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spm_defaults.m
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spm_defaults.m
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function spm_defaults
% Sets the defaults which are used by SPM
%_______________________________________________________________________
%
% This file is intended to be customised for the site.
% Individual users can make copies which can be stored in their own
% matlab subdirectories. If ~/matlab is ahead of the SPM directory
% in the MATLABPATH, then the users own personal defaults are used.
%
% This function 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.
%
% Care must be taken when modifying this file.
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: spm_defaults.m 3953 2010-06-28 16:58:48Z guillaume $
%-Prevent users from making direct calls to this function
%-----------------------------------------------------------------------
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
global defaults
% Command Line Usage default
%=======================================================================
defaults.cmdline = 0;
% User Interface defaults
%=======================================================================
defaults.ui.print = struct('opt',{{'-dpsc2','-append'}},'append',true,'ext','.ps');
defaults.ui.colour = [0.73 0.78 0.96];
defaults.renderer = 'zbuffer';
defaults.ui.fs = 14; % unused
% 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 = 'img'; % used for DICOM, ECAT and MINC import
% DICOM Import defaults
%=======================================================================
defaults.dicom.root = 'flat'; % Folder hierarchy
% Stats defaults
%=======================================================================
defaults.stats.maxmem = 2^26;
defaults.stats.maxres = 64;
defaults.stats.fmri.ufp = 0.001; % Upper tail F-probability
defaults.stats.pet.ufp = 0.05;
defaults.stats.eeg.ufp = 1;
defaults.stats.topoFDR = 1;
defaults.stats.rft.nonstat = 0;
% Mask defaults
%=======================================================================
defaults.mask.thresh = -Inf;
% fMRI design defaults
%=======================================================================
defaults.stats.fmri.fmri_t = 16;
defaults.stats.fmri.fmri_t0 = 1;
defaults.stats.fmri.hpf = 128;
defaults.stats.fmri.cvi = 'AR(1)';
% 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.smooth.prefix = 's';
% Realignment defaults
%=======================================================================
defaults.realign.estimate.quality = 0.9;
defaults.realign.estimate.weight = {''};
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 = 1;
defaults.coreg.write.wrap = [0 0 0];
defaults.coreg.write.mask = 0;
% Spatial Normalisation defaults
%=======================================================================
defaults.normalise.estimate.smosrc = 8;
defaults.normalise.estimate.smoref = 0;
defaults.normalise.estimate.regtype = 'mni';
defaults.normalise.estimate.weight = '';
defaults.normalise.estimate.cutoff = 25;
defaults.normalise.estimate.nits = 16;
defaults.normalise.estimate.reg = 1;
defaults.normalise.estimate.wtsrc = 0;
defaults.normalise.write.preserve = 0;
defaults.normalise.write.bb = [[-90 -126 -72];[ 90 90 108]];
defaults.normalise.write.vox = [2 2 2];
defaults.normalise.write.interp = 1;
defaults.normalise.write.wrap = [0 0 0];
% VBM Preprocessing defaults
%=======================================================================
defaults.preproc.tpm = cellstr(char(...
fullfile(spm('Dir'),'tpm','grey.nii'),...
fullfile(spm('Dir'),'tpm','white.nii'),...
fullfile(spm('Dir'),'tpm','csf.nii'))); % Prior probability maps
defaults.preproc.ngaus = [2 2 2 4]'; % Gaussians per class
defaults.preproc.warpreg = 1; % Warping Regularisation
defaults.preproc.warpco = 25; % Warp Frequency Cutoff
defaults.preproc.biasreg = 0.0001; % Bias regularisation
defaults.preproc.biasfwhm = 60; % Bias FWHM
defaults.preproc.regtype = 'mni'; % Affine Regularisation
defaults.preproc.samp = 3; % Sampling distance
defaults.preproc.output.GM = [0 0 1];
defaults.preproc.output.WM = [0 0 1];
defaults.preproc.output.CSF = [0 0 0];
defaults.preproc.output.biascor = 1;
defaults.preproc.output.cleanup = 0;
% Smooth defaults
%=======================================================================
defaults.smooth.fwhm = [8 8 8];