Home > vbmeg > functions > template > vb_set_brain_parm_fsaverage.m

vb_set_brain_parm_fsaverage

PURPOSE ^

Set parameters to make cortical surface model 'fsaverage'.

SYNOPSIS ^

function brain_parm = vb_set_brain_parm_fsaverage(fsaverage_dir,sbj_dir)

DESCRIPTION ^

 Set parameters to make cortical surface model 'fsaverage'. 

 'fsaverage' data is used to performe inter-subject analysis of cortical
 current estimated on cortical surface models of individual
 subjects. This function is used with vb_job_brain and
 vb_job_brain_add_sph_coord (see example). The following files are
 required for making cortical surface model: 

  surf/[lh/rh].smoothwm.asc
  surf/[lh/rh].inflated.asc
  surf/[lh/rh].curv.asc
  surf/[lh/rh].sphere.reg.asc
  mri/T1.[hdr/img/nii] (ANALYZE or NIfTI)

 These files are not included in FreeSurfer package. You need to convert
 original files by using FreeSurfer's commands as follows: 

  cd $SUBJECTS_DIR/fsaverage/surf
  mris_convert [lh/rh].smoothwm [lh/rh].smoothwm.asc
  mris_convert [lh/rh].inflated [lh/rh].inflated.asc
  mris_convert -c curv [lh/rh].smoothwm [lh/rh].curv.asc
  mris_convert [lh/rh].sphere.reg [lh/rh].sphere.reg.asc
  cd $SUBJECTS_DIR/fsaverage/mri
  mri_convert --out_type [analyze/nifti1] T1.mgz T1

 Where $SUBJECTS_DIR is FreeSurfer's subject directory. 

 [syntax]
 brain_parm = vb_set_brain_parm_fsaverage(fsaverage_dir,sbj_dir)

 [input]
 fsaverage_dir: <<string>> Directory of subject 'fsaverage'. 
 sbj_dir      : <<string>> VBMEG subject directory for 'fsaverage'. New
                files (.brain.mat etc.) are put on this directory. This
                must be a relative path from 'proj_root' directory,
                which is given to vb_job_brain and
                vb_job_brain_add_sphcoord.

 [output]
 brain_parm: <<struct>> Parameter set for vb_job_brain and
             vb_job_brain_add_sphcoord.

 [example]
 >> fsavr_dir = '/home/cbi-data5/taku-y/analysis/freesurfer/fsaverage';
 >> sbj_dir   = 'brain/fsaverage';
 >> brain_parm = vb_set_brain_parm_fsaverage(fsavr_dir,sbj_dir);
 >> vb_job_brain(proj_root,brain_parm);
 >> vb_job_inflate(proj_root,brain_parm);
 >> vb_job_brain_add_sphcoord(proj_dir,brain_parm);

 [history]
 2010-11-30 Taku Yoshioka

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

CROSS-REFERENCE INFORMATION ^

This function calls: This function is called by:

SOURCE CODE ^

0001 function brain_parm = vb_set_brain_parm_fsaverage(fsaverage_dir,sbj_dir)
0002 % Set parameters to make cortical surface model 'fsaverage'.
0003 %
0004 % 'fsaverage' data is used to performe inter-subject analysis of cortical
0005 % current estimated on cortical surface models of individual
0006 % subjects. This function is used with vb_job_brain and
0007 % vb_job_brain_add_sph_coord (see example). The following files are
0008 % required for making cortical surface model:
0009 %
0010 %  surf/[lh/rh].smoothwm.asc
0011 %  surf/[lh/rh].inflated.asc
0012 %  surf/[lh/rh].curv.asc
0013 %  surf/[lh/rh].sphere.reg.asc
0014 %  mri/T1.[hdr/img/nii] (ANALYZE or NIfTI)
0015 %
0016 % These files are not included in FreeSurfer package. You need to convert
0017 % original files by using FreeSurfer's commands as follows:
0018 %
0019 %  cd $SUBJECTS_DIR/fsaverage/surf
0020 %  mris_convert [lh/rh].smoothwm [lh/rh].smoothwm.asc
0021 %  mris_convert [lh/rh].inflated [lh/rh].inflated.asc
0022 %  mris_convert -c curv [lh/rh].smoothwm [lh/rh].curv.asc
0023 %  mris_convert [lh/rh].sphere.reg [lh/rh].sphere.reg.asc
0024 %  cd $SUBJECTS_DIR/fsaverage/mri
0025 %  mri_convert --out_type [analyze/nifti1] T1.mgz T1
0026 %
0027 % Where $SUBJECTS_DIR is FreeSurfer's subject directory.
0028 %
0029 % [syntax]
0030 % brain_parm = vb_set_brain_parm_fsaverage(fsaverage_dir,sbj_dir)
0031 %
0032 % [input]
0033 % fsaverage_dir: <<string>> Directory of subject 'fsaverage'.
0034 % sbj_dir      : <<string>> VBMEG subject directory for 'fsaverage'. New
0035 %                files (.brain.mat etc.) are put on this directory. This
0036 %                must be a relative path from 'proj_root' directory,
0037 %                which is given to vb_job_brain and
0038 %                vb_job_brain_add_sphcoord.
0039 %
0040 % [output]
0041 % brain_parm: <<struct>> Parameter set for vb_job_brain and
0042 %             vb_job_brain_add_sphcoord.
0043 %
0044 % [example]
0045 % >> fsavr_dir = '/home/cbi-data5/taku-y/analysis/freesurfer/fsaverage';
0046 % >> sbj_dir   = 'brain/fsaverage';
0047 % >> brain_parm = vb_set_brain_parm_fsaverage(fsavr_dir,sbj_dir);
0048 % >> vb_job_brain(proj_root,brain_parm);
0049 % >> vb_job_inflate(proj_root,brain_parm);
0050 % >> vb_job_brain_add_sphcoord(proj_dir,brain_parm);
0051 %
0052 % [history]
0053 % 2010-11-30 Taku Yoshioka
0054 %
0055 % Copyright (C) 2011, ATR All Rights Reserved.
0056 % License : New BSD License(see VBMEG_LICENSE.txt)
0057 
0058 % Input files
0059 brain_parm.FS_left_file       = [fsaverage_dir '/surf/lh.smoothwm.asc'];
0060 brain_parm.FS_right_file      = [fsaverage_dir '/surf/rh.smoothwm.asc'];
0061 brain_parm.FS_left_infl_file  = [fsaverage_dir '/surf/lh.inflated.asc'];
0062 brain_parm.FS_right_infl_file = [fsaverage_dir '/surf/rh.inflated.asc'];
0063 brain_parm.FS_left_curv_file  = [fsaverage_dir '/surf/lh.curv.asc'];
0064 brain_parm.FS_right_curv_file = [fsaverage_dir '/surf/rh.curv.asc'];
0065 brain_parm.brain_sphL = [fsaverage_dir '/surf/lh.sphere.reg.asc'];
0066 brain_parm.brain_sphR = [fsaverage_dir '/surf/rh.sphere.reg.asc'];
0067 
0068 brain_parm.analyze_file = [fsaverage_dir '/mri/T1.hdr'];
0069 brain_parm.spm_normalization_file = [];
0070 
0071 % Output files (relative path from proj_root)
0072 brain_parm.brain_file  = [sbj_dir filesep 'fsaverage.brain.mat'];
0073 brain_parm.area_file   = [sbj_dir filesep 'fsaverage.area.mat'];
0074 brain_parm.act_file    = [sbj_dir filesep 'fsaverage.act.mat'];
0075 
0076 % ID of sphere coordinate
0077 brain_parm.key         = 'sphere.reg';
0078 
0079 %
0080 % --- Advanced parameters
0081 %  Do not change, unless you understand the meaning of the parameters!!
0082 %
0083 
0084 % Maximum radius for neighbor search
0085 brain_parm.R_max = 18e-3; % 18mm
0086 
0087 % Total Vertex number after reduction(Priority:Nvertex>reduce_ratio)
0088 brain_parm.Nvertex = 20000;
0089 
0090 % Reduce ratio for BV surface data
0091 brain_parm.reduce_ratio = 0.1;
0092 
0093 % Division number of z axis in matching between BV and MRI points
0094 brain_parm.N_step = 50;
0095 
0096 % Display progress for this steps
0097 brain_parm.display = 200;
0098 
0099 return;

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