[X-batch-news] x_batch x_run_protocol.m,1.5,1.6

[Xenia H. <sa...@us...>]

Update of /cvsroot/x-batch/x_batch
In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv4344

Modified Files:
	x_run_protocol.m 
Log Message:
Save information about processed session ONLY if processing succeeded.


Index: x_run_protocol.m
===================================================================
RCS file: /cvsroot/x-batch/x_batch/x_run_protocol.m,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** x_run_protocol.m	10 Feb 2005 05:32:04 -0000	1.5
--- x_run_protocol.m	8 Aug 2005 02:08:16 -0000	1.6
***************
*** 1,381 ****
! function varargout = x_run_protocol(varargin)
! % X_RUN_PROTOCOL is a gateway to starting actual batch processing with a chosen protocol. 
! % it allows the user to specify file locations for particular subject(s)
! % use the 'new subject' button to create a new subject entry in the database (for Protege database)
! % use 'run' button to start the batch processing session
! global defaults;
! global version_number;
! global global_params;
! global spm_results_dir;
! global display_graphix;
! global log_file_fid;
! constants;
! 
! if nargin == 0  % LAUNCH GUI
!     SPMid = spm('FnBanner',mfilename, version_number);
! 	fig = openfig(mfilename,'reuse');
! 	% Use system color scheme for figure:
! 	set(fig,'Color',get(0,'defaultUicontrolBackgroundColor'));
! 	% Generate a structure of handles to pass to callbacks, and store it. 
! 	handles = guihandles(fig);
! 	guidata(fig, handles);   
! 	if nargout > 0
! 		varargout{1} = fig
! 	end
!     version_number = '2.2 - beta';
! elseif ischar(varargin{1}) % INVOKE NAMED SUBFUNCTION OR CALLBACK
!     try
! 		[varargout{1:nargout}] = feval(varargin{:}); % FEVAL switchyard
! 	catch
! 		disp(lasterr);
! 	end
! 
! end
! 
! % --------------------------------------------------------------------
! function varargout = new_patient_Callback(h, eventdata, handles, varargin)
! % create a new patient in the Protege database. A new patient is only
! % identified by his/her subject id, which MUST be unique
! constants;
! subject_id = spm_input('subject_id', '+1', 's', 'X2003');
! ids = x_get_instances_ids('Subject', SUBJECT);
! % make sure subject ids are unique
! unique = 0;
! while(~unique)
!     check_again  = 0;
!    for i = 1:size(ids,2)
!            if strcmpi(subject_id, ids(i))
!               spm_input(['Subject with the id ' subject_id ' already exists!'], 1,'bd','OK')
!               subject_id = spm_input('subject_id', '+1', 's', 'X2003');
!               check_again = 1;
!            end;     
!     end;
!     if (~check_again) unique = 1; end;     
! end;
! spm_protege_interface('new subject', subject_id);
! closereq;
! 
! %###########################
! %TODO: print errors if any
! %###########################
! % --------------------------------------------------------------------
! function varargout = choose_patient_Callback(h, eventdata, handles, varargin)
! % Stub for Callback of the uicontrol handles.choose.
! global subject_id;
! constants;
! val = get(handles.choose_patient, 'Value'); 
! subject_ids = x_get_instances_ids('Subject', SUBJECT);
! subject_id = subject_ids(val);
! 
! % --------------------------------------------------------------------
! function varargout = execute_Callback(h, eventdata, handles, varargin)
! % Stub for Callback of the uicontrol handles.pushbutton12.
! global global_params;
! global spm_results_dir;
! global log_file_fid;
! constants;
! 
! num_subj = spm_input('Num subjects', 1, 'e', 1);
! 
! for i = 1:num_subj
!    subjects(i) = struct('subject_id', [], ...
!                              'subject_num', [], ... % this is just to display 'processing subject number X' message
!                              'struct_imgs', [], ... % note that I assume that there is essentially ONE struct per subject                              'struct_dir', '', ...
!                              'weight_image', [], ...
!                              'root_dir', [], ...
!                              'sessions', []); 
! end
! 
! for i = 1:num_subj,
!       %  subjects(i) = struct('subject_id', [], ...
!       %                       'subject_num', [], ... % this is just to display 'processing subject number X' message
!       %                       'struct_imgs', [], ... % note that I assume that there is essentially ONE struct per subject                              'struct_dir', '', ...
!       %                       'weight_image', [], ...
!       %                       'root_dir', [], ...
!       %                       'sessions', [])  %semicolon
!       %                   subjects
!         % collect subject-specific info         
!         % get a subject_id 
!        
!         subject_ids = sort(x_get_instances_ids('Subject', SUBJECT, ['Please choose a subject #' i]));            
!         subjects(i).subject_id = spm_input(['Please choose subject # ' num2str(i)], '2','m',subject_ids, subject_ids);
!         subjects(i).subject_num = i;    
!         spm_input(['Subject ' num2str(i) ': ' subjects(i).subject_id{1}], 3 ,'d');
!         
!         % collect info about the structural images, which are SAME for all
!         % sessions
!          subjects(i).root_dir = spm_get(-1, '',['Indicate the root directory for this subject']);
!          % the normalisation may be performed on either struct or func
!          % images. Here, we determine what images it is performed on, so
!          % that we do not ask the user unneccessary question
!          norm_struct = 0;
!          if(~isempty(global_params.normalise_params))
!             norm_struct = global_params.normalise_params.normalise_struct; 
!            % if global_params.normalise_params.option == 2
!            %     global_params.normalise_params.file_to_write_from = spm_get(1, norm_file_extention, ['Parameters to write']);
!            % end;          
!         end;         
!          if ~(isempty(global_params.coreg_params) & isempty(global_params.segment_params) & ~norm_struct)  
!              subjects(i).struct_imgs = spm_get(Inf, 'IMAGE', ['Choose the structural image for this subject']);
!          end;
!          
!          if(~isempty(subjects(i).struct_imgs))
!            [dir, name, ext] = fileparts(subjects(i).struct_imgs(1, :));
!            subjects(i).struct_dir = dir;
!          end;
!                
!          % if the images are weighted, ask for weight images   
!          % TODO: now, are weight images session-specific or
!          % patient-specific? Are the 'other' images sessions speciic
!          % or subjct-specific
!          if (~isempty(global_params.realign_params) & (global_params.realign_params.weight_option))
!                subjects(i).weight_image =  spm_get(1, 'IMAGE', 'Weight image for the this session'); 
!          end;
!          
!         % collect info about all sessions
!         num_sessions = 1;
!         if ~isempty(global_params.analysis_params)
!             % do a little directory switcheroo to insure against 
!             % MATLAB path problems
!             my_dir = pwd;
!             x_batch_dir = fullfile(spm('dir'), 'toolbox', 'x_batch');
!             cd(x_batch_dir);
!             nscan = x_deal_SPM_mat('nscan');
!             cd(my_dir);
!             num_sessions = length(nscan);
!             spm_input(['    ' ,num2str(num_sessions), ' sessions are defined in analysis:	', ],'+1','d');
!         else 
!             num_sessions = spm_input('How many sessions?', '+1', 'e', 1);
!         end
!         
!         for s = 1:num_sessions
!             done = 0;
!             while ~done
!                 sessions(s)  = struct('func_dir','',...
!                                       'num_slices', 0, ...
!                                       'other_dir', '', ...
!                                       'func_imgs','', ...
!                                       'other_imgs', '', ...
!                                       'target_image', '', ...
!                                       'source_image', '', ...
!                                       'other_image', '', ...
!                                       'images', [], ... 
!                                       'results_dir' , '',...
!                                       'mat_file', '', ...
!                                       'session_num', '');                  
!                               
!                 
!                 % I assume that there WILL be some functional images to process.
!                 % After all, this IS the utility for FMRI processing ....
!                 % this, of course, might be reconsidered later - perhaps somebody would
!                 % only do the norm-struct and segment ...
!                 sessions(s).session_num = s;
!                 sessions(s).func_imgs = spm_get(Inf, 'IMAGE', ['Session # ', num2str(s), ' functional images']);
!                 n_imgs = size(sessions(s).func_imgs,1);
!                 if ~isempty(global_params.analysis_params)
!                     while nscan(s) ~= n_imgs
!                         spm_input(['Number of images (' num2str(n_imgs),  ') is different from number specified in analysis (', num2str(nscan(s)), ')']  ,'+1','bd','OK');
!                         sessions(s).func_imgs = spm_get(Inf, 'IMAGE', ['Session # ', num2str(s), ' functional images']);    
!                         n_imgs = size(sessions(s).func_imgs,1);
!                     end
!                 end
!                 sessions(s).other_image = [];%spm_get('Files', subjects(i).other_dir, '*img');
!                 %subjects(i).other_dir = spm_get(Inf, '*', ['Other images directory']);      
!                 % fill the dir info
!                 if(~isempty(sessions(s).func_imgs))
!                     [dir, name, ext] = fileparts(sessions(s).func_imgs(1, :));
!                     sessions(s).func_dir = dir;
! 
!                 end;
!         
!                 % TODO: hmmm - what is THAT?
!                 %********************* OTHER IMAGES ***********************
!                 %if ~isempty(subjects(i).other_imgs)
!                 %   [dir, name, ext] = fileparts(subjects(i).other_imgs(1, :));
!                 %   subjects(i).struct_dir = dir;
!                 %end;
!             
!                 % the following will just give the user a chance to double-check
!                 % the inputs, in case they mess up the images or something ...
!                 % note that the struct directory is SAME for all session
!                 if(~isempty(subjects(i).struct_dir))
!                     spm_input(['      Structural images in ' subjects(i).struct_dir ], '+1' ,'d');
!                 end;
!                 if(~isempty(sessions(s).func_dir))
!                     spm_input(['      Functional images in ' sessions(s).func_dir ], '+1' ,'d');
!                 end;      
!     
!                 if(~isempty(sessions(s).other_dir))
!                     spm_input(['      Other images; ' sessions(s).other_dir ], '+1' ,'d');
!                 end;
!                 done = spm_input(['Accept subject ', num2str(i), ' session # ', num2str(s) ] , '+1', 'b','Yes| Redo',[1 , 0]);
!             
!                 % set up the 'results' dir
!                 if (done)  
!                     % note that this logic for subdir making is based on
!                     % assumption that a subject may have a structural image
!                     % and, say, 1-n sessions of functional image. NOT !!!! many
!                     % sessions of structural images
!                     results_dir_name = strcat(['results_' ,subjects(i).subject_id{1}, '_sess', num2str(s), '_', global_params.protocol_name]);
!                     if ~isempty(sessions(s).func_dir)
!                         mkdir(sessions(s).func_dir, results_dir_name);
!                         sessions(s).results_dir = strcat([sessions(s).func_dir, filesep, results_dir_name]);
!                     elseif ~isempty(subjects(i).struct_dir) & ~made_result_dir % only make one structural results directory per subject
!                         mkdir(sessions(s).struct_dir, results_dir_name);
!                         sessions(s).results_dir = strcat([sessions(s).struct_dir filesep results_dir_name]);
!                         made_result_dir = 1;
!                     end;
!                 %   spm_results_dir = sessions(s).results_dir;
!                 end;
!             
!             end; % end while
!     end; %end sessions input
!  subjects(i).sessions = sessions;
!  
!     %TODO: get 'other images  
!     %subjects(i).images = subjects(i).func_imgs; %spm_get('Files', subjects(i).func_dir, '*.img') ;
! spm_protege_interface('save scan', subjects(i));
! 'about to finish patients input'
! subjects
! end; %end patient's input
! display_graphix = spm_input(['Display graphics (progress bars, windows etc.) while processing?']  ,'+1','bd','Yes|No');
! 
! % create a log file
! str = strcat(['log_', datestr(now, 30), '.txt']);
! d = fullfile(spm('dir'), 'toolbox', 'x_batch', 'logs');
! % TODO: have the user choose log location?
! if(exist(d) ~= 7) % if the 'logs' directory does not exist
!     mkdir(fullfile(spm('dir'), 'toolbox', 'x_batch'), 'logs');
! end
! str = fullfile(spm('dir'), 'toolbox', 'x_batch', 'logs', str);
! log_file_fid = fopen(str, 'at' ); 
! %run the batch job
! for i = 1:num_subj
!     fprintf(log_file_fid, strcat(['subject #', num2str(i), '\n\n']));
!     if strcmpi(display_graphix, 'No')
!     % compliments of SPM mailing list
!         names = {'Graphics', 'Interactive'};%, 'Menu'};
!             for n = 1:length(names)
!                 f = findobj('tag', names{n});
!                 set(f, 'visible', 'off');
!             end;
!     %%%        
!     end;
!     try
!         x_process_subject(subjects(i));
!         
!     catch
!         disp(['error processing subject ', subjects(i).subject_id{1}]);
!         disp(lasterr);
!         fprintf(log_file_fid, strcat(['Error processing subject ', subjects(i).subject_id{1}, ': ', lasterr, '\n']));
!     end
! end
! fclose(log_file_fid);
! spm_input(['        DONE   ' ]  ,'+1','bd','OK');
! %==========================================================================
! % --- Executes on button press in delete_button.
! function delete_button_Callback(hObject, eventdata, handles)
! % hObject    handle to delete_button (see GCBO)
! % eventdata  reserved - to be defined in a future version of MATLAB
! % handles    structure with handles and user data (see GUIDATA)
! x_subjects_delete;
! 
! %==========================================================================
! function x_process_subject(subject)
! % X_PROCESS_SUBJECT executes stages specified in the protocol in correct order
! % then moves the files into separate directories
! global defaults;
! global global_params;
! global subject_id;
! global kb;
! global images;
! global log_file_fid;
! import java.util.*;
! spm_defaults;
! constants;
! 
! %TODO: check if there is anything to process
! %if isempty(subject.images)
! %    disp('no images to process');
! %    return;
! %end
! 
! params_cell = cell(7, 1);
! if(~isempty(global_params.coreg_params))
!     params_cell(global_params.coreg_params.order) = {COREG};
! end
! if(~isempty(global_params.realign_params))
!     params_cell(global_params.realign_params.order) = {REALIGN};
! end
! if(~isempty(global_params.normalise_params))
!     params_cell(global_params.normalise_params.order) = {NORMALIZE};
! end
! if(~isempty(global_params.smooth_params))
!     params_cell(global_params.smooth_params.order) = {SMOOTH};
! end
! if(~isempty(global_params.slice_timing_params))
!     params_cell(global_params.slice_timing_params.order) = {SLICE_TIME};
! end
! if(~isempty(global_params.segment_params))
!     params_cell(global_params.segment_params.order) = {SEGMENT};
! end
! % assumption: analysis is ALWAYS after preprocessing
! if(~isempty(global_params.analysis_params))
!     params_cell(7) = {ANALYSIS};
! end
! 
! %images = subject.images;
! 
! % TODO: note that the following will only work with MATLAB 6.5 or higher
! ps_file = spm_get('files', pwd, 'spm2.ps');
! if ~isempty(ps_file)
!     movefile(ps_file, 'spm2_old.ps');
! end
! 
! clear ps_file;
! 
! for i = 1:size(params_cell,1)
!      if ~isempty(params_cell{i})
!          try
!             subject = x_process_stage(params_cell{i}, subject);
!             fprintf(log_file_fid, '\n   completed successfully \n');
!         catch
!             fprintf(log_file_fid, ['failed: ', lasterr, '\n']);
!             disp(lasterr);
!         end
!      end   
! end
! %##############################################
! %TODO: Make sure that moving is only accomplished when the processing was more or less successful
! %###########################################################################
! %==========================================================================
! function execute_stage( Tag, subject )
! global defaults;
! spm_defaults;
! global global_params;
! global images;
! 
! %skip stages which are not filled
! if isempty(Tag)    
!     return; 
! end;
! 
! % switch on the parameters' type
! switch(char(Tag))
! case COREG
!     subject = x_coreg_batch( subject, global_params.coreg_params );
! case REALIGN
!     subject = x_realign_batch( subject, global_params.realign_params ) ;  
! case NORMALIZE 
!     subject = x_norm_batch( subject, global_params.normalise_params );    
! case SMOOTH
!     subject = x_smooth_batch(subject, global_params.smooth_params)
! case SEGMENT
!     subject = x_segment_batch(subject, global_params.segment_params);  
! case SLICE_TIME   
!     subject = x_slice_timing_batch(subject, global_params.slice_timing_params );
! case ANALYSIS
!     subject = x_analysis_batch(subject, global_params.analysis_params);
! otherwise
!     disp('no such stage. yet')
  end
\ No newline at end of file
--- 1,380 ----
! function varargout = x_run_protocol(varargin)
! % X_RUN_PROTOCOL is a gateway to starting actual batch processing with a chosen protocol. 
! % it allows the user to specify file locations for particular subject(s)
! % use the 'new subject' button to create a new subject entry in the database (for Protege database)
! % use 'run' button to start the batch processing session
! global defaults;
! global version_number;
! global global_params;
! global spm_results_dir;
! global display_graphix;
! global log_file_fid;
! constants;
! 
! if nargin == 0  % LAUNCH GUI
!     SPMid = spm('FnBanner',mfilename, version_number);
! 	fig = openfig(mfilename,'reuse');
! 	% Use system color scheme for figure:
! 	set(fig,'Color',get(0,'defaultUicontrolBackgroundColor'));
! 	% Generate a structure of handles to pass to callbacks, and store it. 
! 	handles = guihandles(fig);
! 	guidata(fig, handles);   
! 	if nargout > 0
! 		varargout{1} = fig
! 	end
!     version_number = '2.2 - beta';
! elseif ischar(varargin{1}) % INVOKE NAMED SUBFUNCTION OR CALLBACK
!     try
! 		[varargout{1:nargout}] = feval(varargin{:}); % FEVAL switchyard
! 	catch
! 		disp(lasterr);
! 	end
! 
! end
! 
! % --------------------------------------------------------------------
! function varargout = new_patient_Callback(h, eventdata, handles, varargin)
! % create a new patient in the Protege database. A new patient is only
! % identified by his/her subject id, which MUST be unique
! constants;
! subject_id = spm_input('subject_id', '+1', 's', 'X2003');
! ids = x_get_instances_ids('Subject', SUBJECT);
! % make sure subject ids are unique
! unique = 0;
! while(~unique)
!     check_again  = 0;
!    for i = 1:size(ids,2)
!            if strcmpi(subject_id, ids(i))
!               spm_input(['Subject with the id ' subject_id ' already exists!'], 1,'bd','OK')
!               subject_id = spm_input('subject_id', '+1', 's', 'X2003');
!               check_again = 1;
!            end;     
!     end;
!     if (~check_again) unique = 1; end;     
! end;
! spm_protege_interface('new subject', subject_id);
! closereq;
! 
! %###########################
! %TODO: print errors if any
! %###########################
! % --------------------------------------------------------------------
! function varargout = choose_patient_Callback(h, eventdata, handles, varargin)
! % Stub for Callback of the uicontrol handles.choose.
! global subject_id;
! constants;
! val = get(handles.choose_patient, 'Value'); 
! subject_ids = x_get_instances_ids('Subject', SUBJECT);
! subject_id = subject_ids(val);
! 
! % --------------------------------------------------------------------
! function varargout = execute_Callback(h, eventdata, handles, varargin)
! % Stub for Callback of the uicontrol handles.pushbutton12.
! global global_params;
! global spm_results_dir;
! global log_file_fid;
! constants;
! 
! num_subj = spm_input('Num subjects', 1, 'e', 1);
! 
! for i = 1:num_subj
!    subjects(i) = struct('subject_id', [], ...
!                              'subject_num', [], ... % this is just to display 'processing subject number X' message
!                              'struct_imgs', [], ... % note that I assume that there is essentially ONE struct per subject                              'struct_dir', '', ...
!                              'weight_image', [], ...
!                              'root_dir', [], ...
!                              'sessions', []); 
! end
! 
! for i = 1:num_subj,
!       %  subjects(i) = struct('subject_id', [], ...
!       %                       'subject_num', [], ... % this is just to display 'processing subject number X' message
!       %                       'struct_imgs', [], ... % note that I assume that there is essentially ONE struct per subject                              'struct_dir', '', ...
!       %                       'weight_image', [], ...
!       %                       'root_dir', [], ...
!       %                       'sessions', [])  %semicolon
!       %                   subjects
!         % collect subject-specific info         
!         % get a subject_id 
!        
!         subject_ids = sort(x_get_instances_ids('Subject', SUBJECT, ['Please choose a subject #' i]));            
!         subjects(i).subject_id = spm_input(['Please choose subject # ' num2str(i)], '2','m',subject_ids, subject_ids);
!         subjects(i).subject_num = i;    
!         spm_input(['Subject ' num2str(i) ': ' subjects(i).subject_id{1}], 3 ,'d');
!         
!         % collect info about the structural images, which are SAME for all
!         % sessions
!          subjects(i).root_dir = spm_get(-1, '',['Indicate the root directory for this subject']);
!          % the normalisation may be performed on either struct or func
!          % images. Here, we determine what images it is performed on, so
!          % that we do not ask the user unneccessary question
!          norm_struct = 0;
!          if(~isempty(global_params.normalise_params))
!             norm_struct = global_params.normalise_params.normalise_struct; 
!            % if global_params.normalise_params.option == 2
!            %     global_params.normalise_params.file_to_write_from = spm_get(1, norm_file_extention, ['Parameters to write']);
!            % end;          
!         end;         
!          if ~(isempty(global_params.coreg_params) & isempty(global_params.segment_params) & ~norm_struct)  
!              subjects(i).struct_imgs = spm_get(Inf, 'IMAGE', ['Choose the structural image for this subject']);
!          end;
!          
!          if(~isempty(subjects(i).struct_imgs))
!            [dir, name, ext] = fileparts(subjects(i).struct_imgs(1, :));
!            subjects(i).struct_dir = dir;
!          end;
!                
!          % if the images are weighted, ask for weight images   
!          % TODO: now, are weight images session-specific or
!          % patient-specific? Are the 'other' images sessions speciic
!          % or subjct-specific
!          if (~isempty(global_params.realign_params) & (global_params.realign_params.weight_option))
!                subjects(i).weight_image =  spm_get(1, 'IMAGE', 'Weight image for the this session'); 
!          end;
!          
!         % collect info about all sessions
!         num_sessions = 1;
!         if ~isempty(global_params.analysis_params)
!             % do a little directory switcheroo to insure against 
!             % MATLAB path problems
!             my_dir = pwd;
!             x_batch_dir = fullfile(spm('dir'), 'toolbox', 'x_batch');
!             cd(x_batch_dir);
!             nscan = x_deal_SPM_mat('nscan');
!             cd(my_dir);
!             num_sessions = length(nscan);
!             spm_input(['    ' ,num2str(num_sessions), ' sessions are defined in analysis:	', ],'+1','d');
!         else 
!             num_sessions = spm_input('How many sessions?', '+1', 'e', 1);
!         end
!         
!         for s = 1:num_sessions
!             done = 0;
!             while ~done
!                 sessions(s)  = struct('func_dir','',...
!                                       'num_slices', 0, ...
!                                       'other_dir', '', ...
!                                       'func_imgs','', ...
!                                       'other_imgs', '', ...
!                                       'target_image', '', ...
!                                       'source_image', '', ...
!                                       'other_image', '', ...
!                                       'images', [], ... 
!                                       'results_dir' , '',...
!                                       'mat_file', '', ...
!                                       'session_num', '');                  
!                               
!                 
!                 % I assume that there WILL be some functional images to process.
!                 % After all, this IS the utility for FMRI processing ....
!                 % this, of course, might be reconsidered later - perhaps somebody would
!                 % only do the norm-struct and segment ...
!                 sessions(s).session_num = s;
!                 sessions(s).func_imgs = spm_get(Inf, 'IMAGE', ['Session # ', num2str(s), ' functional images']);
!                 n_imgs = size(sessions(s).func_imgs,1);
!                 if ~isempty(global_params.analysis_params)
!                     while nscan(s) ~= n_imgs
!                         spm_input(['Number of images (' num2str(n_imgs),  ') is different from number specified in analysis (', num2str(nscan(s)), ')']  ,'+1','bd','OK');
!                         sessions(s).func_imgs = spm_get(Inf, 'IMAGE', ['Session # ', num2str(s), ' functional images']);    
!                         n_imgs = size(sessions(s).func_imgs,1);
!                     end
!                 end
!                 sessions(s).other_image = [];%spm_get('Files', subjects(i).other_dir, '*img');
!                 %subjects(i).other_dir = spm_get(Inf, '*', ['Other images directory']);      
!                 % fill the dir info
!                 if(~isempty(sessions(s).func_imgs))
!                     [dir, name, ext] = fileparts(sessions(s).func_imgs(1, :));
!                     sessions(s).func_dir = dir;
! 
!                 end;
!         
!                 % TODO: hmmm - what is THAT?
!                 %********************* OTHER IMAGES ***********************
!                 %if ~isempty(subjects(i).other_imgs)
!                 %   [dir, name, ext] = fileparts(subjects(i).other_imgs(1, :));
!                 %   subjects(i).struct_dir = dir;
!                 %end;
!             
!                 % the following will just give the user a chance to double-check
!                 % the inputs, in case they mess up the images or something ...
!                 % note that the struct directory is SAME for all session
!                 if(~isempty(subjects(i).struct_dir))
!                     spm_input(['      Structural images in ' subjects(i).struct_dir ], '+1' ,'d');
!                 end;
!                 if(~isempty(sessions(s).func_dir))
!                     spm_input(['      Functional images in ' sessions(s).func_dir ], '+1' ,'d');
!                 end;      
!     
!                 if(~isempty(sessions(s).other_dir))
!                     spm_input(['      Other images; ' sessions(s).other_dir ], '+1' ,'d');
!                 end;
!                 done = spm_input(['Accept subject ', num2str(i), ' session # ', num2str(s) ] , '+1', 'b','Yes| Redo',[1 , 0]);
!             
!                 % set up the 'results' dir
!                 if (done)  
!                     % note that this logic for subdir making is based on
!                     % assumption that a subject may have a structural image
!                     % and, say, 1-n sessions of functional image. NOT !!!! many
!                     % sessions of structural images
!                     results_dir_name = strcat(['results_' ,subjects(i).subject_id{1}, '_sess', num2str(s), '_', global_params.protocol_name]);
!                     if ~isempty(sessions(s).func_dir)
!                         mkdir(sessions(s).func_dir, results_dir_name);
!                         sessions(s).results_dir = strcat([sessions(s).func_dir, filesep, results_dir_name]);
!                     elseif ~isempty(subjects(i).struct_dir) & ~made_result_dir % only make one structural results directory per subject
!                         mkdir(sessions(s).struct_dir, results_dir_name);
!                         sessions(s).results_dir = strcat([sessions(s).struct_dir filesep results_dir_name]);
!                         made_result_dir = 1;
!                     end;
!                 %   spm_results_dir = sessions(s).results_dir;
!                 end;
!             
!             end; % end while
!     end; %end sessions input
!  subjects(i).sessions = sessions;
!  
!     %TODO: get 'other images  
!     %subjects(i).images = subjects(i).func_imgs; %spm_get('Files', subjects(i).func_dir, '*.img') ;
! %spm_protege_interface('save scan', subjects(i));
! end; %end patient's input
! display_graphix = spm_input(['Display graphics (progress bars, windows etc.) while processing?']  ,'+1','bd','Yes|No');
! 
! % create a log file
! str = strcat(['log_', datestr(now, 30), '.txt']);
! d = fullfile(spm('dir'), 'toolbox', 'x_batch', 'logs');
! % TODO: have the user choose log location?
! if(exist(d) ~= 7) % if the 'logs' directory does not exist
!     mkdir(fullfile(spm('dir'), 'toolbox', 'x_batch'), 'logs');
! end
! str = fullfile(spm('dir'), 'toolbox', 'x_batch', 'logs', str);
! log_file_fid = fopen(str, 'at' ); 
! %run the batch job
! for i = 1:num_subj
!     fprintf(log_file_fid, strcat(['subject #', num2str(i), '\n\n']));
!     if strcmpi(display_graphix, 'No')
!     % compliments of SPM mailing list
!         names = {'Graphics', 'Interactive'};%, 'Menu'};
!             for n = 1:length(names)
!                 f = findobj('tag', names{n});
!                 set(f, 'visible', 'off');
!             end;
!     %%%        
!     end;
!     try
!         x_process_subject(subjects(i));
! 	  spm_protege_interface('save scan', subjects(i));
!         
!     catch
!         disp(['error processing subject ', subjects(i).subject_id{1}]);
!         disp(lasterr);
!         fprintf(log_file_fid, strcat(['Error processing subject ', subjects(i).subject_id{1}, ': ', lasterr, '\n']));
!     end
! end
! fclose(log_file_fid);
! spm_input(['        DONE   ' ]  ,'+1','bd','OK');
! %==========================================================================
! % --- Executes on button press in delete_button.
! function delete_button_Callback(hObject, eventdata, handles)
! % hObject    handle to delete_button (see GCBO)
! % eventdata  reserved - to be defined in a future version of MATLAB
! % handles    structure with handles and user data (see GUIDATA)
! x_subjects_delete;
! 
! %==========================================================================
! function x_process_subject(subject)
! % X_PROCESS_SUBJECT executes stages specified in the protocol in correct order
! % then moves the files into separate directories
! global defaults;
! global global_params;
! global subject_id;
! global kb;
! global images;
! global log_file_fid;
! import java.util.*;
! spm_defaults;
! constants;
! 
! %TODO: check if there is anything to process
! %if isempty(subject.images)
! %    disp('no images to process');
! %    return;
! %end
! 
! params_cell = cell(7, 1);
! if(~isempty(global_params.coreg_params))
!     params_cell(global_params.coreg_params.order) = {COREG};
! end
! if(~isempty(global_params.realign_params))
!     params_cell(global_params.realign_params.order) = {REALIGN};
! end
! if(~isempty(global_params.normalise_params))
!     params_cell(global_params.normalise_params.order) = {NORMALIZE};
! end
! if(~isempty(global_params.smooth_params))
!     params_cell(global_params.smooth_params.order) = {SMOOTH};
! end
! if(~isempty(global_params.slice_timing_params))
!     params_cell(global_params.slice_timing_params.order) = {SLICE_TIME};
! end
! if(~isempty(global_params.segment_params))
!     params_cell(global_params.segment_params.order) = {SEGMENT};
! end
! % assumption: analysis is ALWAYS after preprocessing
! if(~isempty(global_params.analysis_params))
!     params_cell(7) = {ANALYSIS};
! end
! 
! %images = subject.images;
! 
! % TODO: note that the following will only work with MATLAB 6.5 or higher
! ps_file = spm_get('files', pwd, 'spm2.ps');
! if ~isempty(ps_file)
!     movefile(ps_file, 'spm2_old.ps');
! end
! 
! clear ps_file;
! 
! for i = 1:size(params_cell,1)
!      if ~isempty(params_cell{i})
!          try
!             subject = x_process_stage(params_cell{i}, subject);
!             fprintf(log_file_fid, '\n   completed successfully \n');
!         catch
!             fprintf(log_file_fid, ['failed: ', lasterr, '\n']);
!             disp(lasterr);
!         end
!      end   
! end
! %##############################################
! %TODO: Make sure that moving is only accomplished when the processing was more or less successful
! %###########################################################################
! %==========================================================================
! function execute_stage( Tag, subject )
! global defaults;
! spm_defaults;
! global global_params;
! global images;
! 
! %skip stages which are not filled
! if isempty(Tag)    
!     return; 
! end;
! 
! % switch on the parameters' type
! switch(char(Tag))
! case COREG
!     subject = x_coreg_batch( subject, global_params.coreg_params );
! case REALIGN
!     subject = x_realign_batch( subject, global_params.realign_params ) ;  
! case NORMALIZE 
!     subject = x_norm_batch( subject, global_params.normalise_params );    
! case SMOOTH
!     subject = x_smooth_batch(subject, global_params.smooth_params)
! case SEGMENT
!     subject = x_segment_batch(subject, global_params.segment_params);  
! case SLICE_TIME   
!     subject = x_slice_timing_batch(subject, global_params.slice_timing_params );
! case ANALYSIS
!     subject = x_analysis_batch(subject, global_params.analysis_params);
! otherwise
!     disp('no such stage. yet')
  end
\ No newline at end of file