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nic_spm_defaults

PURPOSE ^

Sets the defaults which are used by SPM

SYNOPSIS ^

function nic_spm_defaults

DESCRIPTION ^

 Sets the defaults which are used by SPM

 FORMAT spm_defaults
_______________________________________________________________________

 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.

 Care must be taken when modifying this file
_______________________________________________________________________
 Copyright (C) 2005 Wellcome Department of Imaging Neuroscienic_e

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

DOWNLOAD ^

nic_spm_defaults.m

SOURCE CODE ^

0001 function nic_spm_defaults
0002 % Sets the defaults which are used by SPM
0003 %
0004 % FORMAT spm_defaults
0005 %_______________________________________________________________________
0006 %
0007 % This file is intended to be customised for the site.
0008 % Individual users can make copies which can be stored in their own
0009 % matlab subdirectories. If ~/matlab is ahead of the SPM directory
0010 % in the MATLABPATH, then the users own personal defaults are used.
0011 %
0012 % Care must be taken when modifying this file
0013 %_______________________________________________________________________
0014 % Copyright (C) 2005 Wellcome Department of Imaging Neuroscienic_e
0015 
0016 % John Ashburner, Andrew Holmes
0017 % $Id: spm_defaults.m 256 2005-10-17 18:57:24Z guillaume $
0018 
0019 
0020 global defaults
0021 
0022 % Misc
0023 %=======================================================================
0024 defaults.grid     = 0.4;
0025 defaults.cmdline  = 0;
0026 
0027 % File format specific
0028 %=======================================================================
0029 defaults.analyze.multivol = 0;
0030 defaults.analyze.flip     = 1; % <<= Very important.  Relates to L/R
0031 
0032 % Stats defaults
0033 %=======================================================================
0034 defaults.stats.maxmem   = 2^20;
0035 defaults.stats.maxres   = 64;
0036 defaults.stats.fmri.ufp = 0.001;
0037 defaults.stats.pet.ufp  = 0.05;
0038 defaults.stats.eeg.ufp  = 1;
0039 
0040 % Mask defaults
0041 %=======================================================================
0042 defaults.mask.thresh    = 0.8;
0043 
0044 % Realignment defaults
0045 %=======================================================================
0046 defaults.realign.estimate.quality = 0.9;
0047 defaults.realign.estimate.weight = 0;
0048 defaults.realign.estimate.interp = 2;
0049 defaults.realign.estimate.wrap   = [0 0 0];
0050 defaults.realign.estimate.sep    = 4;
0051 defaults.realign.estimate.fwhm   = 5;
0052 defaults.realign.estimate.rtm    = 1;
0053 defaults.realign.write.mask      = 1;
0054 defaults.realign.write.interp    = 4;
0055 defaults.realign.write.wrap      = [0 0 0];
0056 
0057 % Unwarp defaults
0058 %=======================================================================
0059 defaults.unwarp.estimate.fwhm    = 4;
0060 defaults.unwarp.estimate.basfcn  = [12 12];
0061 defaults.unwarp.estimate.regorder= 1;
0062 defaults.unwarp.estimate.regwgt  = 1e5;
0063 defaults.unwarp.estimate.soe     = 1;
0064 defaults.unwarp.estimate.rem     = 1;
0065 defaults.unwarp.estimate.jm      = 0;
0066 defaults.unwarp.estimate.noi     = 5;
0067 defaults.unwarp.estimate.expround= 'Average';
0068 %
0069 % Unwarp uses defaults.realign.write
0070 % defaults for writing.
0071 %
0072 
0073 % Coregistration defaults
0074 %=======================================================================
0075 defaults.coreg.estimate.cost_fun = 'nmi';
0076 defaults.coreg.estimate.sep      = [4 2];
0077 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];
0078 defaults.coreg.estimate.fwhm     = [7 7];
0079 defaults.coreg.write.interp      = 1;
0080 defaults.coreg.write.wrap        = [0 0 0];
0081 defaults.coreg.write.mask        = 0;
0082 
0083 % Spatial Normalisation defaults
0084 %=======================================================================
0085 defaults.normalise.estimate.smosrc  = 8;
0086 defaults.normalise.estimate.smoref  = 0;
0087 defaults.normalise.estimate.regtype = 'mni';
0088 defaults.normalise.estimate.weight  = '';
0089 defaults.normalise.estimate.cutoff  = 25;
0090 defaults.normalise.estimate.nits    = 16;
0091 defaults.normalise.estimate.reg     = 1;
0092 defaults.normalise.estimate.wtsrc   = 0;
0093 defaults.normalise.write.preserve   = 0;
0094 defaults.normalise.write.bb         = [[-78 -112 -50];[78 76 85]];
0095 defaults.normalise.write.vox        = [2 2 2];
0096 defaults.normalise.write.interp     = 1;
0097 defaults.normalise.write.wrap       = [0 0 0];
0098 
0099 % Segmentation defaults
0100 %=======================================================================
0101 defaults.segment.estimate.priors = char(...
0102     fullfile(nic_spm('Dir'),'apriori','grey.nii'),...
0103     fullfile(nic_spm('Dir'),'apriori','white.nii'),...
0104     fullfile(nic_spm('Dir'),'apriori','csf.nii'));
0105 defaults.segment.estimate.reg    = 0.01;
0106 defaults.segment.estimate.cutoff = 30;
0107 defaults.segment.estimate.samp   = 3;
0108 defaults.segment.estimate.bb     =  [[-88 88]' [-122 86]' [-60 95]'];
0109 defaults.segment.estimate.affreg.smosrc = 8;
0110 defaults.segment.estimate.affreg.regtype = 'mni';
0111 %defaults.segment.estimate.affreg.weight = fullfile(spm('Dir'),'apriori','brainmask.nii');
0112 defaults.segment.estimate.affreg.weight = '';
0113 defaults.segment.write.cleanup   = 1;
0114 defaults.segment.write.wrt_cor   = 1;
0115 defaults.segment.write.wrt_brV   = 1;
0116 
0117 % Bias field estimation defaults (UNUSED)
0118 %=======================================================================
0119 defaults.bias.nbins  = 256;    % Number of histogram bins
0120 defaults.bias.reg    = 0.01;    % Regularisation
0121 defaults.bias.cutoff = 30;    % DCT frequenic_y cutoff (mm)
0122 
0123 % VBM Preprocessing defaults
0124 %=======================================================================
0125 defaults.preproc.tpm     = char(...
0126     fullfile(nic_spm('Dir'),'tpm','grey.nii'),...
0127     fullfile(nic_spm('Dir'),'tpm','white.nii'),...
0128     fullfile(nic_spm('Dir'),'tpm','csf.nii')); % Prior probability maps
0129 defaults.preproc.ngaus    = [2 2 2 4];     % Gaussians per class
0130 defaults.preproc.warpreg  = 1;             % Warping Regularisation
0131 defaults.preproc.warpco   = 25;            % Warp Frequenic_y Cutoff
0132 defaults.preproc.biasreg  = 0.0001;        % Bias regularisation
0133 defaults.preproc.biasfwhm = 60;            % Bias FWHM
0134 defaults.preproc.regtype  = 'mni';         % Affine Regularisation
0135 defaults.preproc.samp     = 3;             % Sampling distanic_e
0136 
0137 % ImCalc defaults
0138 %=======================================================================
0139 defaults.imcalc.dmtx   = 0;                 % Data Matrix
0140 defaults.imcalc.mask   = 0;                 % Masking
0141 defaults.imcalc.interp = 1;                 % Interpolation
0142 defaults.imcalc.dtype  = nic_spm_type('int16'); % Data Type
0143 
0144 % User Interface Defaults
0145 %=======================================================================
0146 defaults.ui.print   = struct('opt',{{'-dpsc2','-append'}},'append',true,'ext','.ps');
0147 defaults.ui.colour1 = [0.8 0.8 1.0];
0148 defaults.ui.colour2 = [1.0 1.0 0.8];
0149 defaults.ui.colour3 = [0.0 0.0 0.0];
0150 defaults.ui.fs      = 14;
0151 
0152 % EEG specific
0153 %=======================================================================
0154 defaults.eeg.dtype = 'float';
0155

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