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prt_defaults

PURPOSE ^

Sets the defaults which are used by the Pattern Recognition for

SYNOPSIS ^

function prt_defaults

DESCRIPTION ^

 Sets the defaults which are used by the Pattern Recognition for
 Neuroimaging Toolbox, aka. PRoNTo.

 FORMAT prt_defaults
_______________________________________________________________________

 This file can be customised to any the site/person own setup.
 Individual users can make copies which can be stored on their own
 matlab path. Make sure your 'prt_defaults' is the first one found in the
 path. See matlab documentation for details on setting path.

 Care must be taken when modifying this file!

 The structure and content of this file are largely inspired by SPM:
 http://www.fil.ion.ucl.ac.uk/spm
_______________________________________________________________________
 Copyright (C) 2011 Machine Learning & Neuroimaging Laboratory

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function prt_defaults
0002 % Sets the defaults which are used by the Pattern Recognition for
0003 % Neuroimaging Toolbox, aka. PRoNTo.
0004 %
0005 % FORMAT prt_defaults
0006 %_______________________________________________________________________
0007 %
0008 % This file can be customised to any the site/person own setup.
0009 % Individual users can make copies which can be stored on their own
0010 % matlab path. Make sure your 'prt_defaults' is the first one found in the
0011 % path. See matlab documentation for details on setting path.
0012 %
0013 % Care must be taken when modifying this file!
0014 %
0015 % The structure and content of this file are largely inspired by SPM:
0016 % http://www.fil.ion.ucl.ac.uk/spm
0017 %_______________________________________________________________________
0018 % Copyright (C) 2011 Machine Learning & Neuroimaging Laboratory
0019 
0020 % Written by Christophe Phillips
0021 % $Id$
0022 
0023 %%
0024 global prt_def
0025 
0026 % Global defaults
0027 % prt_loc = which('prt_batch');
0028 % prt_def.global.install_dir = fileparts(prt_loc);
0029 prt_def.global.install_dir = prt('dir');
0030 
0031 % Default colors of the different elements
0032 %-----------------------------------------------
0033 % prt_def.color.bg1=[0 0.8 1];
0034 % prt_def.color.bg2=[0.9,0.6,0.3];
0035 % prt_def.color.fr=[1,0.5,0.7];
0036 % prt_def.color.high=[0.2,0.2,0.8];
0037 
0038 prt_def.color.bg1  = [0.83,0.83,0.83];
0039 prt_def.color.bg2  = [0.88,0.88,0.88];
0040 prt_def.color.fr   = [0.92,0.92,0.92];
0041 prt_def.color.high = [0.8 0 0];
0042 prt_def.color.black = [0 0 0];
0043 
0044 % Parameters for the data and design
0045 %-----------------------------------------------
0046 prt_def.datad.hrfd = 0; % HRF delay in seconds
0047 prt_def.datad.hrfw = 0; % HRF FWHM, used to compute the overlap between conditions
0048 
0049 prt_def.prep.default_mask  = fullfile(prt('dir'),'masks', ...
0050                                 'SPM_mask_noeyes.hdr');% default mask
0051 
0052 % Preprocessing defaults
0053 %------------------------------------------------
0054 % memory limit for kernel/file arrays construction
0055 prt_def.fs.mem_limit = 256*1024*1024;  % bytes of memory to use
0056 prt_def.fs.writeraw  = 0;              % flag to write the data detrended (default) or raw (to set to 1).
0057 
0058 % Default atlas for ROI defintion
0059 prt_def.fs.atlasroi  = cellstr(fullfile(prt('dir'),'atlas', ...
0060     'aal_79x91x69.img')); 
0061 
0062 % Design specification default
0063 prt_def.dspec.use3 = [1 2];
0064 
0065 
0066 
0067 % Specify model: Parameters of the different machines
0068 %--------------------------------------------------
0069 prt_def.model.svmargs     = 1;
0070 prt_def.model.libsvmargs  = '-q -s 0 -t 4 -c ';
0071 prt_def.model.gpcargs     = '-l erf -h';%-h
0072 prt_def.model.gpclapargs  = '-h'; %'-h';
0073 prt_def.model.gprargs     = '-l gauss -h'; % -h
0074 prt_def.model.krrargs     = 1;
0075 prt_def.model.rtargs      = 601;
0076 prt_def.model.l1MKLargs   = 1;
0077 prt_def.model.l1MKLmaxitr = 250;
0078 
0079 % Parralelization of the code
0080 %--------------------------------------------------
0081 prt_def.paral.allow     = false; % use (or not) 'parfor' loops
0082 prt_def.paral.ncore     = 3;     % number of cores that can be used.
0083 
0084 return

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