Home > batch > prt_cfg_weights.m

prt_cfg_weights

PURPOSE ^

Preprocessing of the data.

SYNOPSIS ^

function weights = prt_cfg_weights

DESCRIPTION ^

 Preprocessing of the data.
_______________________________________________________________________
 Copyright (C) 2011 Machine Learning & Neuroimaging Laboratory

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SUBFUNCTIONS ^

SOURCE CODE ^

0001 function weights = prt_cfg_weights
0002 % Preprocessing of the data.
0003 %_______________________________________________________________________
0004 % Copyright (C) 2011 Machine Learning & Neuroimaging Laboratory
0005 
0006 % Written by M.J.Rosa
0007 % $Id$
0008 
0009 % ---------------------------------------------------------------------
0010 % filename Filename(s) of data
0011 % ---------------------------------------------------------------------
0012 infile        = cfg_files;
0013 infile.tag    = 'infile';
0014 infile.name   = 'Load PRT.mat';
0015 infile.filter = 'mat';
0016 infile.num    = [1 1];
0017 infile.help   = {['Select PRT.mat (file containing data/design/models ',...
0018                  'structure).']};
0019 
0020 % ---------------------------------------------------------------------
0021 % model_name Feature set name
0022 % ---------------------------------------------------------------------
0023 model_name         = cfg_entry;
0024 model_name.tag     = 'model_name';
0025 model_name.name    = 'Model name';
0026 model_name.help    = {'Name of a model. Must correspond with one ' ...
0027                       'specified in ''Run model'' and ''Specify model'''...
0028                       'batch modules.' };
0029 model_name.strtype = 's';
0030 model_name.num     = [1 Inf];
0031 
0032 % ---------------------------------------------------------------------
0033 % img_name Feature set name
0034 % ---------------------------------------------------------------------
0035 img_name         = cfg_entry;
0036 img_name.tag     = 'img_name';
0037 img_name.name    = 'Image name (optional)';
0038 img_name.help    = {['Name of the file with weights (optional). If left empty ',...
0039                     ' an automatic name will be generated.']};
0040 img_name.strtype = 's';
0041 img_name.num     = [0 Inf];
0042 img_name.val     = {''};
0043 
0044 % ---------------------------------------------------------------------
0045 % flag_cwi Build the weight images for each permutation (optional)
0046 % ---------------------------------------------------------------------
0047 flag_cwi         = cfg_menu;
0048 flag_cwi.tag     = 'flag_cwi';
0049 flag_cwi.name    = 'Build weight images for permutations';
0050 flag_cwi.help    = {['Set to Yes to compute the weight images obtained ' ...
0051     'from each permutation. This is to further assess the significance ' ...
0052     'of the ranking distance between two models.']};
0053 flag_cwi.labels  = {
0054                'Yes'
0055                'No'
0056 }';
0057 flag_cwi.values  = {1 0};
0058 flag_cwi.val     = {0};
0059 
0060 % ---------------------------------------------------------------------
0061 % atl_name Filename for the atlas to compute the weights per ROI
0062 % ---------------------------------------------------------------------
0063 atl_name         = cfg_files;
0064 atl_name.tag     = 'atl_name';
0065 atl_name.name    = 'Load Atlas';
0066 atl_name.ufilter = '.*';
0067 atl_name.filter  = 'image';
0068 atl_name.num     = [0 1];
0069 atl_name.val     = {{''}};
0070 atl_name.def     = @(val)prt_get_defaults('fs.atlasroi', val{:});
0071 atl_name.help    = {'Select atlas file to build weights per ROI.'};
0072 
0073 % ---------------------------------------------------------------------
0074 % no_atl No weight per ROI
0075 % ---------------------------------------------------------------------
0076 no_atl         = cfg_const;
0077 no_atl.tag     = 'no_atl';
0078 no_atl.name    = 'No weight per ROI';
0079 no_atl.val     = {0};
0080 no_atl.help    = {'Not computing weight per ROI.'};
0081 
0082 % ---------------------------------------------------------------------
0083 % build_wpr Build the weight images per ROI
0084 % ---------------------------------------------------------------------
0085 build_wpr         = cfg_choice;
0086 build_wpr.tag     = 'build_wpr';
0087 build_wpr.name    = 'Build weight images per ROI';
0088 build_wpr.help    = {['Set to Yes to compute the weight images per ROI ' ...
0089     'You need then to select the atlas image.']};
0090 % build_wpr.labels  = {
0091 %                'Yes'
0092 %                'No'
0093 % }';
0094 build_wpr.values  = {no_atl atl_name};
0095 build_wpr.val     = {no_atl};
0096 
0097 % ---------------------------------------------------------------------
0098 % flag_wroi Build the weight images for each ROI (optional)
0099 % ---------------------------------------------------------------------
0100 flag_wroi         = cfg_menu;
0101 flag_wroi.tag     = 'flag_cwi';
0102 flag_wroi.name    = 'Build weight images per ROI';
0103 flag_wroi.help    = {['Set to Yes to compute the weight images obtained ' ...
0104     'from each ROI.']};
0105 flag_wroi.labels  = {
0106                'Yes'
0107                'No'
0108 }';
0109 flag_wroi.values  = {1 0};
0110 flag_wroi.val     = {0};
0111 
0112 % ---------------------------------------------------------------------
0113 % cv_model Preprocessing
0114 % ---------------------------------------------------------------------
0115 weights        = cfg_exbranch;
0116 weights.tag    = 'weights';
0117 weights.name   = 'Compute weights';
0118 weights.val    = {infile model_name img_name build_wpr flag_cwi};
0119 weights.help   = {[
0120     'Compute weights. This module computes the linear weights of a classifier ',...
0121     'and saves them as a 4D image. 3 dimensions correspond to the image dimensions specified in ',...
0122     'the second-level mask, while the extra dimension corresponds to the number of folds. ',...
0123     'There is one 3D weights image per fold.']};
0124 weights.prog   = @prt_run_weights;
0125 weights.vout   = @vout_data;
0126 
0127 %------------------------------------------------------------------------
0128 %% Output function
0129 %------------------------------------------------------------------------
0130 function cdep = vout_data(job)
0131 % Specifies the output from this modules, i.e. the filename of the mat file
0132 
0133 cdep(1)            = cfg_dep;
0134 cdep(1).sname      = 'PRT.mat file';
0135 cdep(1).src_output = substruct('.','files');
0136 cdep(1).tgt_spec   = cfg_findspec({{'filter','mat','strtype','e'}});
0137 cdep(2)            = cfg_dep;
0138 cdep(2).sname      = 'Weight image file';
0139 cdep(2).src_output = substruct('.','files');
0140 cdep(2).tgt_spec   = cfg_findspec({{'filter','img','strtype','e'}});
0141 %------------------------------------------------------------------------

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