vb_set_brain_parm

 Set parameters to create brain model.
    brain_parm = vb_set_brain_parm([fs_dir]);

 [Input]
         fs_dir : freesurfer subject directory.
 [Output]
    brain_parm : import parameters to create brain model.

 [See also]
    vb_job_brain.m

 2016-06-02 Masa-aki Sato

 Copyright (C) 2011, ATR All Rights Reserved.
 License : New BSD License(see VBMEG_LICENSE.txt)

0001 function [brain_parm] = vb_set_brain_parm(fs_dir)
0002 % Set parameters to create brain model.
0003 %    brain_parm = vb_set_brain_parm([fs_dir]);
0004 %
0005 % [Input]
0006 %         fs_dir : freesurfer subject directory.
0007 % [Output]
0008 %    brain_parm : import parameters to create brain model.
0009 %
0010 % [See also]
0011 %    vb_job_brain.m
0012 %
0013 % 2016-06-02 Masa-aki Sato
0014 %
0015 % Copyright (C) 2011, ATR All Rights Reserved.
0016 % License : New BSD License(see VBMEG_LICENSE.txt)
0017 
0018 %
0019 % --- Standard parameters
0020 %
0021 
0022 %
0023 % Input file(absolute path)
0024 %
0025 if ~exist('fs_dir', 'var')
0026     fs_dir = '';
0027 end
0028 
0029 surf_dir   = fullfile(fs_dir, 'bem');
0030 label_dir  = fullfile(fs_dir, 'label');
0031 
0032 % FreeSurfer model(.asc)
0033 % (check : Version 4.2 and 4.5)
0034 brain_parm.FS_left_file         = fullfile(surf_dir,  'lh.smoothwm.asc');
0035 brain_parm.FS_right_file        = fullfile(surf_dir,  'rh.smoothwm.asc');
0036 brain_parm.FS_left_infl_file    = fullfile(surf_dir,  'lh.inflated.asc');
0037 brain_parm.FS_right_infl_file   = fullfile(surf_dir,  'rh.inflated.asc');
0038 brain_parm.FS_left_curv_file    = fullfile(surf_dir,  'lh.curv.asc');
0039 brain_parm.FS_right_curv_file   = fullfile(surf_dir,  'rh.curv.asc');
0040 brain_parm.FS_left_sphere_file  = fullfile(surf_dir,  'lh.sphere.reg.asc');
0041 brain_parm.FS_right_sphere_file = fullfile(surf_dir,  'rh.sphere.reg.asc');
0042 brain_parm.FS_sphere_key        = 'sphere.reg';
0043 brain_parm.FS_left_label_file   = fullfile(label_dir, 'lh.cortex.label');
0044 brain_parm.FS_right_label_file  = fullfile(label_dir, 'rh.cortex.label');
0045 
0046 % registration method to standard brain model.
0047 %     = 'FS' : Freesurfer sphere file is used.
0048 brain_parm.registration_mode='FS';
0049 
0050 % MRI image
0051 brain_parm.analyze_file = 'Subject.nii';
0052 
0053 %
0054 % Output file(relative path from proj_root)
0055 %
0056 brain_parm.brain_file = 'Subject.brain.mat';
0057 brain_parm.area_file  = 'Subject.area.mat';
0058 brain_parm.act_file   = 'Subject.act.mat';
0059 
0060 
0061 %
0062 % --- Advanced parameters
0063 %  Do not change, unless you understand the meaning of the parameters!!
0064 %
0065 
0066 % coordinate space of brain model
0067 brain_parm.brain_space = 'mni'; % = 'mni'  : MNI space(default)
0068                                 % = 'subj' : individual space
0069 
0070 % Maximum radius for neighbor search
0071 brain_parm.R_max = 0.018;
0072 
0073 % Total Vertex number(Priority:Nvertex>reduce_ratio)
0074 brain_parm.Nvertex = 10000;
0075 
0076 % Reduce ratio for original surface data
0077 brain_parm.reduce_ratio = 0.1;
0078 
0079 % Division number of z axis in matching between BV and MRI points
0080 brain_parm.N_step = 50;
0081 
0082 % Display progress for this steps
0083 brain_parm.display = 200;