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# subject_editor

## (Toolbox/subject_editor.m in BrainStorm 2.0 (Alpha))

### Function Synopsis

    varargout = subject_editor(action,varargin)

### Help Text

    SUBJECT_EDITOR - GUI to edit the BrainStorm Subject information, case switchyard
     function varargout = subject_editor(action,varargin)
     R11 Case Switchyard, Creates/Edits a brainstormsubject.mat file
     Invoke as subject_editor('create');
     [FIG,HANDLES] = subject_editor(action) returns the figure and handles

### Cross-Reference Information

This function calls

    bst_color_scheme                   C:\BrainStorm_2001\Toolbox\bst_color_scheme.m
    bst_layout                         C:\BrainStorm_2001\Toolbox\bst_layout.m
    bst_message_window                 C:\BrainStorm_2001\Toolbox\bst_message_window.m
    bst_mriviewer                      C:\BrainStorm_2001\Toolbox\bst_mriviewer.m
    bst_win_manager                    C:\BrainStorm_2001\Toolbox\bst_win_manager.m
    fidufit                            C:\BrainStorm_2001\Toolbox\fidufit.m
    file_selection_win                 C:\BrainStorm_2001\Toolbox\file_selection_win.m
    find_brainstorm_files              C:\BrainStorm_2001\Toolbox\find_brainstorm_files.m
    get_user_directory                 C:\BrainStorm_2001\Toolbox\get_user_directory.m
    makeuswait                         C:\BrainStorm_2001\Toolbox\makeuswait.m
    mesh2brainstorm                    C:\BrainStorm_2001\Toolbox\mesh2brainstorm.m
    readdfs                            C:\BrainStorm_2001\Toolbox\readdfs.m
    readdsgl                           C:\BrainStorm_2001\Toolbox\readdsgl.m
    tess_align_tool                    C:\BrainStorm_2001\Toolbox\tess_align_tool.m
    tri2brainstorm                     C:\BrainStorm_2001\Toolbox\tri2brainstorm.m

This function is called by

    bst_static_taskbar                 C:\BrainStorm_2001\Toolbox\bst_static_taskbar.m
    data_manager                       C:\BrainStorm_2001\Toolbox\data_manager.m
    fidufit                            C:\BrainStorm_2001\Toolbox\fidufit.m

### Listing of function C:\BrainStorm_2001\Toolbox\subject_editor.m

    function varargout = subject_editor(action,varargin)
    %SUBJECT_EDITOR - GUI to edit the BrainStorm Subject information, case switchyard
    % function varargout = subject_editor(action,varargin)
    % R11 Case Switchyard, Creates/Edits a brainstormsubject.mat file
    % Invoke as subject_editor('create');
    % [FIG,HANDLES] = subject_editor(action) returns the figure and handles

    %<autobegin> ---------------------- 12-Oct-2004 01:12:37 -----------------------
    % --------- Automatically Generated Comments Block Using AUTO_COMMENTS ---------
    %
    % CATEGORY: GUI and Related
    %
    % Alphabetical list of external functions (non-Matlab):
    %   toolbox\bst_color_scheme.m
    %   toolbox\bst_layout.m
    %   toolbox\bst_message_window.m
    %   toolbox\bst_mriviewer.m
    %   toolbox\bst_win_manager.m
    %   toolbox\fidufit.m
    %   toolbox\file_selection_win.m
    %   toolbox\find_brainstorm_files.m
    %   toolbox\get_user_directory.m
    %   toolbox\makeuswait.m
    %   toolbox\mesh2brainstorm.m
    %   toolbox\readdfs.m
    %   toolbox\readdsgl.m
    %   toolbox\subject_editor.m  NOTE: Routine calls itself explicitly
    %   toolbox\tess_align_tool.m
    %   toolbox\tri2brainstorm.m
    %
    % Group : Preference data and their calls in this file:
    %   Studies = getpref('BrainStorm','Studies',[]);
    %
    % Application data and their calls in this file:
    %   'Comment'
    %   'CreateFlag'
    %   'DataDir'
    %   'TessellationFiles'
    %   'TileType'
    %   'nFaces'
    %   'nVertices'
    %
    %   setappdata(TriList,'TileType','T')
    %   setappdata(fig,'Comment',Comment)
    %   setappdata(fig,'CreateFlag',0)
    %   setappdata(fig,'CreateFlag',1);
    %   setappdata(fig,'DataDir',DataDir);
    %   setappdata(fig,'TessellationFiles',TessFiles);
    %   setappdata(fig,'TileType','T')
    %   setappdata(fig,'nFaces',nFaces)
    %   setappdata(fig,'nVertices',nVertices)
    %   setappdata(hf,'TileType','T')
    %
    %   DataDir = getappdata(fig,'DataDir');
    %   TessFiles = getappdata(fig,'TessellationFiles');
    %   nFaces = getappdata(fig,'nFaces');
    %   nVertices = getappdata(fig,'nVertices');
    %   switch getappdata(fig,'CreateFlag')
    %
    % Figure Files opened by this function:
    %   'generic_listbox_win.fig'
    %   mfilename
    %
    %   Format of strings below: Type:Style:Tag, "String", CallBack Type and Call
    %   <automatic> callback is <Tag>_Callback by Matlab default
    %
    % Callbacks by figure generic_listbox_win.fig
    %   uicontrol:pushbutton:DONE "Done" uses Callback for subject_editor ImportTriDone
    %
    % Callbacks by figure subject_editor.fig
    %   uicontrol:listbox:e_comment "" uses Callback for subject_editor CurrentEnvelopeInfo
    %   uicontrol:popupmenu:listboxx "''" uses Callback for subject_editor listboxx
    %   uicontrol:popupmenu:Tesselation "N/A" uses Callback for subject_editor TessellationFileInfo
    %   uicontrol:pushbutton:Cancel "Cancel" uses Callback for delete(gcbf)
    %   uicontrol:pushbutton:fit "Adjust" uses Callback for subject_editor fit
    %   uicontrol:pushbutton:pushbutton10 "View" uses Callback for subject_editor ViewEnvelope
    %   uicontrol:pushbutton:pushbutton100 "Save as" uses Callback for subject_editor saveas
    %   uicontrol:pushbutton:pushbutton11 "Swap faces" uses Callback for subject_editor SwapFaces
    %   uicontrol:pushbutton:pushbutton12 "Align" uses Callback for subject_editor AlignTessellation
    %   uicontrol:pushbutton:pushbutton2 "Import" uses Callback for subject_editor ImportAnatomy
    %   uicontrol:pushbutton:pushbutton4 "Import" uses Callback for subject_editor ImportTessellation
    %   uicontrol:pushbutton:pushbutton5 "Rename" uses Callback for subject_editor RenameEnvelope
    %   uicontrol:pushbutton:pushbutton7 "Delete" uses Callback for subject_editor DeleteEnvelope
    %   uicontrol:pushbutton:Pushbutton8 "Save" uses Callback for subject_editor save
    %   uicontrol:pushbutton:pushbutton8 "Downsize" uses Callback for subject_editor DownsizeEnvelope
    %   uicontrol:pushbutton:pushbutton9 "Concatenate" uses Callback for
    %     subject_editor ConcatenateEnvelope
    %   uicontrol:pushbutton:QuitPushbutton1 "Done" uses Callback for subject_editor quit
    %
    % At Check-in: $Author: Mosher $  $Revision: 45 $  $Date: 10/11/04 11:34p $
    %
    % This software is part of BrainStorm Toolbox Version 2.0 (Alpha) 23-Sep-2004
    %
    % Principal Investigators and Developers:
    % ** Richard M. Leahy, PhD, Signal & Image Processing Institute,
    %    University of Southern California, Los Angeles, CA
    % ** John C. Mosher, PhD, Biophysics Group,
    %    Los Alamos National Laboratory, Los Alamos, NM
    % ** Sylvain Baillet, PhD, Cognitive Neuroscience & Brain Imaging Laboratory,
    %    CNRS, Hopital de la Salpetriere, Paris, France
    %
    % See BrainStorm website at http://neuroimage.usc.edu for further information.
    %
    % Copyright (c) 2004 BrainStorm by the University of Southern California
    % This software distributed  under the terms of the GNU General Public License
    % as published by the Free Software Foundation. Further details on the GPL
    % license can be found at http://www.gnu.org/copyleft/gpl.html .
    %
    % FOR RESEARCH PURPOSES ONLY. THE SOFTWARE IS PROVIDED "AS IS," AND THE
    % UNIVERSITY OF SOUTHERN CALIFORNIA AND ITS COLLABORATORS DO NOT MAKE ANY
    % WARRANTY, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO WARRANTIES OF
    % MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE, NOR DO THEY ASSUME ANY
    % LIABILITY OR RESPONSIBILITY FOR THE USE OF THIS SOFTWARE.
    %<autoend> ------------------------ 12-Oct-2004 01:12:37 -----------------------

    % /---Script Author--------------------------------------\
    % |                                                      |
    % | *** Sylvain Baillet, Ph.D.                           |
    % | Cognitive Neuroscience & Brain Imaging Laboratory    |
    % | CNRS UPR640 - LENA                                   |
    % | Hopital de la Salpetriere, Paris, France             |
    % | sylvain.baillet@chups.jussieu.fr                     |
    % |                                                      |
    % |  *** John C. Mosher, Ph.D.                           |
    % |  Biophysics Group                                    |
    % |  Los Alamos National Laboratory                      |
    % |  Los Alamos, New Mexico, USA                         |
    % |  mosher@lanl.gov                                     |
    % |                                                      |
    % |  *** Dimitrios Pantazis                              |
    % |  Univerisity of Southern California                  |
    % \------------------------------------------------------/
    %
    % Date of creation: January 1999
    %
    % Script History -----------------------------------------------------------------------------------------------------------
    % SB  28-Mar-2002  Systematic use of getappdata to access DataBase information
    % SB  16-Apr-2002  Changed findobj calls to handles. referencing via guihandles
    % ...............  Fixed bug on tessellation file naming (which is supposed
    %                  to be relative to the subject's folder)
    % SB  23-May-2002  Moving to new Tessellation File format
    % ...............  Removed _brainstormsubject.mat filename tails in file display
    % JCM 24-May-2002  changed name to subject_editor to match the GUI, altered GUI calls
    % ...............  altered flow of cases to be more efficient, added handles output
    % SB  27-May-2002  Changed the location of the set(fig,'visible','on') command so
    %                  that SUBJECTEDITOR can be created by direct call
    % ...............  to subject_editor('loadfile',FILENAME) as well
    % JCM 6-June-2002  Fixed 'loadfile' comment above, it was transposed in the arguments.
    % JCM 11-Jun-2002  Auto comments, watch pointers, fixed bug in "save" routine
    % JCM 20-Jun-2002  "Go" button still calling old routine, fixed.
    %                  Bug with "No Subject Files . . ."
    %                  needs to be a cell array to work with empty case in listboxx. Reworked
    %                  this tool such that DataDir is stored in the Application data as unaltered.
    %                  If DataDir is empty, then no data, and listboxx displays "No subject files"
    %                  Changed SUBJECTEDITOR to fig for readability.
    %                  "Loadfile" no longer used, case removed.
    %                  Changed all explicit subject_editor calls to feval(mfilename).
    %                  generic_listbox_win called old _cb routine as well. Definitely CBB.
    %                  If "Save" does not detect filenames, defaults to "Save As"
    % SB 01-Jul-2002   Fixed bugs occuring whem hitting the 'Load' button for
    %                  loading a tessellation file
    % SB 22-Jul-2002   Misc. display enhancements
    % SB 28-Jul-2002   _brainstormsubject is not longer a mandatory suffix
    % ..............   Fixed loading issues when some DataBase elements
    %                  (such as some SubjectFiles or StudyFile)
    % ..............   are not up to date
    % SB 22-Oct-2002   Fixed bugs for TessFile access when importing .tri files.
    % SB 05-Nov-2002   Updated GUI and Import callbacks - BrainSuite tri files can now
    %                  be imported into BsT
    % JCM 06-Nov-2002  Handle case of no studies, just a subject file, don't close GUI.
    %                  Changed the Quit button label to "Done"
    % SB  20-Nov-2002  Save the Anatomy field when a subjectimage is available
    % SB  28-Feb-2003  Added the SwapFaces feature for tessellated envelopes
    % SB  03-Jun-2003  Compliant with the new Tiling of GUIs
    % JCM 19-Aug-2003  Handle new database cases, switch back to arrows.
    % JCM  5-Sep-2003  handle start of new gui better
    % JCM 11-May-2004  Handle case of missing datamanager GUI (e.g. straight to
    %                  subject editor). Set anatomy and tesselation searches to the
    %                  correct paths (find_brainstorm_files).
    % JCM 15-May-2004  Added changes from Pantazis for tesselation management
    % DP  17-May-2004  More mods from Pantazis for "dfs" file types, other
    %                  tesselation problems.
    % DP  18-May-2004  Minor changes for better visualization of surfaces and remove error messages
    %                  Also fix downsize button to give proper name to the generated files
    % DP  08-Oct-2004  Supress warning for matlab 6.5 (since tess_align_tool.fig was created in matlab 7)
    %------------------------------------------------------------------------------------------------

    VERBOSE = 1; % for tri2brainstorm import routine

    % old fashioned R11 case switchyard, instead of newer R12.1 feval
    %  switchyard
    % reacquire the figure handle, or open a new one

    fig = findobj(0,'tag','subjecteditor');

    if(isempty(fig)),
       % doesn't exist
       fig = openfig(mfilename,'new'); % opens as invisible
       bst_color_scheme(fig);
       setappdata(fig,'TileType','T')
       bst_layout('align',fig,2,1,2)
       set(fig,'visible','on'); % .fig saved as invisible until ready
       setappdata(fig,'CreateFlag',1); % Set a flag stating that window was just created
    end

    fig = fig(1); % only the first occurence

    handles = guihandles(fig); % reacquire all handles

    % get some common data
    Users = get_user_directory;

    if(nargout),
       varargout{1} = fig; % send back the handles
       varargout{2} = handles;
    end

    % now switch

    switch(action)
       %-----------------------------------------------------------------------
    case 'create'

       drawnow % takes a long time to do the rest, let user see the figure

       makeuswait('start')

       DataDir = find_brainstorm_files('Subjects',Users.SUBJECTS,'');

       % store the results in Application Data
       setappdata(fig,'DataDir',DataDir);

       % prepare the display strings
       if isempty(DataDir)
          cStr = {'No Subject files available in current path'};
       else
          % strip the suffix off for display purposes
          cStr = strrep(DataDir,'_brainstormsubject.mat','');
       end

       set(handles.listboxx,'String',cStr); % load the listbox
       set(handles.DOM,'string',date); % show today's date

       % Now get selected study from DataManager window and display information from corresponding subject
       GUIs = bst_win_manager;
       switch getappdata(fig,'CreateFlag') % Was subject_editor GUI freshly created
           case 1 % Yes - go and see which study was selected in DataManager
               if ~isempty(GUIs.DataManager), % data manager exists
                   DMhandles = guihandles(GUIs.DataManager); % Handles from DataManager GUI
                   iStudy = get(DMhandles.listbox_Study,'Value'); % Current study
               else
                   iStudy = 1; % just set to default
               end

               % Load subject info from selected study
               Studies = getpref('BrainStorm','Studies',[]);
               if(~isempty(Studies)),
                   load(fullfile(Users.STUDIES,Studies(iStudy).StudyFile),'BrainStormSubject')
                   BrainStormSubject = strrep(BrainStormSubject,'_brainstormsubject.mat','');
                   % Find subject in list
                   iSubject = find(strcmp(cStr,BrainStormSubject));
               else
                   iSubject = 1; % Studies are empty, just set iSubject to the first
               end
               if isempty(iSubject)
                   % We have studies, but could not find this subject.
                   % Subject was not found for this study
                   % ask user to update his/her database
                   errordlg(...
                       sprintf('SubjectFile ''%s'' from StudyFile ''%s'' was not found in ''%s''',...
                       BrainStormSubject,Studies(iStudy).StudyFile,Users.SUBJECTS),...
                       'DataBase needs updating');
                   bst_message_window('wrap',{...
                           sprintf('SubjectFile ''%s'' from StudyFile ''%s'' was not found in ''%s''',...
                           BrainStormSubject,Studies(iStudy).StudyFile,Users.SUBJECTS),...
                           ' ',...
                           'Please update or remove problematic files in/from DataBase before going on with BrainStorm'...
                       })
                   iSubject = 1; % don't close this figure, just set it to the first
               end

               set(handles.listboxx,'Value',iSubject);

               setappdata(fig,'CreateFlag',0) % That's it - GUI is created and initialized.

           case 0 % No - leave subject selection alone

               % Leave things alone
       end

       feval(mfilename,'listboxx');  % Reload current subject information

       makeuswait('stop')

       %-----------------------------------------------------------------------
    case 'listboxx'
       % Get the current pointer of the subject listbox and display data available

       cd(Users.SUBJECTS)
       DataDir = getappdata(fig,'DataDir'); % get the list of subject files

       if(isempty(DataDir)), % there are no files, listbox displays "No files"
          Val = 0; % listbox is pointing at "No files"
          return % there is nothing to process
       else
          Val = get(handles.listboxx,'Value'); % which file are we pointed at?
       end

       SubjectPath = fileparts(DataDir{Val}); % extract the referential path

       % JCM, my preferred style is to load into structure for easier tracking
       Subject = load(DataDir{Val}); % load the brainstormsubject

       set(handles.Name,'String',Subject.Name)

       % the following fields may not be defined, so test accordingly

       if ~isfield(Subject,'DateOfAcquisition')
          Subject.DateOfAcquisition = '';
       end
       set(handles.DOA,'String',Subject.DateOfAcquisition)

       if ~isfield(Subject,'DateOfModification') | isempty(Subject.DateOfModification)
          Subject.DateOfModification = date;
       end
       set(handles.DOM,'String',Subject.DateOfModification)

       if ~isfield(Subject,'Comments')
          Subject.Comments = '';
       end
       set(handles.Comments,'String',Subject.Comments)

       AnatFiles = find_brainstorm_files('anatomy',fullfile(Users.SUBJECTS,SubjectPath));
       if isempty(AnatFiles)
          AnatFiles = 'N/A';
          set(handles.Anatomy,'Enable','off')
          nfiles = 0;
       else
          set(handles.Anatomy,'Enable','on')
          nfiles = length(AnatFiles);
       end
       set(handles.Anatomy,'String',AnatFiles,'Value',1,'Max',nfiles);
       set(handles.B_Anatomy,'String',sprintf('%d Anatomy - MRI file(s)',nfiles))

       TessFiles = find_brainstorm_files('tess',fullfile(Users.SUBJECTS,SubjectPath));
       if isempty(TessFiles)
          TessFiles = {'N/A'};
          set(handles.Tesselation,'Enable','off')
          nfiles = 0;
       else
          set(handles.Tesselation,'Enable','on')
          nfiles = length(TessFiles);
       end
       set(handles.Tesselation,'String',TessFiles,'Value',1,'Max',nfiles)
       set(handles.B_Tessellation,'String',sprintf('%d Tessellation file(s)',nfiles'))

       % Store tessellation files
       setappdata(fig,'TessellationFiles',TessFiles);

       % Display info about first tessellation in list
       subject_editor TessellationFileInfo

       %-----------------------------------------------------------------------
    case 'TessellationFileInfo' % Display information about selected tessellation file

       set(fig,'pointer','watch')
       drawnow

       set(handles.e_comment,'Value',1)

       TessFiles = getappdata(fig,'TessellationFiles');
       iFile = get(handles.Tesselation,'Value'); % Which file is selected
       if strcmpi(TessFiles{iFile},'N/A') % No file available, return
          set(fig,'pointer','arrow')
          return
       end

       cd(Users.SUBJECTS)

          DataDir = getappdata(fig,'DataDir'); % get the list of subject files

          if(isempty(DataDir)), % there are no files, listbox displays "No files"
             Val = 0; % listbox is pointing at "No files"
             set(fig,'pointer','arrow')
             return % there is nothing to process
          else
             Val = get(handles.listboxx,'Value'); % which file are we pointed at?
          end

          SubjectPath = fileparts(DataDir{Val}); % extract the referential path
          if ~isempty(SubjectPath)
             cd(SubjectPath)
          end

       load(TessFiles{iFile},'Comment','Faces','Vertices')

       if isempty(Comment)
          % empty tessellation file - delete
          ButtonName=questdlg('This file is apparently empty - would you like to remove it from disk?', ...
             'DataBase Cleaning', ...
             'Yes','No','No');
          switch(ButtonName)
          case 'No'
             set(fig,'pointer','arrow')
             return
          case 'Yes'
             switch(upper(computer))
             case('PCWIN')
                dos(sprintf('del %s', TessFiles{iFile}));
             case ('UNIX')
                unix(sprintf('rm %s %s', TessFiles{iFile}));
             end
             subject_editor listboxx
          end
       else
          set(handles.e_comment,'string',Comment)

          for k = 1:length(Faces);
             nFaces(k) = size(Faces{k},1);
          end
          clear Faces
          for k = 1:length(Vertices);
             nVertices(k) = size(Vertices{k},2);
          end
          clear Vertices

          setappdata(fig,'Comment',Comment)
          setappdata(fig,'nFaces',nFaces)
          setappdata(fig,'nVertices',nVertices)

          subject_editor CurrentEnvelopeInfo
          set(handles.t_envelopes,'String',sprintf('%d Envelope(s)',length(Comment)));
          set(handles.e_comment,'Max',length(Comment))

       end

       set(fig,'pointer','arrow')

       %-----------------------------------------------------------------------
    case 'CurrentEnvelopeInfo' % Display info related to selected envelope in tessellation file
       iCurrent = get(handles.e_comment,'Value'); % what's the current envelope ?
       %     if length(iCurrent) > 1
       %         set(handles.e_comment,'Value', min(iCurrent));
       %         subject_editor CurrentEnvelopeInfo
       %         return
       %     end

       nFaces = getappdata(fig,'nFaces');
       nVertices = getappdata(fig,'nVertices');

       try
          if length(nFaces) == length(nVertices) % several envelopes of different tissues are stored (pre-MMII convention)
             set(handles.t_faces_vertices,'String',sprintf('%d Faces - %d Vertices',nFaces(iCurrent),nVertices(iCurrent)))
          else % Variations of the same envelope: number of faces and vertices is the same for all variations
             set(handles.t_faces_vertices,'String',sprintf('%d Faces - %d Vertices',nFaces(1),nVertices(1)))
          end
       catch
          set(handles.e_comment,'Value', min(iCurrent));
          subject_editor CurrentEnvelopeInfo
          return
       end

       %-----------------------------------------------------------------------
    case 'ConcatenateEnvelope' % Concatenate selected envelopes in a single tessellation

        makeuswait('start')

        TessFiles = getappdata(fig,'TessellationFiles');
       % Tessellation file
       iFile = get(handles.Tesselation,'Value'); % Which file is selected
       % Envelope in tessellation file
       iCurrent = get(handles.e_comment,'Value'); % what's the current envelope ?

       if length(iCurrent) == 1 % Concatenate tessellation from 2 different files
          % Open specific GUI for file selection
          TriList = openfig('generic_listbox_win.fig');
          setappdata(TriList,'TileType','T')
          bst_color_scheme(TriList)
          bst_layout('align',TriList,2,2,1)
          set(TriList,'Visible','on')

          TriHandles = guihandles(TriList);
          set(TriHandles.listbox,'String',TessFiles,'ListboxTop',2,'Max',2)
          set(TriList,'Name','Select tessellation files to concatenate')
          set(TriHandles.DONE,'Callback','subject_editor ConcatenateEnvelope_Done')

          return
       elseif length(iCurrent) ~= 2
          errordlg('Please select 2 envelopes only from list.')
          return
       end

       % Go into proper folder
       cd(Users.SUBJECTS)
       DataDir = getappdata(fig,'DataDir'); % get the list of subject files
       if(isempty(DataDir)), % there are no files, listbox displays "No files"
          Val = 0; % listbox is pointing at "No files"
          return % there is nothing to process
       else
          Val = get(handles.listboxx,'Value'); % which file are we pointed at?
       end
       SubjectPath = fileparts(DataDir{Val}); % extract the referential path
       if ~isempty(SubjectPath)
          cd(SubjectPath)
       end

       oldTess = load(TessFiles{iFile});

       % As per MMII convention - there should be one tessellation file per envelope
       % A downsized version of e.g. a cortex is considered as a different envelope
       % ans is therefore saved in a separate tessellation file than the original.
       Vertices{1} = [oldTess.Vertices{iCurrent(1)},oldTess.Vertices{iCurrent(2)}]  ;
       Faces{1} = [oldTess.Faces{iCurrent(1)}; oldTess.Faces{iCurrent(2)}+size(oldTess.Vertices{iCurrent(1)},2)];
       Comment{1} = [oldTess.Comment{iCurrent(1)},oldTess.Comment{iCurrent(2)}]  ;
       clear oldTess

       newTessFile = strrep(TessFiles{iFile},'tess',[Comment{1},'_tess']);
       save(newTessFile,'Faces','Comment','Vertices')

       subject_editor listboxx
       bst_message_window({...
             ' ',...
             'Wrote new envelope in',...
             newTessFile,...
             ' '})

       makeuswait('stop')

       %-----------------------------------------------------------------------
    case 'ConcatenateEnvelope_Done' % Two files were selected - concatenate their envelopes

       set(fig,'pointer','watch'), drawnow
       % Assume there is only one envelope per file
       TriList = openfig('generic_listbox_win.fig','reuse');
       TriHandles = guihandles(TriList);

       iCurrent = get(TriHandles.listbox,'Value'); % Selected tess files

       if length(iCurrent) ~= 2
          errordlg('Please select 2 envelopes only from list.')
          return
       end

       delete(TriList);

       TessFiles = getappdata(fig,'TessellationFiles');

       % Go into proper folder
       cd(Users.SUBJECTS)
       DataDir = getappdata(fig,'DataDir'); % get the list of subject files
       if(isempty(DataDir)), % there are no files, listbox displays "No files"
          Val = 0; % listbox is pointing at "No files"
          return % there is nothing to process
       else
          Val = get(handles.listboxx,'Value'); % which file are we pointed at?
       end
       SubjectPath = fileparts(DataDir{Val}); % extract the referential path
       if ~isempty(SubjectPath)
          cd(SubjectPath)
       end

       for k = 1:length(iCurrent)
          oldTess{k} = load(TessFiles{iCurrent(k)});
       end

       % As per MMII convention - there should be one tessellation file per envelope
       % A downsized version of e.g. a cortex is considered as a different envelope
       % ans is therefore saved in a separate tessellation file than the original.
       Vertices{1} = [oldTess{1}.Vertices{1},oldTess{2}.Vertices{1}]  ;
       Faces{1} = [oldTess{1}.Faces{1}; oldTess{2}.Faces{1}+size(oldTess{1}.Vertices{1},2)];
       Comment{1} = [oldTess{1}.Comment{1},oldTess{2}.Comment{1}]  ;
       clear oldTess

       newTessFile = [Comment{1},'_tess.mat'];
       save(newTessFile,'Faces','Comment','Vertices')

       subject_editor listboxx
       bst_message_window({...
             ' ',...
             'Wrote new envelope in',...
             newTessFile,...
             ' '})

       set(fig,'pointer','arrow'), drawnow

       %-----------------------------------------------------------------------
    case 'RenameEnvelope' % Change the comment entry to selected envelope

       TessFiles = getappdata(fig,'TessellationFiles');
       % Tessellation file
       iFile = get(handles.Tesselation,'Value'); % Which file is selected
       % Envelope in tessellation file
       iCurrent = get(handles.e_comment,'Value'); % what's the current envelope ?
       if length(iCurrent) > 1
          set(handles.e_comment,'Value', min(iCurrent));
          subject_editor RenameEnvelope
          return
       end

       % Go into proper folder
       cd(Users.SUBJECTS)
       DataDir = getappdata(fig,'DataDir'); % get the list of subject files
       if(isempty(DataDir)), % there are no files, listbox displays "No files"
          Val = 0; % listbox is pointing at "No files"
          return % there is nothing to process
       else
          Val = get(handles.listboxx,'Value'); % which file are we pointed at?
       end
       SubjectPath = fileparts(DataDir{Val}); % extract the referential path
       if ~isempty(SubjectPath)
          cd(SubjectPath)
       end

       load(TessFiles{iFile},'Comment')
       newComment = inputdlg('Enter a new name for selected envelope','Edit tessellation file',1,{Comment{iCurrent}});
       if isempty(newComment), return, end

       Comment{iCurrent} = char(newComment);

       save(TessFiles{iFile},'Comment','-append')
       set(handles.e_comment,'string',Comment)
       setappdata(fig,'Comment',Comment)

       %-----------------------------------------------------------------------

    case 'SwapFaces' % Swap vertex ordering for face definition as some pacthes normal may happen to be oriented inwards and therefore look dark in 3d

       set(fig,'pointer','watch')
       TessFiles = getappdata(fig,'TessellationFiles');
       % Tessellation file
       iFile = get(handles.Tesselation,'Value'); % Which file is selected
       % Envelope in tessellation file
       iCurrent = get(handles.e_comment,'Value'); % what's the current envelope ?
       if length(iCurrent) > 1
          set(handles.e_comment,'Value', min(iCurrent));
          subject_editor RenameEnvelope
          return
       end

       % Go into proper folder
       cd(Users.SUBJECTS)
       DataDir = getappdata(fig,'DataDir'); % get the list of subject files
       if(isempty(DataDir)), % there are no files, listbox displays "No files"
          Val = 0; % listbox is pointing at "No files"
          return % there is nothing to process
       else
          Val = get(handles.listboxx,'Value'); % which file are we pointed at?
       end
       SubjectPath = fileparts(DataDir{Val}); % extract the referential path
       if ~isempty(SubjectPath)
          cd(SubjectPath)
       end

       load(TessFiles{iFile},'Faces')

       Faces{iCurrent} = Faces{iCurrent}(:,[2 1 3]);

       save(TessFiles{iFile},'Faces','-append')

       set(fig,'pointer','arrow')

       %-----------------------------------------------------------------------
    case 'DeleteEnvelope' % Delete selected envelope

       TessFiles = getappdata(fig,'TessellationFiles');
       % Tessellation file
       iFile = get(handles.Tesselation,'Value'); % Which file is selected
       % Envelope in tessellation file
       iCurrent = get(handles.e_comment,'Value'); % what's the current envelope ?

       % Go into proper folder
       cd(Users.SUBJECTS)
       DataDir = getappdata(fig,'DataDir'); % get the list of subject files
       if(isempty(DataDir)), % there are no files, listbox displays "No files"
          Val = 0; % listbox is pointing at "No files"
          return % there is nothing to process
       else
          Val = get(handles.listboxx,'Value'); % which file are we pointed at?
       end
       SubjectPath = fileparts(DataDir{Val}); % extract the referential path
       if ~isempty(SubjectPath)
          cd(SubjectPath)
       end

       ButtonName=questdlg('Are you sure you want to delete permanently the selected envelope(s) ?', ...
          'Warning', ...
          'Yes','No','No');

       switch(ButtonName)

       case 'No'
          return
       case 'Yes'
          set(fig,'pointer','watch'), drawnow

          load(TessFiles{iFile},'Comment','Vertices','Faces')
          iValidSet = setdiff(1:length(Comment),iCurrent); % Set of remaining envelopes
          if length(Faces) == length(Comment)
             Faces = Faces(iValidSet);
          end
          Comment = Comment(iValidSet);
          Vertices = Vertices(iValidSet);

          save(TessFiles{iFile},'Comment','Vertices','Faces')
          set(handles.e_comment,'string',Comment)
       end

       % Update display
       if length(Comment) < 1 % Empty tessellation file
          subject_editor listboxx
          return
       end

       for k = 1:length(Faces);
          nFaces(k) = size(Faces{k},1);
       end
       clear Faces
       for k = 1:length(Vertices);
          nVertices(k) = size(Vertices{k},2);
       end
       clear Vertices

       setappdata(fig,'Comment',Comment)
       setappdata(fig,'nFaces',nFaces)
       setappdata(fig,'nVertices',nVertices)

       subject_editor CurrentEnvelopeInfo

       set(handles.t_envelopes,'String',sprintf('%d Envelope(s)',length(Comment)));

       set(fig,'pointer','arrow')

       %-----------------------------------------------------------------------

    case 'ViewEnvelope' % View of selected envelope

       TessFiles = getappdata(fig,'TessellationFiles');
       % Tessellation file
       iFile = get(handles.Tesselation,'Value'); % Which file is selected
       % Envelope in tessellation file
       iCurrent = get(handles.e_comment,'Value'); % what's the current envelope ?
       if length(iCurrent) > 1
          set(handles.e_comment,'Value', min(iCurrent));
          subject_editor DownsizeEnvelope
          return
       end

       % Go into proper folder
       cd(Users.SUBJECTS)
       DataDir = getappdata(fig,'DataDir'); % get the list of subject files
       if(isempty(DataDir)), % there are no files, listbox displays "No files"
          Val = 0; % listbox is pointing at "No files"
          return % there is nothing to process
       else
          Val = get(handles.listboxx,'Value'); % which file are we pointed at?
       end
       SubjectPath = fileparts(DataDir{Val}); % extract the referential path
       if ~isempty(SubjectPath)
          cd(SubjectPath)
       end

       load(TessFiles{iFile});
       Faces = Faces{iCurrent};
       Vertices = Vertices{iCurrent};
       Comment = Comment{iCurrent};

       hf =  figure('visible','off');
       bst_color_scheme(hf);
       setappdata(hf,'TileType','T')
       set(hf,'menubar','figure','toolbar','figure');
       bst_layout('align',hf,1,1,1);
       set(hf,'visible','on');
       set(hf,'name','Tessellation Viewer');
       light
       %    h = light('visible','off');
       %    set(h,'position',[0 -1 0],'visible','on');
       lighting gouraud
       axis equal
       axis off
       axis vis3d

        FV.vertices = Vertices';
        FV.faces = Faces;
        nVertices = size(FV.vertices,1);
        figure(hf);
        hpatch = patch(FV,'FaceColor','interp','EdgeColor','none','FaceVertexCData',ones(nVertices,3)*0.9,'faceAlpha',1); %plot surface
        lighting gouraud

       %-----------------------------------------------------------------------

    case 'DownsizeEnvelope' % Create a new version of selected envelope with a reduced number of faces and vertices

       TessFiles = getappdata(fig,'TessellationFiles');
       % Tessellation file
       iFile = get(handles.Tesselation,'Value'); % Which file is selected
       % Envelope in tessellation file
       iCurrent = get(handles.e_comment,'Value'); % what's the current envelope ?
       if length(iCurrent) > 1
          set(handles.e_comment,'Value', min(iCurrent));
          subject_editor DownsizeEnvelope
          return
       end

       % Go into proper folder
       cd(Users.SUBJECTS)
       DataDir = getappdata(fig,'DataDir'); % get the list of subject files
       if(isempty(DataDir)), % there are no files, listbox displays "No files"
          Val = 0; % listbox is pointing at "No files"
          return % there is nothing to process
       else
          Val = get(handles.listboxx,'Value'); % which file are we pointed at?
       end
       SubjectPath = fileparts(DataDir{Val}); % extract the referential path
       if ~isempty(SubjectPath)
          cd(SubjectPath)
       end

       load(TessFiles{iFile});

       newVertices = ...
          inputdlg('New number of vertices for selected envelope',...
          'Tessellation downsizing',...
          1,{num2str(size(Vertices{iCurrent},2))});

       if isempty(newVertices), return, end

       nfv.faces = double(Faces{iCurrent});
       nfv.vertices = double(Vertices{iCurrent}');
       dsFactor = str2num(newVertices{1})/size(Vertices{iCurrent},2); % Downsize factor
       clear Faces Vertices

       makeuswait('start')

       NFV = reducepatch(nfv, dsFactor);

       clear nfv

       % As per MMII convention - there should be one tessellation file per envelope
       % A downsized version of e.g. a cortex is considered as a different envelope
       % ans is therefore saved in a separate tessellation file than the original.

       Faces{1} = NFV.faces;
       Vertices{1} = NFV.vertices';
       clear NFV
       OldComment = Comment;
       clear Comment
       Comment{1} = [OldComment{iCurrent},'_',num2str(newVertices{1}),'V'];%num2str(dsFactor)];
       newTessFile = strrep(TessFiles{iFile},'tess',[num2str(newVertices{1}) 'V_tess']);
       save(newTessFile,'Faces','Comment','Vertices')

       subject_editor listboxx
       bst_message_window({...
             ' ',...
             'Wrote new envelope in',...
             newTessFile,...
             ' '})

     makeuswait('stop')

       %-----------------------------------------------------------------------

    case 'save'

       DataDir = getappdata(fig,'DataDir');

       if(isempty(DataDir)),
          % there is no subject, call as a "save as"
          feval(mfilename,'saveas'); % no filename

       else
          % use the existing filename to save
          ifile = get(handles.listboxx,'value'); % what is selected in the listbox?

          file = DataDir{ifile}; % referential filename

          feval(mfilename,'saveas',file) % save with this name
       end

       %-----------------------------------------------------------------------
    case 'saveas'

       % called with optional argument of referential filename

       cd(Users.SUBJECTS)

       Name = get(handles.Name,'String');
       DateOfAcquisition = get(handles.DOA,'String');
       DateOfModification = date;
       set(handles.DOM,'String', date);
       Comments = get(handles.Comments,'String');
       Anatomy = get(handles.Anatomy,'String');

       try
           Anatomy = fullfile(fileparts(varargin{1}),Anatomy{get(handles.Anatomy,'Value')}); % referential name
       catch
           Anatomy = '';
       end

       Tesselation = get(handles.Tesselation,'Userdata');
       if isempty(Tesselation)
           Tesselation = '';
       end

       if nargin == 1 % No handles.Name was specified
           DefaultLeader = strrep(Name,' ',''); % Default prefix to Subject filename.
           if ~isempty(DefaultLeader)
               DefaultLeader = [DefaultLeader,'_brainstormsubject.mat'];
           else
               DefaultLeader = ['brainstormsubject.mat'];
           end

           [file,path] = uiputfile(DefaultLeader, 'Save Subject Information');

           if file == 0,
               return,
           end

           if isempty(findstr(lower(file),'brainstormsubject.mat'));
               file = [file,'_brainstormsubject.mat']; % Add the BST suffix if not entered by user
           end
           % file is name only, but path is absolute
       else
           file = varargin{1}; % referential name
           path = Users.SUBJECTS;
           ifile = get(handles.listboxx,'Value'); % What's the value of the subject file lisbox for future display
       end

       save(fullfile(path,file),'Name','DateOfAcquisition','DateOfModification','Comments',...
           'Anatomy','Tesselation')
       bst_message_window('wrap',{sprintf('Saved to %s',path),file}); % filename on second line

       % now reinitialize the GUI to seek out the new subject file and load the gui

       feval(mfilename,'create');

       if nargin > 1
           set(handles.listboxx,'Value',ifile)
       end

       %-----------------------------------------------------------------------
    case 'ImportAnatomy'

       bst_mriviewer;

       %-----------------------------------------------------------------------

    case 'ImportTessellation'

        % Move to current subject's folder
        DataDir = getappdata(fig,'DataDir'); % referential filenames
        if(isempty(DataDir)),
            % no current subject
            bst_message_window('append','No valid subject file selected');
            return
        else
            CurrentSubjectFile = DataDir{get(handles.listboxx,'Value')};
        end

        % strip the folder name, add to the filename
        CurrentSubjectFolder = fileparts(fullfile(Users.SUBJECTS,CurrentSubjectFile));

        %Open window to ask for tesselation files
        filetype{1} = '.tri';
        filetype{2} = '.dsgl';
        filetype{3} = '.dfs';
        filetype{4} = '.mesh';

        [Files Filenames] = file_selection_win(filetype,CurrentSubjectFolder);

        if(isempty(Files{1})) %if no files are loaded
            return
        end

        %separate Tri from Dsgl and Dfs files
        TriFiles = {};
        DsglFiles = {};
        DfsFiles = {};
        ndxTri = 1;
        ndxMesh = 1;
        ndxDsgl = 1;
        ndxDfs = 1;
        for k = 1:size(Files,2)
            if strcmp(Files{k}(end-3:end),'.tri')
                TriFiles{ndxTri} = Files{k};
                ndxTri = ndxTri + 1;
            end
            if strcmp(Files{k}(end-4:end),'.mesh')
                TriFiles{ndxMesh} = Files{k};
                ndxMesh = ndxMesh + 1;
            end
            if strcmp(Files{k}(end-4:end),'.dsgl')
                DsglFiles{ndxDsgl} = Files{k};
                ndxDsgl = ndxDsgl + 1;
            end
            if strcmp(Files{k}(end-3:end),'.dfs')
                DfsFiles{ndxDfs} = Files{k};
                ndxDfs = ndxDfs + 1 ;
            end
        end
        ndxTri = ndxTri - 1;
        ndxMesh = ndxMesh - 1;
        ndxDsgl = ndxDsgl - 1;
        ndxDfs = ndxDfs - 1;

        if(ndxTri>0) %if any tri files
            [oVertices, oFaces, oComment] = tri2brainstorm(TriFiles,VERBOSE);
        elseif(ndxMesh>0) %if any MESH files
            for k=1:length(ndxMesh)
                [oVertices{k},oFaces{k},normal,vertex_number,faces_number] = mesh2brainstorm(TriFiles{k});
                oVertices{k} = oVertices{k}';
                oFaces{k} = oFaces{k}+1;
                oComment{k} = TriFiles{k};
            end
        end

        %The following code may be used in the future, to automatically align dsgl files

    %     %we need to check if PCS is present in the subjectimage file:
    %     %get subject file, to get a link to anatomy file
    %     % Move to current subject's folder
    %     CurrentSubjectFile = DataDir{get(handles.listboxx,'Value')};
    %     SubjectFile = fullfile(Users.SUBJECTS,CurrentSubjectFile);
    %     warning off %we don't want to scare the user if no anatomy is present
    %     load(CurrentSubjectFile,'Anatomy');
    %     warning on
    %     if(~exist('Anatomy'))
    %         bst_message_window({' ','-------------------------------------------------',...
    %                 'Import an anatomy file and define a Patient Coordinate System before importing Dsgl files...'});
    %         return
    %     end
    %     SubjectImageFile = fullfile(Users.SUBJECTS,Anatomy);
    %
    %     %check whether PCS from Anatomy file is defined
    %     %we need this to align dsgl with mri and channels
    %     warning off %we don't want to scare the user if no PCS is present
    %     load(SubjectImageFile,'PCS')
    %     warning on
    %     if(~exist('PCS') | ~isfield(PCS,'PERM'))
    %         bst_message_window({' ','-------------------------------------------------',...
    %                 'Define a Patient Coordinate System using the MRI Tool before importing Dsgl files...'});
    %         return
    %     end
    %     %now we can use bsuite2PCS function

        %load dsgl files
        for k = 1:size(DsglFiles,2)
            FV = readdsgl(DsglFiles{k});
            %now in cube coords, make it engineering dimensions, in meters
            FV.vertices(:,1) = FV.vertices(:,1)*(FV.res(1)/1000);  %this should not be used with bsuite2PCS
            FV.vertices(:,2) = FV.vertices(:,2)*(FV.res(2)/1000);  %this should not be used with bsuite2PCS
            FV.vertices(:,3) = FV.vertices(:,3)*(FV.res(3)/1000);  %this should not be used with bsuite2PCS
            FV_PCS = FV; %temp code
            clear FV;
    %        FV_PCS = bsuite2PCS(FV,SubjectImageFile);
            oVertices{k+ndxTri} = FV_PCS.vertices'; %append info
            oFaces{k+ndxTri} = FV_PCS.faces;
            [ignore,fileComment] = fileparts(DsglFiles{k});
            oComment{k+ndxTri} = fileComment;
        end

        %load dfs files
        for k = 1:size(DfsFiles,2)
            FV = readdfs(DfsFiles{k});
            FV.vertices = FV.vertices / 1000;  %make mm into m
            oVertices{k+ndxTri+ndxDsgl} = FV.vertices'; %append info
            oFaces{k+ndxTri+ndxDsgl} = FV.faces;
            [ignore,fileComment] = fileparts(DfsFiles{k});
            oComment{k+ndxTri+ndxDsgl} = fileComment;
        end

        % BST.MMII innovation:
        % Now save each in a separate tess file
        %TessFileLeader = strrep(TriFiles{1},Leader,'');
        %TessFileLeader = strrep(TessFileLeader,'.tri',''); % Common leader for every new tessellation file

        bst_message_window({' ','-------------------------------------------------',...
                'Saving envelopes in separate files...'});
        drawnow
        for k = 1: length(TriFiles)

            % Get corresponding surface specs
            Faces{1} = oFaces{k};
            Vertices{1} = oVertices{k};
            Comment{1} = oComment{k};

            % Generate file name
            [PATHSTR,NAME,EXT,VERSN] = fileparts(Files{k});

            TessFile{k} = strrep(Files{k},EXT,'_tess.mat');

            save(TessFile{k},'Comment','Faces','Vertices','-mat');

            bst_message_window('wrap',{...
                    ['Saving envelope ''',Comment{1},''' in '],...
                    TessFile{k},...
                });

        end

        for k = ndxTri+1: ndxTri+ size(DsglFiles,2)

            % Get corresponding surface specs
            Faces{1} = oFaces{k};
            Vertices{1} = oVertices{k};
            Comment{1} = oComment{k};

            % Generate file name
            TessFile{k}= strrep(Files{k},'.dsgl','_tess.mat');

            save(TessFile{k},'Comment','Faces','Vertices','-mat');

            bst_message_window('wrap',{...
                    ['Saving envelope ''',Comment{1},''' in '],...
                    TessFile{k},...
                });

        end

        for k = ndxTri+ndxDsgl+1: ndxTri+ndxDsgl +  size(DfsFiles,2)

            % Get corresponding surface specs
            Faces{1} = oFaces{k};
            Vertices{1} = oVertices{k};
            Comment{1} = oComment{k};

            % Generate file name
            TessFile{k}= strrep(Files{k},'.dfs','_tess.mat');

            save(TessFile{k},'Comment','Faces','Vertices','-mat');

            bst_message_window('wrap',{...
                    ['Saving envelope ''',Comment{1},''' in '],...
                    TessFile{k},...
                });

        end

        bst_message_window({'Saving envelopes in separate files -----> DONE',...
                '-------------------------------------------------',' '});

        DataDir = getappdata(fig,'DataDir');
        if(isempty(DataDir)),
            bst_message_window('No valid subject name')
            return
        end
        CurrentSubjectFile = DataDir{get(handles.listboxx,'Value')};

        % extract the referential folder name
        CurrentSubjectFolder = fileparts(CurrentSubjectFile);

        %set(handles.Tesselation,'string',TessFile,'Value',1,'Userdata',fullfile(CurrentSubjectFolder,TessFile))
        set(handles.Tesselation,'string',TessFile,'Value',1,'Userdata',TessFile)

        subject_editor('listboxx');

       %-----------------------------------------------------------------------

    case 'quit'
       close gcbf

       %-----------------------------------------------------------------------

    case 'anatomy'
       cd(Users.SUBJECTS)
       [file,path] = uigetfile(['*subjectimage.mat'], 'Select a BrainStorm ''subjectimage'' file');
       if file == 0, return, end

       if isempty(findstr(lower(Users.SUBJECTS),lower(path))) % Check if the subjectimage file is in Users.SUBJECTS for correct relative indexing
          errordlg(sprintf('Please place %s in %s first',file,Users.SUBJECTS))
          return
       end

       if findstr(lower(fullfile(path,file)),lower(Users.SUBJECTS)) ~=1 % Automount issus on some Linux systems - remove the automount prefix
          fname = fullfile(path,file);
          istrip = findstr(lower(fullfile(path,file)),lower(Users.SUBJECTS));
          fname = fname(istrip:end);
       else
          fname = fullfile(path,file);
       end

       fname = strrep(fname,(Users.SUBJECTS),''); % strip the user location

       set(handles.Anatomy,'String',file,'Userdata',fname)
       cd(path)
       set(findobj(gcbf,'Tag','fit'),'Enable','on')

       %-----------------------------------------------------------------------

    case 'tesselation'

       [file,path] = uigetfile(['*tess*.mat'], 'Select a handles.Tesselation file');
       if file == 0, return, end

       if findstr(lower(fullfile(path,file)),lower(Users.SUBJECTS)) ~=1 % Automount issues on some Linux systems
          % Remove the automount prefix
          fname = fullfile(path,file);
          istrip = findstr(lower(fullfile(path,file)),lower(Users.SUBJECTS));
          fname = fname(istrip:end);
       else
          fname = fullfile(path,file);
       end

       fname = strrep(fname,Users.SUBJECTS,''); % strip the user location

       set(handles.Tesselation,'String',file)
       set(handles.Tesselation,'Enable','on')
       nfiles = 1;
       set(handles.Tesselation,'String',fname,'Value',1,'Max',nfiles)
       set(handles.B_Tessellation,'String',sprintf('%d Tessellation file(s)',nfiles'))

       cd(path)

       %-----------------------------------------------------------------------

    case 'TriConn'

       [file,path] = uigetfile(['*.mat'], 'Triangle Connectivity file');
       if file == 0, return, end
       if isempty(strmatch((Users.SUBJECTS),(path))) % Check if the handles.Tesselation file is in Users.SUBJECTS for correct relative indexing
          errordlg(sprintf('Please place %s in %s first',file,Users.SUBJECTS))
          return
       end

       fname = strrep((fullfile(path,file)),(Users.SUBJECTS),''); % strip the user location
       set(handles.TriConn,'String',file,'Userdata',fname)
       cd(path)

       %-----------------------------------------------------------------------

    case 'VertConn'

       [file,path] = uigetfile(['*.mat'], 'Vertex Connectivity file');
       if file == 0, return, end
       if isempty(strmatch((Users.SUBJECTS),(path))) % Check if the handles.Tesselation file is in Users.SUBJECTS for correct relative indexing
          errordlg(sprintf('Please place %s in %s first',file,Users.SUBJECTS))
          return
       end

       fname = strrep((fullfile(path,file)),(Users.SUBJECTS),''); % strip the user location
       set(handles.VertConn,'String',file,'Userdata',fname)
       cd(path)

       %-----------------------------------------------------------------------

    case 'fit' % Scale the MRI to the true fiducials
       fidufit

       load(get(handles.Anatomy,'Userdata'),'PCS');
       if ~exist('PCS','var')
          errordlg('Please use the original dummy MRI scan')
          return
       end

       PCS.PCSFiducial(abs(PCS.PCSFiducial) < 1e-4) = 0;

       set(findobj(gcf,'Tag','old1'),'String',(num2str(PCS.PCSFiducial(:,1)','%3.1f %3.1f %3.1f')));
       set(findobj(gcf,'Tag','old2'),'String',(num2str(PCS.PCSFiducial(:,2)','%3.1f %3.1f %3.1f')));
       set(findobj(gcf,'Tag','old3'),'String',(num2str(PCS.PCSFiducial(:,3)','%3.1f %3.1f %3.1f')));

       %-----------------------------------------------------------------------

    case 'fitdone' % Scale the MRI to the true fiducials

       %-----------------------------------------------------------------------

       new1 = str2num(get(findobj(gcbf,'Tag','new1'),'String'));
       new2 = str2num(get(findobj(gcbf,'Tag','new2'),'String'));
       new3 = str2num(get(findobj(gcbf,'Tag','new3'),'String'));
       load(get(handles.Anatomy,'Userdata'),'PCS');
       tmp = mean(abs([new2;new3]));
       newfid = [new1',tmp',[0 0 1]'];
       tmp = mean(abs(PCS.PCSFiducial(:,2:3)'));
       scale_fiducials = newfid*inv([PCS.PCSFiducial(:,1),tmp',[0 0 1]']);
       PCS.PCSFiducial = [new1',new2',new3',[0 0 0]'];
       save(get(handles.Anatomy,'Userdata'),'PCS','scale_fiducials','-append')
       bst_message_window(' ')
       bst_message_window('Fiducials points have been properly updated')
       bst_message_window(' ')
       close(gcbf)

       %-----------------------------------------------------------------------

    case 'AlignTessellation'

       %-----------------------------------------------------------------------
       % Align the tesselation to the Subject Coordinate System

           %get current subject directory
        DataDir = getappdata(fig,'DataDir'); % referential filenames
        if(isempty(DataDir)),
            % no current subject
            bst_message_window('append','No valid subject file selected');
            return
        else
            CurrentSubjectFile = DataDir{get(handles.listboxx,'Value')};
        end
        % strip the folder name, add to the filename
        CurrentSubjectFolder = fileparts(fullfile(Users.SUBJECTS,CurrentSubjectFile));

        %launch tesselation alignment tool
        warning off; %supress warning for matlab 6.5 (window created on matlab 7)
        tess_align_tool('dummy',CurrentSubjectFolder);
        warning on;

       %-----------------------------------------------------------------------

    end % case switches

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