Home > fmri > simulate > simulate_defaults.m

simulate_defaults

PURPOSE ^

Defaults _ copied from ts1, initially created for Schubert batch analyses

SYNOPSIS ^

This is a script file.

DESCRIPTION ^

 Defaults _ copied from ts1, initially created for Schubert batch analyses

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 %
0002 % Defaults _ copied from ts1, initially created for Schubert batch analyses
0003 %
0004 
0005 %
0006 % Defaults for analysis 'defaults_edit'
0007 %
0008 
0009 %
0010 % NOTE: It is better to set normalization defaults in the script that handles
0011 % all the normalization batching.  If they are set here, any values set in the
0012 % normalization batch script are not used!
0013 %
0014 
0015 % Set general defaults
0016 
0017 defaults_edit = struct( ...
0018    'type_area', [1 2], ...
0019    'index',     [1 1] ...
0020 );
0021 
0022 defaults_edit(2) = struct( ...
0023     'type_area', 4, ...
0024     'index', 1 ...
0025     );
0026 
0027 type_area = {'Misc','Printing','Hdr','Statistics', ...
0028       'Normalisation','RealignCoreg','Reset'};
0029        
0030 Misc = struct( ...
0031     'log_to_file', 1, ...
0032     'log_file_name', sprintf('analysis_log_%s', datestr(now,1)), ...
0033     'cmdline', 1, ...
0034     'grid', 0.1 ...
0035     );
0036 
0037 Printing(1) = struct( ...
0038    'printing_mode', 1,  ...
0039    'postscript_filename', sprintf('realign_%s_%s', datestr(now,1), datestr(now,15)),  ...
0040    'postscript_type', 1,  ...
0041    'default_printer', 0,  ...
0042    'printer_name', '',  ...
0043    'post_type', '-dps',  ...
0044    'graphics_filename', '',  ...
0045    'graph_type', 3,  ...
0046    'print_string', '' ...
0047 );
0048 
0049 Printing(2) = Printing(1);
0050 Printing(2).postscript_filename = sprintf('coregister_%s', datestr(now,1));
0051 Printing(2).postscript_type = 2;
0052 
0053 Hdr = struct( ...
0054    'defaults_area',  3, ...
0055    'image_size_voxels',  '10 20 30', ...
0056    'voxel_size_mm',  '4 4 4', ...
0057    'scale',  1, ...
0058    'data_type',  16, ...
0059    'offset',  0, ...
0060    'origin_voxels',  '1 1 1', ...
0061    'description',  'oufff' ...
0062    );
0063 
0064 RealignCoreg = struct( ...
0065     'defaults_area', 4, ...
0066     'separate_combine' , -11, ...
0067     'create' , 1, ...
0068     'adjust', 0, ...
0069     'mask', 1, ...
0070     'reg_quality', 1.0 ...   
0071     );
0072 
0073 Normalisation(1) = struct( ...
0074    'defaults',  1, ...
0075    'estimates',  1, ...
0076    'custom_estimates',  ones(1,12), ...
0077    'custom_norm',  -1, ...
0078    'nonlin_func_nb', 13, ...        %  7=4x5x4
0079    'func_nb',  0, ...
0080    'nonlin_ite_nb',  12, ...
0081    'nonlin_regular',  0.01, ...
0082    'mask_brain',  0, ...
0083    'mask_object_brain',  0 ...
0084 );
0085 
0086 Normalisation(2).defaults = 0;
0087 Normalisation(2).bounding_box = [1];
0088 Normalisation(2).voxel_sizes = 0;
0089 Normalisation(2).voxel_sizes_custom = [3.5 3.5 5];
0090 
0091 Statistics = struct( ...
0092    'fMRI_T',        16, ...
0093    'fMRI_T0',        1, ...
0094    'F_threshold',  1 ...
0095 );
0096

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