=====  VBMEG ꡼Ρ

С0.5-1.a.0
CVSversion_0_5_1_a_0

=====  CVS

CVSROOT
  :pserver:username@lobule2:/home/cbi/rhayashi/cvs_repository/vbmeg_genesis

===== С(0.5-0.b.0)νɲùܰ

()ϴؿ󥿥եѹѥ᡼ѹեեޥåȤѹ

ܰ
1.brain
  1-1.()job_brainؤεǽɲäȤȼatlas2vbġؿλѹ
2.fmri
3.meg
  3-1.()megmatեѹ
  3-2.load_megؿEEGб
  3-3.()EEGǡcalibrationǽɲ
  3-4.()12/16bitMEGǡб
4.basis
  4-1.()job_leadfieldƹ
  4-2.()EEG꡼ɥեɻإإåб
  4-3.¿ض̥ǥˤ붭̷ؿ
5.bayes
  5-1.()ʿ경ե륿ȾȺȾ¤Ϳ褦ˤ뽤
  5-2.MEGŸץѹ
6.current
  6-1.ή׻˶ʿ경ǳĥ줿ΰޤʤ褦ˤ뽤
  6-2.job_current, job_current_trcurrent_parm¸ɲ
  6-3.ή׻ؿν
7.GUI
  7-1.()job_plot_megεǽɲ
  7-2.GUIѹ(Rfilter, Rfilter_globalνѹб)
  7-3.job_select_areaλѹ
  7-4.()project_mgrǽɲ
  7-5.job_plot_currentmapήɽ˴ؤ뽤
  7-6.brainGUIFreeSurferб
  7-7.ή׻ѤGUIɲ
  7-8.Activity map ԽGUI(job_edit_act)ɲ
  7-9.MRI¸GUIɲ
8.¾ѹ
  8-1.()ɽ̤Ƭɽ̤Υ饤ɽˡѹ
  8-2.ʿ경르ꥺѹ
  8-3.()Curry ǡMatlab̾ι®
  8-4.atlasϢν
  8-5.()change_file_basename()ؿλѹ
  8-6.()ݡϢ⥸塼ν
  8-7.plotؿɲá
  8-8.ե̤ĥʿ경, Хͥǥɽʿ경ؿɲ
  8-9.ĺꥹȤϢΰФؿɲ
  8-10.get_class_color()ؿɲ
  8-11.load_analyze_noflip()ؿɲ
  8-12.Ѳǽʥ֤ɽġ(for MATLAB6.5)ɲ
  8-13.ݡϢ⥸塼ɲ
  8-14.MNIƥץ졼Ȳɲ
  8-15.MEG/EEG١饤桼ƥƥؿο
  8-16.meg.matեؿο
  8-17.ؿplot_brain_inflate_new.mɲ
  8-18.surface, maskǡνؿɲá
  8-19.ɸǾ٥ĿǾ˼ؿɲ
  8-20.ɸѴؿɲ
  8-21.եå桼ƥƥؿɲ
  8-22.stackؿɲ
  8-23.()dipoleؿ
  8-24.ĥݡ⥸塼ɲ
  8-25.()load_cortex()
  8-26.HEAD-MATեheadǡؿɲ
  8-27.̵ʺɸͤؿɲ
  8-28.eegֹ碌ؿɲ
  8-29.Script-Mեǥ쥯ȥκ
  8-30.ʸӴؿɲ
  8-31.žִؿɲ
  8-32.2˵ؿɲ
  8-33.surf_file, analyze_filebrain,area,actfileؿɲ

9.Х
  9-1.ݥꥴǥϢ̼ФؿΥХ
  9-2.vbmeg_current_reconstruct_tr.m Υǥ쥯ȥ
  9-3.job_plot_currentmap, job_edit_areaǾǥɽ˴ؤԶ罤
  9-4.job_preprocess_meg3ΥХ
  9-5.job_view_cortexХ
  9-6.surface, maskǡؿΥХ
  9-7.GUIԶ罤
  9-8.job_plot_currentmapԶ罤

===== ܺ

ܾܺ
1.brain
  1-1.()job_brainؤεǽɲäȤȼatlas2vbġؿλѹ

    brain_parm.spm_normalization_fileꤵ줿
     1. job_brainMNIɸTalairachɸ׻뵡ǽɲä
     2. ˶ʬ䥨ꥢե뵡ǽä

    [ѹ]
      job/
        job_brain.m, 
      tool_box/atlas2vb/
        calc_mni_coord.m,
        atlas2vb.m,
        atlas2vb_aal.m,
        script_atlas2vb.m, 
      brain/
        make_brain_data.m,
        make_brain_data2.m
    [ɲ]
      tool_box/atlas2vb/
        spm_dctmtx.m

    [ѥ᡼ѹ]
       brain_parm
            : brain_parm.spm_normalization_file(ץʥ)ɲá
       atlas2vb.m, atlas2vb_aal.m, calc_mni_coord
            : parm.save_xyzfile  ѻ
    [եѹ]
       brainfile:
         ѿ  Vmni, Vtal, derrɲá
         Vmni,VtalϡĿǾĺˤMNIɸTalairachɸ
         derrϡĿǾĺɸǾΥܥκǶ˵ȤεΥ
         줾ñ̤ϥ᡼ȥ롣
    []
       MNIɸTalairachɸϡ̥ե(xyzfile)˽񤭽Ф
       顢brainfileѿȤƽ񤭹褦ˤʤäΤǡ
       atlas2vb 桼դ뤳ȡ

2.fmri
3.meg
  3-1.()MEGinfoνѹ
    - MEGinfo.MEGch_name, MEGinfo.EEGinfo.*_ch_name
      ºݤΥֹ+1ͤäƤΤ
    - ե󥹥󥵾eegǡȤ¸褦ˤ
      (ɲ)
        MEGinfo.EEGinfo.refmg_ch_name
                       .refmg_ch_ix
    - MEG-MATե(.meg.mat)ˡMeasurementȤѿɲä
        Measurement = 'MEG';

    []
      device/meg/yokogawa
          load_yokogawa_meg_header.m make_yokogawa_meg_data.m 
      device/meg/yokogawa/readfunc
          read_yokogawa_channel_def.m read_yokogawa_data.m

    [ؿ󥿥եѹ]
      ͤch_nameɲ
      [channel_def] = read_yokogawa_channel_def(fid);
                      
      [channel_def, ch_name] = read_yokogawa_channel_def(fid);

  3-2.load_megؿEEGб
    load_meg_data  load_meg_info ؿeeg-mat(.eeg.mat)ե
    Ϥ褦ɲä
    []
      common/loadfunc/
        load_meg_data.m, load_meg_info.m
    [ɲ]
      common/loadfunc/
        load_measurement_info.m
    [] load_meg_infoǤϡeeg-matեͿƤMEGinfo֤ͤ

  3-3.()EEGǡcalibrationǽɲ
     MEGEEGΥǡϿݡǡˤϤΥϤʤᡢ
    Ű᤹ͤȤǤʤǡϤ뤿GUI
    yokogawaMEGǡݡGUI顢ϤǤ褦ˤ
    meg_parm.eeg_gainФƥͥ̾ȥ(uV/V)ꤹ뤳Ȥǡ
    make_meg_dataǥǡcalibrationԤ
    
    [ɲ]
     ǡ
      template/
        Modified Files:
          set_yokogawa_meg_parm_test.m set_yokogawa_meg_parm.m
      device/meg/yokogawa
        Modified Files:
          ()load_yokogawa_meg.m load_yokogawa_meg_header.m 
          make_yokogawa_meg_data.m
        Added Files:
          calibrate_yokogawa_eeg_data.m define_yokogawa.m 
          load_yokogawa_calibrated_eeg_data.m load_yokogawa_eeg_header.m 
      device/meg/yokogawa/readfunc
        Modified Files:
          read_yokogawa_data.m

      GUI
       Added Directory:
          gui/eeg_gain_input
        Added Files:
          gui/eeg_gain_input
          eeg_gain_input.fig eeg_gain_input.m

      yokogawaMEGǡݡGUI
        preAnalysis/callback_func
          Modified Files:
            pa_yokogawa_meg_callback.m pa_yokogawa_meg_gui_util.m
        preAnalysis/create_func
          Modified Files:
            pa_yokogawa_meg.fig 
        preAnalysis/init_func
          Modified Files:
            pa_init_yokogawa_meg_gui.m
    [ѥ᡼ѹ]
      meg_parm.eeg_gainɲá
        eeg_gain(:, 1) = Nx1 : ĴEEGֹͥ(MEGΥֹͥ)
        eeg_gain(:, 1) = Nx1 : (ñ:uV/V)
    [եѹ]
      MEG-matե(.meg.mat)ѿeegˤĤơ
      ʲ̤ѹˤʤä
      (ޤ)
         ǥͤȤƵϿ
      (줫)
        ĴԤʤä硧MEGϤ줿Ű(ʥ)ܥȤ¸
        ĴԤä:EEGŰͤܥȤ¸

  3-4.12/16bitMEGǡб
    12bit/16bitMEGǡեɤ߹褦˽
    [ѹ]
      device/meg/yokogawa/
        define_yokogawa.m
        load_yokogawa_calibrated_eeg_data.m 
        ()load_yokogawa_meg.m 
    [ɲ]
      device/meg/yokogawa/yokogawa_lib
        GetMeg160ADbitInfoM.p

4.basis
  4-1.()job_leadfieldƹ
      ꡼ɥեɷ׻ؿιľ
      EEGصǥȤȾ¤ͤå
        Ⱦ¤Ȥ
      job_leadfield_eeg_bem顼ˤʤ
    [ɲ]
      leadfield/
          job_leadfield_meg_sphere.m
          job_leadfield_meg_bem.m
          job_leadfield_meg_harmonics.m
          job_leadfield_eeg_sphere.m
          job_leadfield_eeg_bem.m
          lf_preprocess.m
      leadfield/head
          calc_consistent_eeg_radius.m
    []
        job_leadfield  job/replaced/job_leadfield_old Ȥưư
        job_leadfieldƤӽФƤδؿ leadfield/relaced/ذư
          prepare_lead_field.m
          prepare_bem.m
          calc_lead_field.m

    [եѹ]
       MEG̴ؿ׻˹MEG-MATեhead_fileɲá
       ɲ MEGinfo.SPHinfo Ǥ

       << MEGinfo.SPHinfo>>
       ------------------------------------
        harmo_coef: [1295x416 double]
        func_order: 35
            radius: 0.0796
         head_file: 'sample.head.mat'        <<< ɲåե
        ------------------------------------

  4-2.()EEG꡼ɥեɻإإåб
    EEG꡼ɥեɷ׻(EEG-SPHERE, EEG-BEM)ˡheadǡȤƻإǥͿ롣
    []
      leadfield/
          prepare_lead_field.m prepare_bem.m
      common/loadfunc/
          load_sensor.m
      template/
          set_basis_parm.m, set_basis_parm_test.m
    [ɲ]
      common/loadfunc/
          load_device.m load_eeg_data.m load_eeg_sensor.m
      device/eeg/biosemi/ (new directory)
          load_eeg_data_biosemi.m load_eeg_sensor_biosemi.m
      common/utility/
          util_get_file_body.m util_distance_of_points.m
          util_check_head_shell_info.m
      leadfield/head/ (new directory)
          util_calc_head_radius.m util_make_joined_head_file.m
          util_make_omega_file.m, util_get_specified_layer_headinfo
      device/eeg/
          eeginfo_get_sensor_position.m eeginfo_set_sensor_position.m
    [եѹ]
       '.eeg.mat'եɲ

  4-3.¿ض̥ǥˤ붭̷ؿ
    ñإإåɤˤб
    []
      leadfield/eeg/
        bem_matrix.m

5.bayes
  5-1.()ʿ경ե륿ȾȺȾ¤Ϳ褦ˤ뽤
    ʿ경ե륿ȾȺȾ¤򳰤Ϳ褦ˤ
    Rfilt 顼λȾ
    Rfilt=[R, Rmax] ηǺȾ¤Ϳ

    []
      estimation/bayes
          prepare_leadfield.m
      template/
          set_bayes_default_parameters.m 

    [ѥ᡼ѹ]
      (ѹ)  bayes_parm.Rfilt        = 6e-3;
                bayes_parm.Rfilt_global = bayes_parm.Rfilt
      (ѹ)  bayes_parm.Rfilt        = [6e-3, 6e-3];
                bayes_parm.Rfilt_global = 0;

  5-2.MEGŸץѹ
      ΥץǤϡήʬ׻ݡѥ᡼ˤä
      focal modelglobal modelΤ줫ѤƤfocal 
      modelΥݡfMRIˤäѤ뤿ᡢglobal model
      Ѥ褦ˤơ̤ꤹ褦ˤޤήʬ
      ׻뤿VB르ꥺ¹ԤݡޤǤѤƤ®
      ؽ§ߤơ̾ؽ§Τ߻Ѥ褦ˤ
    [ѹ]
      job/
        job_vb.m
      estimation/bayes/
        vb_baseline_variance_acquisition.m 

6.current
  6-1.ή׻˶ʿ경ǳĥ줿ΰޤʤ褦ˤ뽤
    VB˥ꥢǻꤵ줿ĺΤߤ׻
    []
      estimation/bayes/
          vb_load_result.m

  6-2.job_current, job_current_trcurrent_parm¸ɲ
    ץȥե(.prj.mat)current_parm¸ɲä
    []
      job/
          job_current_tr.m job_current.m

  6-3.ή׻ؿν
    xxLmode=3κݤεưѹˤʤä
    [V,xx] = current_vector(V,xx,Lmode)

    if xx == [] &  Lmode = 3 
        xx(n       ,:) =  [1 0 0]
        xx(n + NV  ,:) =  [0 1 0]
        xx(n + 2*NV,:) =  [0 0 1]

    []
      leadfield/
          current_vector.m

7.GUI
  7-1.()job_plot_megεǽɲ
    - 򥰥վ򤷡ؿƤӽФindex֤ǽ
    - ǡ¿᤯
    - ɽMEGɽθɤ
      (MATLAB ver.6/7ξ򥵥ݡȤ롣)


    [ؿ󥿥եѹ]
      ()                            job_plot_meg(megfile, mode)

      ()[twin_meg, gui_cancelled] = job_plot_meg(megfile, mode, twin_lim, twin_ini)

      twin_meg : 򤵤줿(MEGdatasampleindex)
      gui_cancelled : true/false(closeܥ򲡲trueʳǤfalse)

      twin_lim : ǽʻϰ(MEGdatasampleindexǻꤹ)
      twin_ini : ǽ餫򤵤ƤϰϤꤹ(MEGdatasampleindexǻꤹ)

    []
      job/job_plot_meg/
          job_plot_meg_update_timecourse.m 
          job_plot_meg_update_spatialpattern.m 
          job_plot_meg_change_trial.m job_plot_meg.m job_plot_meg.fig 
    [ɲ]
      job/job_plot_meg/
          define_job_plot_meg_const.m

  7-2.GUIѹ(Rfilter, Rfilter_globalνѹб)
    bayes_parm.Rfilter, Rfilter_globalνѹб
    []
      gui/bayes_parm_editor
          bayes_parm_editor_advanced.fig bayes_parm_advanced_gui.m 

  7-3.job_select_areaλѹ
    job_select_area*.bayes.matɤ߹ߤ*.curr.matɤ߹ߤѹ
    (եեޥåȤѹˤʤꡢɤ߹ե뤬ѹˤʤä)
    ޤTimeWindowǤ褦ˤ
    [ɲ]
      job/job_select_area
          select_time_window_gui.m, select_time_window.m,
          select_time_window_gui.fig
    [ѹ]
      plotfunc/
          select_area.m

  7-4.()project_mgrǽɲ
    1.GUI,GUI,ή׻GUI˥ϵǽ
    2.project_mgrʲΥץꥱưǤ褦ˤ
          job_view_cortex       Ǿǥɽ
          job_plot_meg          MEGɽ
          job_plot_currentmap   ήɽ
          job_edit_area         ꥢκ
          job_select_area       ꥢκ
          job_edit_act          Activity mapԽ
      ưˡ
      (a)project_mgrHistoryɽԤ1Ǳå
         ɽ˥塼顢ץꥱ̾򤹤
      (b)project_mgrTools˥塼饢ץꥱ򤷡
         ɽ줿ɬפʥե򤷤ϡOKܥ򲡲롣
    [ɲ]
       gui/project_mgr/tool_launcher(ġ뵯ưGUI)
    [ѹ]
       ϵǽɲ
         gui/bayes/parm_editor(GUI)
            /current_gui(ή׻GUI)
            /preAnalysis(GUI)
       ץꥱȤϢȵǽɲ
         gui/project_mgr
    [ѥ᡼ѹ]
      GUIѥ᡼Υեɤ˰ʲɲ

      keyword = ե̾ư˻
      comment = ˴ؤ륳¸˻

      brain_parm.keyword
                .comment
      fmri_parm.comment
      meg_parm.keyword
              .comment
      basis_parm.keyword
                .comment
      bayes_parm.comment
      current_parm.comment

  7-5.job_plot_currentmapήɽ˴ؤ뽤
    - patch_norm=ONξˡήñɽѤ褦ˤ
    - ϡ򤷤(򤷤ĺμ)ή٤¤
      ɽƤʿѤɽ褦ѹ
    - ؿload_current()Ѥ褦ˡץ
    []
      job/job_plot_currentmap/
          job_plot_currentmap.m
          job_plot_cmap_update_timecourse.m

  7-6.brainGUIFreeSurferб
    brainGUIFreeSurferΥեꤹ뵡ǽɲä
    []
      gui/preAnalysis/create_func/
          pa_brain.fig
      gui/preAnalysis/init_func
          pa_init_brain_gui.m 
      gui/preAnalysis/callback_func/
          pa_brain_callback.m pa_brain_gui_util.m 

  7-7.ή׻ѤGUIɲ
    ή׻ԤGUIɲäޤ 
    vbmeg_current_reconstruct_tr.mǹԤƤǥ쥯ȥ 
      äǥ쥯ȥꤷݤ˴ʤԤᡢõޤ
    []
      gui/project_mgr
          project_mgr.m project_mgr.fig project_file_mgr.m
    [ɲ]
      gui/current_gui
          current_gui.m current_gui.fig

  7-8.Activity map ԽGUI(job_edit_act)ɲ
    Activity mapԽ뤿Υ桼ƥƥjob_edit_actɲá
    ưޥåפФʿ경(ؿƥå״ؿ)
    [ɲ]
      job/job_edit_actʲδؿ
      brain/
          step_filter.m
    []
      ̤εǽޤ٤ԽȤϤǤ֡
      job_edit_act_spatial_gauss_filter.mϡ衢Ūʴؿ֤롣

  7-9.MRI¸GUIɲ
    analyzeեɤ߹MRI饤ɽ
    ޥǤդ򤷤ơκɸͤե¸GUIɲá
    [ɲ]
      tool_box/mri_toolbox/mri_point_select/
                                           /mps_pointlist
                                           /mps_fileio
                                           /analyze_info

8.¾ѹ
  8-1.()ɽ̤Ƭɽ̤Υ饤ɽˡѹ
    ɽ̤Ƭɽ̤ηå뤿
    MRI饤̤̤ɽؿä
    (ޤǤϡ饤ɽƤ)
    ȼɽ̤Ƭɽ̤򥹥饤ɽ뤳ޤǤδؿ
    []
      plotfunc/
          plot_slice_fit.m plot_slice.m plot_fit_vivid.m plot_fit_scan.m 
          plot_fit.m
      plotfunc/check_model/
          check_brain_model.m
    [ؿ󥿥եѹ]
        plot_slice( B, V, zindx, vertex_mode, Nsubfig, Msize)
                                 
        plot_slice( B, V, zindx, xymode, Nsubfig, Msize)
    []
        check_brain_modelѹˤʤäƤΤǡjob_brainиβ̤
        СȰۤʤ

  8-2.ʿ경르ꥺѹ
    []
      common/boundary/
          surf_smooth_fit.m surf_smooth.m
  8-3.()Curry ǡMatlab̾ι®
      create_curry_patchѤơread_curry_surface®

    [ؿ󥿡եѹ]

      (ѹ)[F,V,xx] = read_curry_surface(curryfile,avwfile)
      (ѹ)[F,V,xx,Ninfo] = read_curry_surface(curryfile)

      (ѹ)job_curry2vbmeg(curryfile,avwfile,headfile)
      (ѹ)job_curry2vbmeg(curryfile,headfile)

    []
      job/
          job_curry2vbmeg.m
      leadfield/curry/
          read_curry_surface.m

    [ɲ]
      leadfield/curry/
          create_curry_patch.m

  8-4.atlasϢν
    1.ꥢե¸Ȥ䤤碌ʤ褦ˤ
    2.ȥ饹٥η侮
    3.Х
    4.ȥ饹ɽɲäȽ
      plot_atlas(brainfile,atlasfile,atlas_id)
      plot_atlas2(brainfile,Atlas)
      plot_atlas_area(brainfile,Atlas)

    []
      tool_box/atlas2vb/ʲ(¿ΤᵭҾά)

  8-5.()change_file_basenameѹ
    [ؿ󥿡եѹ]
        ()[fname ,basename, ext] = change_file_basename(fold, addname)
        ()[fname ,basename, ext] = change_file_basename(fold, addname, ext)

    []
      common/utility/
          change_file_basename.m

    [ؿ]
      change basename of file for predefined extension
       [fname ,basename, ext] = change_file_basename(fold, addname)
       [fname ,basename, ext] = change_file_basename(fold, addname, ext)
      --- Input
      fold    : old file name = [ old_basename  extension ]
      addname : this string is added to the basename of the file name
      --- Optional input
      ext     : extension
         If this variable is not specified, 
         predefined extensions is used
      --- Output
      basename = [ old_basename  addname ]
      fname    : new file name = [ basename  extension ]
      ext      : extension

  8-6.ݡϢ⥸塼ν
    ι«դʤݡˡ
    MATLABŬؿ
    ݡǤդ˻Ǥ
    ͤȤͿοˤʤ
    ǾήΤΥХǥˤɾ
    奢եȤ俴異եȤꤹ뤿
    ӥСȤɾ٤
    ץ륹ץ job_test_dipole.m 򻲾

    [ѹ]
      estimation/dipole/
          ()dipole_search.m
              ݡΰõؿ
          ()dipole_current.m, ()dipole_basis.m
              ݡΰֿή׻
          ()dipole_error.m 
              奢եȤ俴異եȤꤹ뤿
              ӥСȤɾ

  8-7.plotؿɲá
    [ɲ]
      plotfunc/
        plot_2d_image.m
        plot_3d_image.m
        plot_cross_section.m
          get_cross_section.m
        plot_slice_surf.m
        plot_slice_head.m
        plot_head_surf.m
        plot_cross_section.m
        plot_compare_brain.m
        plot_boundary_edge.m
        plot_brain_mask.m
    []
      plotfunc/
        plot_slice_fit.m    顼åɲ
        plot_marker.m       ޡ̾ɲåץåȤ뵡ǽɲ
        
  8-8.ե̤ĥʿ경, Хͥǥɽʿ경ؿɲ
    [ɲ]
      common/boundary/
        surf_smooth_expand.m

  8-9.ĺꥹȤϢΰФؿɲ
    [ɲ]
      common/boundary/
        connected_vertex.m

  8-10.get_class_color()ؿɲ
    [ɲ]
      common/utility/
        rand_index.mat get_class_color.m 
    [ؿ]
      Make color map for class label
       cmap = get_class_color(Nclass)
      --- Input
      Nclass : # of class
      --- Output
      cmap : colormap matrix for class plot
           : [Nclass x 3]

  8-11.load_analyze_noflip()ؿɲ
    [ɲ]
      common/loadfunc/
        load_analyze_noflip.m
    [ؿ]
      load analize image without L-R flip
      Use to read Right-hand analyze image for plot
       [B, Vdim, Vsize] = load_analyze_noflip(analyzefile)
      --- Input
      analyzefile - Analyze filename 
      --- Output
      B     : 3D image data  [Xdim, Ydim, Zdim ]
      Vdim  : image size  [Xdim  Ydim  Zdim ] (voxels)
      Vsize : voxel size  [x y z ] (mm)

  8-12.Ѳǽʥ֤ɽġ(for MATLAB6.5)ɲ
    Ѳǽʥ֤ɽġ(for MATLAB6.5)ɲ
    [ɲ]
      common/utility/
        dumpmemmex.dll
    []
      MATLAB7ʹߤfeature('Dump')ޥɤȤ

  8-13.ݡϢ⥸塼ɲ
    [ɲ]
      leadfield/sphere/
        sarvas_sensor.m, sarvas_basis.m
              ݡѤ˺äǥΥ꡼ɥեɷ׻
      vbmeg/estimation/dipole
        dipole_error_sarvas.m
              ǾήΤΥХǥˤɾ

    []
      ȡ9-6.ݡϢ⥸塼ν

  8-14.MNIƥץ졼Ȳɲ
    ɸǾɲ
    [ɲ]
      tool_box/atlas2vb/MNI_atlas_templates
        ch2bet.img    --- ĿǾ27󥹥󤷤ʿѲ(Ƭդ)
        ch2bet.hdr
        ch2.img       --- ĿǾ27󥹥󤷤ʿѲ(Ƭ̵)
        ch2.hdr
        brain_mask.mat--- ɸǾ̥ޥåץǡ

  8-15.MEG/EEG١饤桼ƥƥؿο
    MEG LaboratoryǤϡûʿΥǡФ
    ١饤ǤʤΤᡢVBMEGǥ١饤
    ԤΥ桼ƥƥؿ򿷵
    [ɲ]
      common/utility/corr_base.m
    []
      ߤϡꤷλʿѤˤΤߥݡȡ

  8-16.meg.matեؿο
    ʣ.meg.matե礹뤿Υ桼ƥƥؿ򿷵
    [ɲ]
      common/utility/combine_meg_files.m
    []
      ߤϡVBMEG ver 0.500ΥեեޥåȤΤߥݡȡ
      եեޥåȤѤСδؿ⽤ɬפ롣

  8-17.ؿplot_brain_inflate_new.mɲ
    plot_brain_inflate.mǥե뤫ǡɤ߹Ǥꡢ
    ΨäΤᡢɬפʥѥ᡼ľѥץå
    ؿȤplot_brain_inflate_new.m
    ǤϡǥɽץबƤӽФؿ˽񤫤
    礬¿

    [ɲ]
      plotfunc/plot_brain_inflate_new.m
    []
      衢δؿȤޤplot_brain_inflate.m
      δؿǴ֤뤳ȤͽꤷƤ롣

  8-18.surface, maskǡνؿɲá
    ɽ̷Խδˤ礭ѹ˾ܺ٤򵭽ҡ
    [ɲ]
      job/
        job_import_cortex.m --- 
      common/boundary/
        boundary_edge.m  --- ̤ζ׻
        close_surf.m     --- surfaceĤ
        close_line.m
        mask_to_surf_expand.m ---ޥǡԽsurfaceǡ
      common/morphology/
        smooth_cortex_LR.m    --- Ⲥʿ경ʿ경ǥ
        surf_to_filled_mask.m --- surfaceޥǡѴ
        get_3d_mask_point.m   --- ޥǡλꥹ饤
        get_3d_mask_slice.m   --- ޥǡλꥹ饤Υޥ
        mask_image_size.m     --- ְƥåפ˱ޥ׻
        make_inner_sphere.m 

    []
      job/
        job_smooth_cortex.m
        job_smooth_head.m 
      common/coordinate
        analyze_right_mm_to_spm_right.m
        analyze_right_to_spm_right.m
      common/morphology/
        smooth_cortex.m 
        cortex_fill.m
        remove_vertex_by_mask.m
        surf_extract.m
        trans_surf_to_vox.m
        trans_vox_to_surf.m 
      common/boundary
        get_boundary.m
        combine_surf.m
        surf_smooth_expand.m
        surf_smooth_fit.m 

    ɽ̷Խδ

    ƬɸɤɬľAnalize-Right-mmѴ
        Analizeեꤷ trans_surf_to_vox Ѵ
        ޥ᡼ trans_surf_to_vox ǵ᤿ Dim ꤷƺ
    ɽԽޥ᡼ Analyze_right [mm] ɸǹԤ
    ¸SPM-Right-m Ѵ
        analyze_right_mm_to_spm_right Ѵ
    Analizeե˥饤ɽ򤹤Analize-Right-voxelѴ
        analyze_mm_to_analyze Ѵ
        Vana = analyze_mm_to_analyze(Vana,Vdim,Vsize)
        [B] = load_analyze_to_right(analyzefile);
        plot_slice_surf( B, Vana, F, zindx, 'z');
    ޥ᡼˥饤ɽ򤹤 Voxel size ΰ㤤
        [B] = surf_to_filled_mask(Vox, F, Dim, step)
        plot_slice_surf( B, Vox/step, F, zindx/step, 'z');

     ɽ̺ɸݡޥɸѴ: Spm_right [m] -> Analyze_right [mm]
    [Vox, Para] = trans_surf_to_vox(V, analyze_file, step)
    % Transform 3D surface coordinate to Analyze_right [mm] to make mask image
    % step  =  Voxel size of mask image [mm]
    % Vox    : voxel coordinate : Analyze_right [mm]
    % Para.Vdim   =  Voxel dimension of Analyze image
    % Para.Vsize  =  Voxel size of Analyze image [mm]
    % Para.vstep  =  Voxel size of mask image [mm] = step
    % Para.Dim    =  Dimension of mask image

     ޥɸݡɽ̺ɸѴ: Analyze_right [mm] -> Spm_right [m]
    ɽ̺ɸե¸ Spm_right [m] Ѵ
    V = analyze_right_mm_to_spm_right(Vox,Vdim,Vsize);

     ɽԽ Analyze_right [mm] ɸѴȤ
    ʲƤδؿ V Analyze_right [mm] ɸǤ뤳ȤꤷƤ

    --------------------------------------------------
     Make smooth cortex from brain model
    [Vx,Fnew,xx,Vindx,Vinfo] = smooth_cortex(V, F, Para)

    --------------------------------------------------
     Expand surface by morphology and smooth surface by spring model
    [V, F, xx, B] = surf_smooth_expand(V, F, xx, Para)

    --------------------------------------------------
     Make filled mask image from surface cordinate
    [B] = surf_to_filled_mask(V, F, Dim, step, X0, Radius)

    --------------------------------------------------
     ̤ɤĤ֤DޥѥѴ
    ̤ʣʤΤsurf_to_filled_maskǤɤĤ֤ʤ
    [B, XL, XR] = cortex_fill(V,F,step,Radius,LR_mode,Dim)

    --------------------------------------------------
     Extract boundary surface from mask image
    [F, V, xx]  = surf_extract(B, step)

     Fit surface to the boundary of mask
    [Vx, Fx, xx] = make_inner_sphere(V, Nvertex);     % ̺ܵ
    [Vx, Fx, xx] = surf_smooth_fit(Vx,Fx,xx, B, Para);% ̤ĥ

  8-19.ɸǾ٥ĿǾ˼ؿɲ
    [ɲ]
      common/morphology/
        map_mask_image.m
        get_brain_mask.m
        make_upsample_vertex.m
        make_mask_from_vertex.m

  8-20.ɸѴؿɲ
    [ɲ]
      common/coodinate/
        analyze_mm_to_analyze.m
        spm_right_to_analyze_right_mm.m
        analyze_to_analyze_mm.m

  8-21.եå桼ƥƥؿɲ
    Axes, Figure˴ޤޤꤷեå֥Ȥ
    طѹ(/̤˰ư)ؿ
    [ɲ]
      common/utility/
        gobject_send_to_back.m
        gobject_bring_to_front.m 

  8-22.stackؿɲ
    StackؿɲäåХåե򡢥塦ե
    ֤뤳ȤǤ롣礭ʥǡ򥹥åϡե
    ˥å롣
    [ɲ]
      common/utility/stack
        stack_delete.m
        stack_get_length.m
        stack_new.m
        stack_pop.m 
        stack_push.m 
      common/utility/stack/tools/
        f_stack_delete.m f_stack_new.m f_stack_pop.m f_stack_push.m 
        m_stack_delete.m m_stack_new.m m_stack_pop.m m_stack_push.m 

    []
    data = 'test_data';
    % create stack(stack size=10, Memory stack)
    stk = stack_new(10, 'M'); 
    % push
    stk = stack_push(stk, data);
    % pop
    [stk, pop_data] = stack_pop(stk);
    % destroy stack(Don't forget)
    stack_delete(stk);

  8-23.()dipoleؿ
    ߤVBMEGΥǡ¤˹礦褦˽
    [ѹ]
      leadfield/sphere/
        ()dipole_gradio.m
      common/loadfunc
        load_basis_info.m 

  8-24.ĥݡ⥸塼ɲ
    եȽΤᡢĥݡɲ
    extra_dipole/ReadME.txt 򸫤Ʋ

    [ɲ]
      job/
        job_add_extra_dipole.m
        job_add_extra_basis.m 
      extra_dipole/
        ReadME.txt
        make_extra_basis.m
        job_add_extra_area.m 
        job_add_extra_act.m
        duplicate_extra_position.m 
        add_extra_brain.m
        add_extra_basis.m
        add_extra_area.m 
        add_extra_act.m
      template/
        set_extra_brain_parm.m
        set_extra_basis_parm.m

  8-25.()load_cortex()
    load_cortexcoord_typeˡĤͤɲä
       'Talairach'
       'MNI'
    ɤcoord_typeˤʬΤˤ

    [ѹ]
      common/loadfunc/
        load_cortex.m
    [ѥ᡼ѹ]
      coord_type - 
    []
      ưǧϡλ̤Τߡ
      coord_typeͤꤷʤ
      coord_type = 'Inflate'
      coord_type = 'Talairach'

  8-26.HEAD-MATեheadǡؿ
    HEAD-MATե뤪ӤȤΥǡؿɲä
    [ɲ]
      leafield/head/

  8-27.̵ʺɸͤؿɲ
    ֹ碌βǡ̵ʺɸͤȯ礬롣
    ̵ʺɸͤؿɲä
    [ɲ]
      common/coordinate/
        is_invalid_coordinate.m
        valid_coordinate_filter_decode.m 
        valid_coordinate_filter_encode.m

      default_param/
        INVALID_COORDINATE_3D.m
    [Ȥ]
      valid_coordinate_filter_encode 
        valid_coordinate_filter_decode Ȥȹ礻ǻѤ
      ͭʺɸͤΤߤоݤȤ򡢤ĤǶࡣ

    <<Ŭ>>
    coord = digit.eeg_sensor.pos;
    [filt_spec] = valid_coordinate_filter_encode(coord);
    % filt_spec ˤϡͭɸоäƤ

    % Фͭɸ˽ä
    % Ǥϡɸɲúϸ(̵ɸ᤻ʤʤ)
    new_coord = filt_spec.valid_coord;
    new_coord(5,1) = 1.1;
    new_coord(5,2) = 1.2;
    new_coord(5,3) = 1.3;

    % filt_specͭɸեɤùκɸȺؤ
    filt_spec.valid_coord = new_coord;
    
    [new_coord] = valid_coordinate_filter_decode(filt_spec);
    % new_coord ϡ̵ɸܲù夵줿ͭɸ

  8-28.eegֹ碌ؿɲ
    [ɲ]
      job/job_vivid_dir/
        job_fit_eeg.m

  8-29.Script-Mեǥ쥯ȥκ
    Sript-Mեǥ쥯ȥVBMEGScript-Mե
    scriptǥ쥯ȥذư
    [ɲ]
      script/
        curry_to_dicom.m
        demo_line.m
        demo_mri.m
        job_load_vivid.m 
        job_test_dipole.m
        job_vivid_marker.m
        script_atlas2vb.m
        set_current_V.m
        set_head_model.m 
        set_sphere_model.m
        test_berg.m
        test_morfology.m 
        proj_run.m 
    []
      common/morphology
        test_morfology.m
      job/job_plot_currentmap_dir/
        job_plot_currentmap.m
      job/job_vivid_dir/
        job_load_vivid.m, job_vivid_marker.m
      template/
        proj_run.m
      leadfield/bem/
        set_head_model.m
      leadfield/curry/
        curry_to_dicom.m
      estimation/dipole
        job_test_dipole.m 
      tool_box/atlas2vb_dir/
        script_atlas2vb.m 
      tool_box/select3d_dir
        demo_line.m, demo_mri.m
      leadfield/eeg
        set_current_V.m, test_berg.m 
      leadfield/sphere
        set_sphere_model.m

  8-30.ʸӴؿɲ
    ĤΥꥹȤξȹ̤indexȤ֤
    [ɲ]
      common/utility/
        util_get_cross_checked_list.m

    []
      list_a , listb
      'aaa'    'ccc'
      'bbb'    'bbb'
      'ccc'    'aaa'
      'ddd'    'ddd'

      util_get_cross_checked_list(list_a, list_b);

      ans = [1 3;
             2 2;
             3 1;
             4 4]

  8-31.žִؿɲ
    [Nx1] or [1xN]Ϥȡ[1xN] or [Nx1]Ѵ롣
    
    [ɲ]
      common/utility/
        util_arrange_list.m

  8-32.2˵ؿɲ
    ABϤȡAγˤĤơB椫
    ǤᤤõФBindexֹ֤
    [ɲ]
      common/coordinate/
        find_min_distance_2d.m

  8-33.surf_file, analyze_filebrain,area,actfileؿɲ
    surf_file('V', 'F', 'xx', 'Xcenter')analyze_fileϤȡ
    Ǿǥʿ경Ԥbrain_file, area_file, act_fileϤ
    ؿɲä
    [ɲ]
      job/
        job_import_cortex.m
      brain/
        get_cortex_info.m

9.Х
  9-1.ݥꥴǥϢ̼ФؿΥХ
    []
      common/boundary
        separate_surf.m
        neighbor_index.m

  9-2.vbmeg_current_reconstruct_tr.m
     ǥ쥯ȥ꤬¸ߤСŪ˺⤦ٺ
     Ȥäǥ쥯ȥ̾λ㤤
     ʤᡢǥ쥯ȥ꤬äƤ⡢ʤ褦ˤ
    []
      estimation/bayes/
          vbmeg_current_reconstruct_tr.m

  9-3.job_plot_currentmap, job_edit_areaǾǥɽ˴ؤԶ罤
     job_plot_currentmap, job_edit_areaMATLAB7ʹߤǼ¹Ԥȡ
     Ǿǥ뤬ɽʤԶ礬ä
     axesǾǥplotaxis tightaxis equal¹Ԥꡢ
     η̡axesXLimMode, YLimMode, ZLimModeMATLAB7ǤmanualȤʤꡢ
     axesΥꤵƤޤäƤ̡axesǾǥplot
     ƤǾǥ뤬ɽƤʤäMATLAB6.5.1ɽǤƤΤϡ
     plotaxis tightaxis equal¹ԤƤ⡢XlimMode, YLimMode, ZLimMode
     autoΤޤޤäᡢplotɬפʥѹԤ졢ɽ
     Ƥ
    []
      job/job_plot_currentmap
          job_plot_currentmap.m job_plot_cmap_update_spatialpattern.m 
      job/job_edit_area
          job_edit_area.m job_edit_area_update_spatialpattern.m

  9-4 job_preprocess_meg3ΥХ
    1.EOGͥ򻲾ȤΤMEGinfo.MEGch_idѤƤΤMEGch_nameѹ 
    2.ɥեȽˡѥ᥿parm.driftremovalmodeˤ'quodra'typoˤ
      ꤹȤ'quadra'ѹ'quodra'⽾ɤѲġˡ
      ˡѥ᥿ꤹȥ顼Ϥ褦ѹ
    3.٤ƤTrial/sensorreject줿бʥ顼ϡˡ
    4.ե̾ϥǥ󥻥뤷бʥ顼ϡˡ
    []
      job/
        job_preprocess_meg3.m
  9-5.job_view_cortexХ
    ѿ'Area'ؿareaȥХåƥ󥰤ƥ顼ˤʤХ
    [ѹ]
      job/
          job_view_cortex.m
  9-6.surface, maskǡؿΥХ
    ޥʡХ
    []
      common/morphology/
        flood_fill_3d.m
        face_to_mask.m
        erosion_3d_int.m
        erosion_3d.m 
        dilation_3d_int.m
        dilation_3d.m 
  9-7.GUIԶ罤
    MATLAB6.5.1(Linux)ǿGUIѤȡAdvanced parameter̤
    basisfile_global˥ե餺ե
   򤹤뤳ȤǤʤääơAdvanced parameter̤
   ⡼Ȥη̡Advanced parameterɽ
   Basic parameter̤Ǥ褦ˤʤꡢʲưɲä
    1.Basic parameterareaե롢basisեѹȡ
      ¨¤Advanced parameter̤ȿǤ롣
    2.ExecܥLoad, Saveܥ󤬲줿ϡץ
      Advanced parameterOKܥ򲡲ΤȤƲ̤Ĥ
      ¹Ԥ롣

   [ѹ]
      gui/bayes_parm_editor/
        bayes_parm_editor_advanced.fig
        bayes_parm_editor.m
        bayes_parm_basic_gui.m
        bayes_parm_advanced_gui.m

  9-8.job_plot_currentmapԶ罤
   "print temporal pattern""print spatial pattern"Ȥȡ
   ץꥱĤƤޤԶ
   [ѹ]
     job/job_plot_currentmap_dir/
       job_plot_cmap_print_temporalpattern.m 
       job_plot_cmap_print_spatialpattern.m 
   
