [2 2 2];
defaults.normalise.write.interp     = 4;

% Old Spatial Normalisation defaults
%==========================================================================
defaults.old.normalise.estimate.smosrc  = 8;
defaults.old.normalise.estimate.smoref  = 0;
defaults.old.normalise.estimate.regtype = 'mni';
defaults.old.normalise.estimate.weight  = '';
defaults.old.normalise.estimate.cutoff  = 25;
defaults.old.normalise.estimate.nits    = 16;
defaults.old.normalise.estimate.reg     = 1;
defaults.old.normalise.write.preserve   = 0;
defaults.old.normalise.write.bb         = [[-78 -112 -70];[78 76 85]];
defaults.old.normalise.write.vox        = [2 2 2];
defaults.old.normalise.write.interp     = 1;
defaults.old.normalise.write.wrap       = [0 0 0];
defaults.old.normalise.write.prefix     = 'w';

% VBM Preprocessing defaults
%==========================================================================
defaults.old.preproc.tpm     = cellstr(char(...
    fullfile(spm('Dir'),'toolbox','OldSeg','grey.nii'),...
    fullfile(spm('Dir'),'toolbox','OldSeg','white.nii'),...
    fullfile(spm('Dir'),'toolbox','OldSeg','csf.nii'))); % Prior probability maps
defaults.old.preproc.ngaus          = [2 2 2 4]'; % Gaussians per class
defaults.old.preproc.warpreg        = 1;          % Warping Regularisation
defaults.old.preproc.warpco         = 25;         % Warp Frequency Cutoff
defaults.old.preproc.biasreg        = 0.0001;     % Bias regularisation
defaults.old.preproc.biasfwhm       = 60;         % Bias FWHM
defaults.old.preproc.regtype        = 'mni';      % Affine Regularisation
defaults.old.preproc.fudge          = 5;          % Fudge factor, can not be set in batch GUI
defaults.old.preproc.samp           = 3;          % Sampling distance
defaults.old.preproc.output.GM      = [0 0 1];
defaults.old.preproc.output.WM      = [0 0 1];
defaults.old.preproc.output.CSF     = [0 0 0];
defaults.old.preproc.output.biascor = 1;
defaults.old.preproc.output.cleanup = 0;

% Smooth defaults
%==========================================================================
defaults.smooth.fwhm = [8 8 8];


%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%-Prevent users from making direct calls to spm_defaults
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
persistent runOnce
try
    if ~isdeployed && isempty(runOnce)
        d = dbstack;
        if isempty(intersect({'spm','spm_get_defaults'},{d.name}))
            fprintf(['Direct calls to spm_defauts are deprecated.\n' ...
                'Please use spm(''Defaults'',modality) ' ...
                'or spm_get_defaults instead.\n']);
            runOnce = 1;
        end
    end
end

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%-Execute user-specified defaults files
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
def = defaults;
user_defaults = 'spm_my_defaults.m';
if exist(user_defaults,'file')
    if isdeployed && exist(fullfile(spm('Dir'),user_defaults),'file')
        user_defaults_file = cellstr(fullfile(spm('Dir'),user_defaults));
    else
        user_defaults_file = cellstr(which(user_defaults,'-ALL'));
    end
    for i=1:numel(user_defaults_file)
        try
            spm('run', user_defaults_file{i});
        catch
            lr = lasterror;
            warning(lr.message);
        end
    end
    if spm_check_version('matlab','8.0') >= 0, my_isequaln = @isequaln;
    else my_isequaln = @isequalwithequalnans; end
    if ~my_isequaln(def,defaults)
        fprintf('Defaults settings have been modified by file(s):\n');
        for i=1:numel(user_defaults_file)
            fprintf('  %s\n',user_defaults_file{i});
        end
        fn0 = fieldnames(def);
        mf = fn0(~cellfun(@(x) my_isequaln(def.(x),defaults.(x)),fn0));
        if ~isempty(mf)
            fprintf('Modified fields: ');
            for i=1:numel(mf)
                fprintf('%s ',mf{i});
            end
            fprintf('\n');
        end
    end
end