基于监督学习的多模态MRI脑肿瘤分割，使用来自超体素的纹理特征（Matlab代码实现）

function varargout = MP3(varargin) % MP3 MATLAB code for MP3.fig % MP3, by itself, creates a new MP3 or raises the existing % singleton*. % % H = MP3 returns the handle to a new MP3 or the handle to % the existing singleton*. % % MP3( ’CALLBACK’ ,hObject,eventData,handles,...) calls the local % function named CALLBACK in MP3.M with the given input arguments. % % MP3( ’Property’ , ’Value’ ,...) creates a new MP3 or raises the % existing singleton*. Starting from the left, property value pairs are % applied to the GUI before MP3_OpeningFcn gets called. An % unrecognized property name or invalid value makes property application % stop. All inputs are passed to MP3_OpeningFcn via varargin. % % *See GUI Options on GUIDE ’s Tools menu. Choose "GUI allows only one % instance to run (singleton)". % % See also: GUIDE, GUIDATA, GUIHANDLES % Edit the above text to modify the response to help MP3 % Last Modified by GUIDE v2.5 17-Jun-2021 14:19:22 % Begin initialization code - DO NOT EDIT gui_Singleton = 1; gui_State = struct(’ gui_Name ’, mfilename, ... ’ gui_Singleton ’, gui_Singleton, ... ’ gui_OpeningFcn ’, @MP3_OpeningFcn, ... ’ gui_OutputFcn ’, @MP3_OutputFcn, ... ’ gui_LayoutFcn ’, [] , ... ’ gui_Callback ’, []); if nargin && ischar(varargin{1}) gui_State.gui_Callback = str2func(varargin{1}); end if nargout [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:}); else gui_mainfcn(gui_State, varargin{:}); end % End initialization code - DO NOT EDIT % --- Executes just before MP3 is made visible. function MP3_OpeningFcn(hObject, ~, handles, varargin) % This function has no output args, see OutputFcn. % hObject handle to figure % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % varargin command line arguments to MP3 (see VARARGIN) % Choose default command line output for MP3 handles.output = hObject; % Add path to all the files in the MATLAB search path p = mfilename(’ fullpath ’); warning off rmpath(genpath(fileparts(p))) warning on addpath(genpath(fileparts(p)),’ -begin ’); % init stuct/variables handles.VOIs = {’ Other ’}; handles.histo = {’ Other ’}; %{’ Pimo ’, ’ ColIV ’, ’ Tc+I_cerveau ’, ’ Tc+I_ref ’}; handles.resolution = [1 64 112 128 192 256 384 512 3000]; handles.colors ={’ b ’, ’ g ’, ’ m ’, ’ c ’, ’ r ’, ’ k ’, ’ y ’, ’ navy ’,... ’ u1 ’,’ turquoise ’,’ slateblue ’, ’ springgreen ’, ’ maroon ’,... ’ purple ’, ’ u2 ’, ’ olive ’, ’ u3 ’,’ chartreuse ’, ’ u4 ’, ’ sky ’,... ’ u5 ’, ’ orange ’, ’ u6 ’, ’ u7 ’, ’ u8 ’, ’ gray ’}; load(which(’ rgb_color_table.mat ’), ’ num ’); handles.colors_rgb = num; handles.colormap = get(handles.MP3_colormap_popupmenu,’ String ’); handles.markers ={’ o ’,’ s ’, ’ d ’, ’ p ’, ’ h ’, ’ + ’, ’ * ’, ’ x ’}; table_data(1,1) = {’ Voxel values ’}; set(handles.MP3_table_pixel_values, ’ Data ’, table_data); set(handles.MP3_table1, ’ Data ’, {’ ’, ’ ’, ’ ’, ’ ’, ’ ’}); handles.table1.cluster = []; handles.table1.cluster_row = []; handles.mode = 1; handles.view_mode = ’ Axial ’; set(handles.MP3_scans_button, ’ ForegroundColor ’, [1 0 0]) set(handles.MP3_scans_button, ’ Value ’, 1) handles.display_option.view_pixel_on_map = 0; handles.display_option.view_pixel_on_plot = 0; handles.display_option.view_plot = 1; handles.display_option.manual_contrast = 0; set(handles.MP3_menu_view_plot, ’ Check ’, ’ on ’); for i=1:4 stri = num2str(i); set(eval([’ handles.MP3_data ’, stri, ’ _echo_slider ’]), ’ Visible ’, ’ off ’); set(eval([’ handles.MP3_data ’, stri, ’ _expt_slider ’]), ’ Visible ’, ’ off ’); end set(handles.MP3_PRM_slider_trans, ’ Visible ’, ’ off ’); % add MRIManager.jar to the classpath (dynamic classpath) [filepath,name,ext] = fileparts(which(’ MRIManager.jar ’)); javaclasspath(fullfile(filepath,[name,ext])); % save the java skin used handles.original_Java_LookAndFeel = javax.swing.UIManager.getLookAndFeel; handles.original_Java_LookAndFeel = sprintf(’ %s ’,handles.original_Java_LookAndFeel); handles.original_Java_LookAndFeel = split(handles.original_Java_LookAndFeel,’ - ’); handles.original_Java_LookAndFeel = extractBefore(handles.original_Java_LookAndFeel{end},’ ] ’); handles.original_Java_LookAndFeel = [’ [LookAndFeel] ’,handles.original_Java_LookAndFeel]; % A = javax.swing.UIManager.getLookAndFeel; % char(A.getClass) % ’ class com.jgoodies.looks.plastic.Plastic3DLookAndFeel ’ Replace class by [LookAndFeel] % Update handles structure guidata(hObject, handles); % UIWAIT makes MP3 wait for user response (see UIRESUME) % uiwait(handles.MP3_GUI); % --- Outputs from this function are returned to the command line. function varargout = MP3_OutputFcn(~, ~, handles) % varargout cell array for returning output args (see VARARGOUT); % hObject handle to figure % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Get default command line output from handles structure varargout{1} = handles.output; % --- Executes when user attempts to close MP3_GUI. function MP3_GUI_CloseRequestFcn(hObject, eventdata, handles) % hObject handle to MP3_GUI (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if ~isfield(handles, ’ database ’) delete(hObject); if ~isempty(findobj(’ type ’, ’ figure ’, ’ name ’, ’ MP3 pipeline Manager ’)) close((findobj(’ type ’, ’ figure ’, ’ name ’, ’ MP3 pipeline Manager ’))); end return else DBFilename = [handles.database.Properties.UserData.MP3_data_path, handles.database.Properties.UserData.db_filename]; SavedDB = load(DBFilename, ’ database ’); Diff = setdiff(SavedDB.database, handles.database); if isempty(Diff) delete(hObject); if ~isempty(findobj(’ type ’, ’ figure ’, ’ name ’, ’ MP3 pipeline Manager ’)) close((findobj(’ type ’, ’ figure ’, ’ name ’, ’ MP3 pipeline Manager ’))); end return end end % Hint: delete(hObject) closes the figure selection = questdlg(’ Before leaving, do you want to save your database? ’,... ’ Warning ’,... ’ Yes ’,’ No ’,’ Yes ’); if isempty(selection) return end switch selection case ’ Yes ’ MP3_menu_save_database_Callback(hObject, eventdata, handles) end if ~isempty(findobj(’ type ’, ’ figure ’, ’ name ’, ’ MP3 pipeline Manager ’)) close((findobj(’ type ’, ’ figure ’, ’ name ’, ’ MP3 pipeline Manager ’))); end delete(hObject); % --- If Enable == ’ on ’, executes on mouse press in 5 pixel border. % --- Otherwise, executes on mouse press in 5 pixel border or over MP3_slider_slice. function MP3_slider_slice_ButtonDownFcn(hObject, eventdata, handles) % hObject handle to MP3_slider_slice (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) handles = guidata(hObject); if ~isfield(handles, ’ data_loaded ’) && ~isfield(handles, ’ data_selected_for_PRM ’) return end Slice_min = get(hObject,’ Min ’); Slice_max = get(hObject,’ Max ’); Position = get(hObject,’ Position ’); SliderBarWidth = Position(3)/Slice_max; set(hObject,’ UserData ’,[Slice_min Slice_max SliderBarWidth]); cp = get(handles.MP3_GUI,’ CurrentPoint ’); newValue = round((cp(1,1))/SliderBarWidth); if newValue == get(handles.MP3_slider_slice,’ Value ’) return elseif newValue > Slice_max newValue = Slice_max; elseif newValue < Slice_min newValue = Slice_min; end set(handles.MP3_slider_slice,’ Value ’,newValue); MP3_update_axes(hObject, eventdata, handles) % % set(handles.MP3_GUI,’ WindowButtonMotionFcn ’,{@MP3_slider_on_move,handles}) % set(handles.MP3_GUI,’ WindowButtonUpFcn ’,{@MP3_slider_release_click,handles}) % --- Executes during object creation, after setting all properties. function MP3_slider_slice_CreateFcn(hObject, ~, ~) % hObject handle to MP3_slider_slice (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: slider controls usually have a light gray background. if isequal(get(hObject,’ BackgroundColor ’), get(0,’ defaultUicontrolBackgroundColor ’)) set(hObject,’ BackgroundColor ’,[.9 .9 .9]); end % --- Executes on selection change in MP3_name_list. function MP3_name_list_Callback(hObject, eventdata, ~) % hObject handle to MP3_name_list (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: contents = cellstr(get(hObject,’ String ’)) returns MP3_name_list contents as cell array % contents{get(hObject,’ Value ’)} returns selected item from MP3_name_list handles = guidata(hObject); if ~isfield(handles, ’ database ’) return end set(handles.MP3_time_points_list, ’ Value ’, 1); set(handles.MP3_scans_list, ’ Value ’, 1); set(handles.MP3_file_list, ’ Value ’, 1); MP3_update_database_display(hObject, eventdata, handles); % --- Executes during object creation, after setting all properties. function MP3_name_list_CreateFcn(hObject, ~, ~) % hObject handle to MP3_name_list (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: listbox controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,’ BackgroundColor ’), get(0,’ defaultUicontrolBackgroundColor ’)) set(hObject,’ BackgroundColor ’,’ white ’); end % --- Executes on selection change in MP3_scans_list. function MP3_scans_list_Callback(hObject, eventdata, handles) % hObject handle to MP3_scans_list (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: contents = cellstr(get(hObject,’ String ’)) returns s_list contents as cell array % contents{get(hObject,’ Value ’)} returns selected item from MP3_scans_list if ~isfield(handles, ’ database ’) return end if numel(get(handles.MP3_name_list, ’ Value ’)) >1 || numel(get(handles.MP3_time_points_list, ’ Value ’)) > 1 return end set(handles.MP3_file_list, ’ Value ’, 1); guidata(hObject, handles); MP3_update_database_display(hObject, eventdata, handles) % --- Executes during object creation, after setting all properties. function MP3_scans_list_CreateFcn(hObject, ~, ~) %#ok<*DEFNU> % hObject handle to MP3_scans_list (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: listbox controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,’ BackgroundColor ’), get(0,’ defaultUicontrolBackgroundColor ’)) set(hObject,’ BackgroundColor ’,’ white ’); end function MP3_update_database_display(hObject, eventdata, handles) % handles = guidata(gcf, findobj(’ Tag ’, ’ MP3_GUI ’)); handles = guidata(handles.MP3_GUI); if ~isfield(handles, ’ database ’) return end if isempty(handles.database) % if the table is empty, clear all lists set(handles.MP3_name_list, ’ String ’, ’ ’, ’ Value ’, 1); set(handles.MP3_time_points_list, ’ String ’, ’ ’, ’ Value ’, 1); set(handles.MP3_scans_list, ’ String ’, ’ ’, ’ Value ’, 1); set(handles.MP3_file_list, ’ String ’, ’ ’, ’ Value ’, 1); return end patient_id = get(handles.MP3_name_list, ’ Value ’); id_listing = unique(handles.database.Patient,’ stable ’); set(handles.MP3_name_list, ’ String ’, char(id_listing)); if numel(patient_id)~= 1 return end Patient_filter = handles.database.Patient== id_listing(patient_id); tp_listing = unique(handles.database.Tp(Patient_filter),’ stable ’); % check if the new time point listing is not shorter than the old one. If % so update MP3_time_points_list ’ Value ’ if numel(tp_listing) < get(handles.MP3_time_points_list, ’ Value ’) set(handles.MP3_time_points_list, ’ String ’, char(tp_listing), ’ Value ’, numel(tp_listing)); else set(handles.MP3_time_points_list, ’ String ’, char(tp_listing)); end time_point = get(handles.MP3_time_points_list, ’ Value ’); if get(handles.MP3_scans_button, ’ Value ’) == 1 %display parameters list is_scan = handles.database.Type == ’ Scan ’; tp_filter = handles.database.Tp== tp_listing(time_point); sequence_listing = handles.database.SequenceName(Patient_filter & tp_filter & is_scan); % check if the sequence listing is not shorter than the old one. If % so update MP3_scans_list ’ Value ’ if numel(sequence_listing) < get(handles.MP3_scans_list, ’ Value ’) set(handles.MP3_scans_list, ’ String ’, char(sequence_listing), ’ Value ’, numel(sequence_listing)); else set(handles.MP3_scans_list, ’ String ’, char(sequence_listing)); end scan = get(handles.MP3_scans_list, ’ Value ’); file_text= cell(1, numel(sequence_listing(scan))); for i=1:numel(sequence_listing(scan)) sequence_filter = handles.database.SequenceName== sequence_listing(scan(i)); file_text(i) = cellstr(handles.database.Filename(Patient_filter & tp_filter & sequence_filter & is_scan)); end set(handles.MP3_file_list, ’ String ’, file_text); elseif get(handles.MP3_VOIs_button, ’ Value ’) == 1 %display VOIs list is_ROI = handles.database.Type == ’ ROI ’ | handles.database.Type == ’ Cluster ’; tp_filter = handles.database.Tp== tp_listing(time_point); sequence_listing = handles.database.SequenceName(Patient_filter & tp_filter & is_ROI); if isempty(sequence_listing) set(handles.MP3_scans_list, ’ String ’, ’ ’); return end scan = get(handles.MP3_scans_list, ’ Value ’); set(handles.MP3_scans_list, ’ String ’, char(sequence_listing)); file_text= cell(1, numel(sequence_listing(scan))); for i=1:numel(sequence_listing(scan)) sequence_filter = handles.database.SequenceName== sequence_listing(scan(i)); if sum(Patient_filter & tp_filter & sequence_filter & is_ROI) == 1 file_text(i) = cellstr(handles.database.Filename(Patient_filter & tp_filter & sequence_filter & is_ROI)); else % in case there are more than two entries in the database --> delete the extra one(s) indexes = find(Patient_filter & tp_filter & sequence_filter & is_ROI); handles.database(indexes(2:end),:)=[]; guidata(hObject, handles) return end end set(handles.MP3_file_list, ’ String ’, file_text); elseif get(handles.MP3_Others_button, ’ Value ’) == 1 %display the "Other" tag list % warndlg(’ not coded yet ’, ’ Warning ’); List_of_types = unique(handles.database.Type); List_of_types = List_of_types( ~sum(List_of_types == {’ Scan ’, ’ ROI ’, ’ Cluster ’}, 2)); is_scan = sum(handles.database.Type == List_of_types’ , 2 ); tp_filter = handles.database.Tp== tp_listing(time_point); sequence_listing = handles.database.SequenceName(Patient_filter & tp_filter & is_scan); if isempty(sequence_listing) set(handles.MP3_scans_list, ’String’ , ’’ ); return end % check if the sequence listing is not shorter than the old one. If % so update MP3_scans_list ’Value’ if numel(sequence_listing) < get(handles.MP3_scans_list, ’Value’ ) set(handles.MP3_scans_list, ’String’ , char(sequence_listing), ’Value’ , numel(sequence_listing)); else set(handles.MP3_scans_list, ’String’ , char(sequence_listing)); end scan = get(handles.MP3_scans_list, ’Value’ ); file_text= cell( 1 , numel(sequence_listing(scan))); for i= 1 :numel(sequence_listing(scan)) sequence_filter = handles.database.SequenceName== sequence_listing(scan(i)); file_text(i) = cellstr(handles.database.Filename(Patient_filter & tp_filter & sequence_filter & is_scan)); end set(handles.MP3_file_list, ’String’ , file_text); end % Update the groupname MP3_show_group_Callback(hObject, eventdata, handles) % if the pipeline Manager is open, update the information : patient selected % update the ’String’ of MP3_pipeline_pushMP3Selection and MP3_pipeline_pushMP3TPSelection push button if ~isempty(findobj( ’type’ , ’figure’ , ’name’ , ’MP3 pipeline Manager’ )) % Get the hObject of MP3_pipeline h = findobj( ’Tag’ , ’MP3_pipeline_manager_GUI’ ); % Get the handles of MP3_pipeline data = guidata(h); % Update the handles of MP3_pipeline by stocking the latest version of % MP3 handles. data.MP3_data = handles; % Don ’t touch the original eventdata, just in case. eventdata2 = eventdata; %Update the MP3_pipeline tmp_database [h, ~, data] = MP3_pipeline(’ UpdateTmpDatabase ’, h, eventdata2, data); [~, ~, data] = MP3_pipeline(’ MP3_pipeline_UpdateTables ’, h, eventdata2, data); clear(’ eventdata2 ’) guidata(h, data) end if ~isempty(findobj(’ Tag ’, ’ MP3_pipeline_pushMP3Selection ’)) data_selected = finddata_selected(handles); if size(char(handles.database.Patient(data_selected)),1) > 1 return else set(findobj(’ Tag ’, ’ MP3_pipeline_pushMP3Selection ’), ’ String ’, [char(handles.database.Patient(data_selected(1))) ’ - ’ char(handles.database.Tp(data_selected(1))) ’ only ’]) set(findobj(’ Tag ’, ’ MP3_pipeline_pushMP3TPSelection ’), ’ String ’, [’ All time point of : ’ char(handles.database.Patient(data_selected(1)))]) end end % --- Executes on selection change in MP3_time_points_list. function MP3_time_points_list_Callback(hObject, eventdata, handles) % hObject handle to MP3_time_points_list (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: contents = cellstr(get(hObject,’ String ’)) returns MP3_time_points_list contents as cell array % contents{get(hObject,’ Value ’)} returns selected item from MP3_time_points_list if ~isfield(handles, ’ database ’) return end set(handles.MP3_scans_list, ’ Value ’, 1); set(handles.MP3_file_list, ’ Value ’, 1); guidata(hObject, handles); if numel(get(handles.MP3_time_points_list, ’ Value ’)) >1 ||... numel(get(handles.MP3_name_list, ’ Value ’)) >1 else MP3_update_database_display(hObject, eventdata, handles) end % --- Executes during object creation, after setting all properties. function MP3_time_points_list_CreateFcn(hObject, ~, ~) % hObject handle to MP3_time_points_list (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: listbox controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,’ BackgroundColor ’), get(0,’ defaultUicontrolBackgroundColor ’)) set(hObject,’ BackgroundColor ’,’ white ’); end % --- Executes on selection change in MP3_file_list. function MP3_file_list_Callback(~, ~, ~) % hObject handle to MP3_file_list (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % Hints: contents = cellstr(get(hObject,’ String ’)) returns MP3_file_list contents as cell array % contents{get(hObject,’ Value ’)} returns selected item from MP3_file_list % --- Executes during object creation, after setting all properties. function MP3_file_list_CreateFcn(hObject, ~, ~) % hObject handle to MP3_file_list (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles empty - handles not created until after all CreateFcns called % Hint: listbox controls usually have a white background on Windows. % See ISPC and COMPUTER. if ispc && isequal(get(hObject,’ BackgroundColor ’), get(0,’ defaultUicontrolBackgroundColor ’)) set(hObject,’ BackgroundColor ’,’ white ’); end % -------------------------------------------------------------------- function MP3_rename_name_Callback(hObject, eventdata, handles) % hObject handle to MP3_rename_name (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if ~isfield(handles, ’ database ’) return end data_selected = finddata_selected(handles); if numel(data_selected) >1 warndlg(’ Please select only one Patient ’, ’ Warning ’); return end name_option = [cellstr(unique(handles.database.Patient(handles.database.Type == ’ Scan ’)))’ ’Other’ ] ’; [new_Patient_name, ok1] = listdlg(’ PromptString ’,’ Select the new scan name: ’,... ’ Name ’, ’ Select a Name ’,... ’ SelectionMode ’,’ single ’,... ’ ListSize ’, [400 300],... ’ ListString ’,name_option); if ok1 == 0 return end if strcmp(’ Other ’,name_option(new_Patient_name)) == 1 NewPatient = inputdlg(’ Name of the new Scan ’, ’ Question? ’, 1, {’ ’}); if isempty(NewPatient) return end else NewPatient =name_option(new_Patient_name); end %% update the database with the new name % but first check if the new scan name does not exist for this patient and % time point if find(handles.database.Patient == handles.database.Patient(data_selected) &... handles.database.Tp == handles.database.Tp(data_selected) & ... handles.database.SequenceName == NewPatient) > 0 msgbox(’ A Scan with the same name already exist for this patient at this time point ’) ; return end idx_scan_to_rename = find(handles.database.Patient == handles.database.Patient(data_selected)); for i=1:numel(idx_scan_to_rename) new_nii_filename = strrep(cellstr(handles.database.Filename(idx_scan_to_rename(i))), cellstr(handles.database.Patient(idx_scan_to_rename(i))), NewPatient); % rename the scan file if exist(fullfilename(handles, idx_scan_to_rename(i), ’ .nii ’), ’ file ’) == 0 warning_text = sprintf(’ ##$ This file no not exist ##$ %s’,... fullfilename(handles, idx_scan_to_rename(i), ’.nii’ )); msgbox(warning_text, ’rename file warning’ ) ; elseif exist(string(strcat(cellstr(handles.database.Path(idx_scan_to_rename(i))),new_nii_filename{:}, ’.nii’ )), ’file’ ) == 2 msgbox( ’The new .nii file exist already!!’ ) ; else movefile(fullfilename(handles, idx_scan_to_rename(i), ’.nii’ ), strcat(char(handles.database.Path(idx_scan_to_rename(i))),new_nii_filename{:}, ’.nii’ ), ’f’ ) if exist(fullfilename(handles, idx_scan_to_rename(i), ’.json’ ), ’file’ ) == 2 movefile(fullfilename(handles, idx_scan_to_rename(i), ’.json’ ), strcat(char(handles.database.Path(idx_scan_to_rename(i))),new_nii_filename{:}, ’.json’ ), ’f’ ); end end % update the Filename field in the table handles.database.Patient(idx_scan_to_rename(i)) = NewPatient; handles.database.Filename(idx_scan_to_rename(i)) = new_nii_filename; end % save the structure guidata(hObject, handles); set(handles.MP3_name_list, ’Value’ , 1 ); % update graph and display MP3_update_database_display(hObject, eventdata, handles); % Save database MP3_menu_save_database_Callback(hObject, eventdata, handles) function MP3_remove_name_Callback(hObject, eventdata, handles) % hObject handle to MP3_remove_name (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if ~isfield(handles, ’database’ ) return end %data_selected = finddata_selected(handles); patient_seleted = get(handles.MP3_name_list, ’String’ ); patient_name = patient_seleted(get(handles.MP3_name_list, ’Value’ ),:); %patient_name = unique(handles.database.Patient(data_selected)); user_response = questdlg([ ’Do you want to delete every data of ’ cellstr(patient_name) ’]’ , ’Warning’ , ’Yes’ , ’No’ , ’Cancel’ , ’Cancel’ ); if strcmp(user_response, ’Cancel’ ) || strcmp(user_response, ’No’ ) || isempty(user_response) return end nii_index = []; for i= 1 :size(patient_name, 1 ) nii_index = [nii_index ’ find(handles.database.Patient == categorical(cellstr(patient_name(i,:))))’ ] ’; end MP3_remove_scan(hObject, eventdata, handles, nii_index) % -------------------------------------------------------------------- function MP3_name_right_click_Callback(hObject, eventdata, handles) % hObject handle to MP3_name_right_click (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if ~isfield(handles, ’ database ’) return end % patient_num = get(handles.MP3_name_list, ’ Value ’); % omit_obj = findobj(handles.MP3_name_right_click, ’ Label ’, ’ Omit ’); % set(omit_obj, ’ Checked ’, ’ off ’); % if numel(patient_num) ==1 && ~isempty(handles.database(patient_num).group) % group_name = handles.database(patient_num).group; % if handles.database(patient_num).omit == 1 % set(omit_obj, ’ Checked ’, ’ on ’); % end % end % % show_menu_obj = findobj(handles.MP3_name_right_click, ’ Label ’, ’ Show ’); % delete(get(show_menu_obj, ’ Children ’)) %remove the ’ old ’ show menu % % group = reshape({handles.database.group},1,[]); % group_list = unique(group); % %group_list = unique(group(1:2:end)); % % if ~isfield(handles, ’ database_all ’) || numel(handles.database_all) == numel(handles.database) % for i = 1:numel(group_list) % uimenu(show_menu_obj, ’ Label ’, group_list{i},... % ’ Callback ’, @(hObject,eventdata)MP3(’ MP3_show_group_submenu ’,hObject,eventdata,guidata(hObject))); % end % else % uimenu(show_menu_obj, ’ Label ’, ’ all ’,... % ’ Callback ’, @(hObject,eventdata)MP3(’ MP3_show_group_submenu ’,hObject,eventdata,guidata(hObject))); % end % guidata(hObject, handles); % % function MP3_show_group_submenu(hObject, eventdata, handles) % % show = get(hObject, ’ Label ’); % if strcmp(’ all ’, show) % database_tmp = handles.database_all; % for i = 1:numel(handles.database) % name_size = numel(handles.database(i).name); % match_name = find(strncmp(handles.database(i).name, {database_tmp.name}’ , name_size) == 1 ); % if numel(match_name) > 1 % for j = 1 :numel(match_name) % if numel(handles.database(match_name(j)).name) == name_size; % tmp = match_name(j); % end % end % match_name = tmp; % end % database_tmp(match_name) = handles.database(i); % end % handles.database = database_tmp; % handles= rmfield(handles, ’database_all’ ); % else % n = 1 ; % for i= 1 :numel(handles.database) % if strncmp(show, handles.database(i).group, numel(show)) == 1 &&... % numel(show) == numel(handles.database(i).group) % database_tmp(n) = handles.database(i); % n=n+ 1 ; % end % end % handles.database_all = handles.database; % handles.database = database_tmp; % end % set(handles.MP3_name_list, ’Value’ , 1 ); % set(handles.MP3_time_points_list, ’Value’ , 1 ); % guidata(handles.MP3_GUI, handles); % MP3_update_database_display(hObject, eventdata, handles); % -------------------------------------------------------------------- function MP3_open_database_ClickedCallback(hObject, eventdata, handles) % hObject handle to MP3_open_database (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if isfield(handles, ’database’ ) selection = questdlg( ’Have you saved the present database?’ ,... ’Warning’ ,... ’Yes’ , ’No’ , ’Yes’ ); switch selection case ’No’ return end end path_root=pwd; %[filename, pathname]=uigetfile( ’*.mat’ , ’Open Mat File’ , ’MultiSelect’ , ’off’ ); selpath = uigetdir(path_root, ’Select the project’ ’s folder you want to open’ ); pathname = selpath; %listfiles = what(selpath) filename = ’MP3_database.mat’ ; if pathname == 0 return else if exist(fullfile(pathname, filename)) ~= 2 % The former name of MP3 is MIA. The following lines allow to open % old projects with the new software. if exist(fullfile(pathname, ’MIA_database.mat’ )) ~= 2 errordlg( ’The folder you selected might be corrupt. Please select a folder containing a MP3_database.mat file.’ , ’Cannot open project’ ); return else movefile(fullfile(pathname, ’MIA_database.mat’ ), fullfile(pathname, filename)); end end cd(pathname); if ~strcmp(class(filename), ’double’ ) % #ok<STISA> %reset everything handles = MP3_clear_data(hObject, eventdata, handles); set(handles.MP3_name_list, ’Value’ , 1 ); set(handles.MP3_time_points_list, ’Value’ , 1 ); set(handles.MP3_scans_button, ’Value’ , 1 ); set(handles.MP3_scans_list, ’Value’ , 1 ); database = load(filename); handles.database = database.database; set(handles.MP3_name_list, ’String’ , handles.database.Properties.UserData.db_filename) % update database path ( in case the directory has moved) handles.database.Properties.UserData.db_filename = filename; new_patient_directory = strcat(pathname, filesep); handles.database.Properties.UserData.MP3_data_path = new_patient_directory; handles.database.Properties.UserData.MP3_Raw_data_path = [new_patient_directory, ’Raw_data’ , filesep]; handles.database.Properties.UserData.MP3_ROI_path = [new_patient_directory, ’ROI_data’ , filesep]; handles.database.Properties.UserData.MP3_Derived_data_path = [new_patient_directory, ’Derived_data’ , filesep]; handles.database.Properties.UserData.PSOM_path = [new_patient_directory, ’PSOM’ , filesep]; handles.database.Properties.UserData.MP3_Others_data_path = [new_patient_directory, ’Others_data’ , filesep]; % update the path in the table %handles.database.Path(handles.database.Type == ’Scan’ ) = handles.database.Properties.UserData.MP3_Raw_data_path; if ~isempty(handles.database) handles.database.Path(handles.database.IsRaw == ’0’ & handles.database.Type == ’Scan’ ,:) = handles.database.Properties.UserData.MP3_Derived_data_path ; handles.database.Path(handles.database.IsRaw == ’1’ & handles.database.Type == ’Scan’ ,:) = handles.database.Properties.UserData.MP3_Raw_data_path; handles.database.Path(handles.database.Type == ’Mfile’ ,:) = handles.database.Properties.UserData.MP3_Others_data_path; handles.database.Path(handles.database.Type == ’ROI’ ) = handles.database.Properties.UserData.MP3_ROI_path; handles.database.Path(handles.database.Type == ’Cluster’ ) = handles.database.Properties.UserData.MP3_ROI_path; end guidata(hObject, handles); end cd(path_root); end MP3_update_figureName(hObject, eventdata, handles) guidata(hObject, handles); MP3_update_database_display(hObject, eventdata, handles); % -------------------------------------------------------------------- function MP3_time_points_right_click_Callback(~, ~, ~) % hObject handle to MP3_time_points_right_click (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) % -------------------------------------------------------------------- function MP3_rename_time_point_Callback(hObject, eventdata,handles) % hObject handle to MP3_rename_time_point (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if ~isfield(handles, ’database’ ) return end data_selected = finddata_selected(handles); if numel(data_selected) > 1 warndlg( ’Please select only one Time point’ , ’Warning’ ); return end name_option = [cellstr(unique(handles.database.Tp(handles.database.Type == ’Scan’ ))) ’ ’ Other ’]’ ; [new_TP_name, ok1] = listdlg( ’PromptString’ , ’Select the new scan name:’ ,... ’Name’ , ’Select a Name’ ,... ’SelectionMode’ , ’single’ ,... ’ListSize’ , [ 400 300 ],... ’ListString’ ,name_option); if ok1 == 0 return end if strcmp( ’Other’ ,name_option(new_TP_name)) == 1 NewTp = inputdlg( ’Name of the new Scan ’ , ’Question?’ , 1 , { ’’ }); else NewTp =name_option(new_TP_name); end %% update the database with the new name % but first check if the new scan name does not exist for this patient and % time point % faire le ROI vs SCAN if find(handles.database.Patient == handles.database.Patient(data_selected) &... handles.database.Tp == handles.database.Tp(data_selected) & ... handles.database.SequenceName == NewTp) > 0 msgbox( ’A Scan with the same name already exist for this patient at this time point’ ) ; return end idx_scan_to_rename = find(handles.database.Patient == handles.database.Patient(data_selected) & handles.database.Tp == handles.database.Tp(data_selected)); for i= 1 :numel(idx_scan_to_rename) new_nii_filename = strrep(cellstr(handles.database.Filename(idx_scan_to_rename(i))), cellstr(handles.database.Tp(idx_scan_to_rename(i))), NewTp); % rename the scan file if exist(fullfilename(handles, idx_scan_to_rename(i), ’.nii’ ), ’file’ ) == 0 && exist(fullfilename(handles, idx_scan_to_rename(i), ’.nii.gz’ ), ’file’ ) == 0 warning_text = sprintf( ’##$ This file no not exist ##$ %s’ ,... fullfilename(handles, idx_scan_to_rename(i), ’.nii’ )); msgbox(warning_text, ’rename file warning’ ) ; elseif exist(string(strcat(cellstr(handles.database.Path(idx_scan_to_rename(i))),new_nii_filename{:}, ’.nii’ )), ’file’ ) == 2 msgbox( ’The new .nii file exist already!!’ ) ; else if exist(fullfilename(handles, idx_scan_to_rename(i), ’.nii’ ), ’file’ ) == 2 movefile(fullfilename(handles, idx_scan_to_rename(i), ’.nii’ ), strcat(char(handles.database.Path(idx_scan_to_rename(i))),new_nii_filename{:}, ’.nii’ ), ’f’ ) end if exist(fullfilename(handles, idx_scan_to_rename(i), ’.nii.gz’ ), ’file’ ) == 2 movefile(fullfilename(handles, idx_scan_to_rename(i), ’.nii.gz’ ), strcat(char(handles.database.Path(idx_scan_to_rename(i))),new_nii_filename{:}, ’.nii.gz’ ), ’f’ ) end if exist(fullfilename(handles, idx_scan_to_rename(i), ’.json’ ), ’file’ ) == 2 movefile(fullfilename(handles, idx_scan_to_rename(i), ’.json’ ), strcat(char(handles.database.Path(idx_scan_to_rename(i))),new_nii_filename{:}, ’.json’ ), ’f’ ); end end % update the Filename field in the table handles.database.Tp(idx_scan_to_rename(i)) = NewTp; handles.database.Filename(idx_scan_to_rename(i)) = new_nii_filename; end % save the structure guidata(hObject, handles); %% update graph and display MP3_update_database_display(hObject, eventdata, handles); % save database MP3_menu_save_database_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- function MP3_rename_scan_Callback(hObject, eventdata, handles) % hObject handle to MP3_rename_scan (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if ~isfield(handles, ’database’ ) || isempty(get(handles.MP3_scans_list, ’String’ )) return end data_selected = finddata_selected(handles); if numel(data_selected) > 1 warndlg( ’Please select only one scan’ , ’Warning’ ); return end if get(handles.MP3_scans_button, ’Value’ ) name_option = [cellstr(unique(handles.database.SequenceName(handles.database.Type == ’Scan’ ))) ’ ’ Other ’]’ ; elseif get(handles.MP3_VOIs_button, ’Value’ ) name_option = [cellstr(unique(handles.database.SequenceName(handles.database.Type == ’ROI’ ))) ’ ’ Other ’]’ ; elseif get(handles.MP3_Others_button_button, ’Value’ ) name_option = [cellstr(unique(handles.database.SequenceName(handles.database.Type ~= ’Scan’ & handles.database.Type ~= ’ROI’ ))) ’ ’ Other ’]’ ; end [new_scan_name, ok1] = listdlg( ’PromptString’ , ’Select the new scan name:’ ,... ’Name’ , ’Select a Name’ ,... ’SelectionMode’ , ’single’ ,... ’ListSize’ , [ 400 300 ],... ’ListString’ ,name_option); if ok1 == 0 return end if strcmp( ’Other’ ,name_option(new_scan_name)) == 1 newparameter = inputdlg( ’Name of the new Scan ’ , ’Question?’ , 1 , { ’’ }); else newparameter =name_option(new_scan_name); end %% update the database with the new name % but first check if the new scan name does not exist for this patient and % time point % faire le ROI vs SCAN if find(handles.database.Patient == handles.database.Patient(data_selected) &... handles.database.Tp == handles.database.Tp(data_selected) & ... handles.database.SequenceName == newparameter) > 0 msgbox( ’A Scan with the same name already exist for this patient at this time point’ ) ; return end new_nii_filename = strrep(cellstr(handles.database.Filename(data_selected)), cellstr(handles.database.SequenceName(data_selected)), newparameter); % rename the scan file if exist(fullfilename(handles, data_selected, ’.nii’ ), ’file’ ) == 0 && exist(fullfilename(handles, data_selected, ’.nii.gz’ ), ’file’ ) == 0 warning_text = sprintf( ’##$ This file no not exist ##$ %s’ ,... fullfilename(handles, data_selected, ’.nii’ )); msgbox(warning_text, ’rename file warning’ ) ; elseif exist(string(strcat(cellstr(handles.database.Path(data_selected)),new_nii_filename{:}, ’.nii’ )), ’file’ ) == 2 msgbox( ’The new .nii file exist already!!’ ) ; else if exist(fullfilename(handles, data_selected, ’.nii’ ), ’file’ ) == 2 movefile(fullfilename(handles, data_selected, ’.nii’ ), strcat(char(handles.database.Path(data_selected)),new_nii_filename{:}, ’.nii’ ), ’f’ ) end if exist(fullfilename(handles, data_selected, ’.nii.gz’ ), ’file’ ) == 2 movefile(fullfilename(handles, data_selected, ’.nii.gz’ ), strcat(char(handles.database.Path(data_selected)),new_nii_filename{:}, ’.nii.gz’ ), ’f’ ) end % rename json file if needed if exist(fullfilename(handles, data_selected, ’.json’ ), ’file’ ) == 2 movefile(fullfilename(handles, data_selected, ’.json’ ), strcat(char(handles.database.Path(data_selected)),new_nii_filename{:}, ’.json’ ), ’f’ ); end % rename mat file if needed if exist(fullfilename(handles, data_selected, ’.mat’ ), ’file’ ) == 2 movefile(fullfilename(handles, data_selected, ’.mat’ ), strcat(char(handles.database.Path(data_selected)),new_nii_filename{:}, ’.mat’ ), ’f’ ); end end % update the Filename field in the table handles.database.SequenceName(data_selected) = newparameter; handles.database.Filename(data_selected) = new_nii_filename; % save the structure guidata(hObject, handles); %% update graph and display MP3_update_database_display(hObject, eventdata, handles); % Save database MP3_menu_save_database_Callback(hObject, eventdata, handles) % -------------------------------------------------------------------- function MP3_remove_scan_Callback(hObject, eventdata, handles) % hObject handle to MP3_remove_scan (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if ~isfield(handles, ’database’ ) return end nii_index = finddata_selected(handles); user_response = questdlg( ’Do you want to delete these data ??’ , ’Warning’ , ’Yes’ , ’No’ , ’Cancel’ , ’Cancel’ ); if strcmp(user_response, ’Cancel’ ) || strcmp(user_response, ’No’ ) || isempty(user_response) return end MP3_remove_scan(hObject, eventdata, handles, nii_index) % -------------------------------------------------------------------- function MP3_remove_time_point_Callback(hObject, eventdata, handles) % hObject handle to MP3_remove_time_point (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) if ~isfield(handles, ’database’ ) return end data_selected = finddata_selected(handles); Time_point_selected = unique(handles.database.Tp(data_selected)); patient_selected = unique(handles.database.Patient(data_selected)); user_response = questdlg([ ’Do you want to delete every data of ’ char(Time_point_selected) ’??’ ], ’Warning’ , ’Yes’ , ’No’ , ’Cancel’ , ’Cancel’ ); if strcmp(user_response, ’Cancel’ ) || strcmp(user_response, ’No’ ) return end nii_index = find(handles.database.Patient == patient_selected & handles.database.Tp == Time_point_selected); MP3_remove_scan(hObject, eventdata, handles, nii_index) % -------------------------------------------------------------------- function MP3_ScanVoi_right_click_Callback(~, ~, ~) % hObject handle to MP3_ScanVoi_right_click (see GCBO) % eventdata reserved - to be defined in a future version of MATLAB % handles structure with handles and user data (see GUIDATA) function MP3_update_figureName(~, ~, handles) num_timepoint = 0 ; patient_listing = unique(handles.database.Patient); for i= 1 :numel(patient_listing) num_timepoint = num_timepoint+ numel(unique(handles.database.Tp(handles.database.Patient == patient_listing(i)))); end Name_soft = ’Medical software for Processing multi-Parametric image Pipelines (Grenoble Institute of neurosciences - France)’ ; Spl = strsplit(handles.database.Properties.UserData.MP3_data_path, filesep); Name_Projet = Spl{end- 1 }; %old_title = get(handles.MP3_GUI, ’Name’ ); title = [Name_soft, ’ ; Projet : ’ , Name_Projet, ’ ; ’ , num2str(numel(patient_listing)),... ’ patients and ’ , num2str(num_timepoint), ’ ’ , ’time points’ ]; set(handles.MP3_GUI, ’Name’ , title); function handles = MP3_update_handles_parameters_VOIs(handles) % parameters_list = []; % Voi_list = []; % for patient= 1 :numel(handles.database) % for time_point = 1 :numel(handles.database(patient).day) % parameters_list = [parameters_list handles.database(patient).day(time_point).parameters]; % Voi_list = [Voi_list handles.database(patient).day(time_point).VOIs]; % end % end % handles.VOIs = [unique(Voi_list) ’Other’ ]; VOIs_list = {}; for i= 1 :numel(handles.database) for j = 1 :numel(handles.database(i).day) VOIs_list = [VOIs_list handles.database(i).day(j).VOIs]; end end handles.VOIs = [unique(VOIs_list), ’Other’ ]; guidata(handles.MP3_GUI, handles); function MP3_load_axes_Callback(hObject, eventdata, handles) if get(handles.MP3_Others_button, ’Value’ ) == 1 warndlg( ’Such files cannot be display in MP3’ , ’Warning’ ); return end % by default this slider is hidded set(handles.MP3_PRM_slider_trans, ’Visible’ , ’off’ ); if ~isfield(handles, ’database’ ) || isempty(handles.database) return end % MP3 cannot load scan(s) if multiple patients are selected if numel(get(handles.MP3_name_list, ’Value’ )) > 1 warndlg( ’Please select only 1 patient before loading scan(s)’ , ’Warning’ ); return end scan = get(handles.MP3_scans_list, ’Value’ ); % Load VOIs if handles.mode == 2 && numel(scan) > 1 if get(handles.MP3_scans_button, ’Value’ ) == 1 warndlg( ’Please select only 1 Scan when using the longitudinal view mode’ , ’Warning’ ); elseif get(handles.MP3_VOIs_button, ’Value’ ) == 1 warndlg( ’Please select only 1 VOI when using the longitudinal view mode’ , ’Warning’ ); end return end if get(handles.MP3_VOIs_button, ’Value’ ) && isfield(handles, ’data_loaded’ ) || ... get(handles.MP3_scans_button, ’Value’ ) && isfield(handles, ’data_selected_for_PRM’ ) handles = MP3_load_VOIs(hObject, eventdata, handles); MP3_update_axes(hObject, eventdata, handles) return elseif get(handles.MP3_VOIs_button, ’Value’ ) && ~isfield(handles, ’data_loaded’ ) warndlg( ’Please load a scan first’ , ’Warning’ ); return end handles = MP3_clear_data(hObject, eventdata, handles); % display a waiting symbol set(handles.MP3_GUI, ’pointer’ , ’watch’ ); % Load Scans if handles.mode == 1 handles = MP3_load_axes_single(hObject, eventdata, handles); else handles = MP3_load_axes_PRM(hObject, eventdata, handles); % if all conditions are not present --> return if ~isfield(handles, ’data_loaded’ ) return end list_day = [ ’-1’ , string(handles.data_loaded.info_data_loaded.Tp) ’]; set(handles.MP3_PRM_ref_popupmenu, ’ String ’, list_day’ , ’Value’ , 2 ); %set MP3_PRM_slider set(handles.MP3_PRM_slider_tp, ’Max’ , handles.data_loaded.number_of_scan); set(handles.MP3_PRM_slider_tp, ’Value’ , 1 ); set(handles.MP3_PRM_slider_tp, ’Min’ , 1 ); set(handles.MP3_PRM_slider_tp, ’Visible’ , ’on’ ); set(handles.MP3_PRM_slider_tp, ’SliderStep’ ,[ 1 /(handles.data_loaded.number_of_scan- 1 ) min( 5 /(handles.data_loaded.number_of_scan- 1 ), 1 )]); end drawnow; MP3_update_axes(hObject, eventdata, handles) set(handles.MP3_GUI, ’pointer’ , ’arrow’ ); %toc(tstart) function handles = MP3_load_VOIs(hObject, ~, handles) data_selected = finddata_selected(handles); handles.data_loaded.info_data_loaded(handles.data_loaded.info_data_loaded.Type == ’ROI’ ,:) =[]; if isfield(handles.data_loaded, ’ROI’ ) handles.data_loaded= rmfield(handles.data_loaded, ’ROI’ ); handles.data_loaded= rmfield(handles.data_loaded, ’number_of_ROI’ ); end if isfield(handles.data_displayed, ’ROI’ ) handles.data_displayed= rmfield(handles.data_displayed, ’ROI’ ); end handles.data_loaded.info_data_loaded(handles.data_loaded.info_data_loaded.Type == ’Cluster’ ,:) =[]; if isfield(handles.data_loaded, ’Cluster’ ) handles.data_loaded= rmfield(handles.data_loaded, ’Cluster’ ); handles.data_loaded= rmfield(handles.data_loaded, ’number_of_Cluster’ ); end if isfield(handles.data_displayed, ’Cluster’ ) handles.data_displayed= rmfield(handles.data_displayed, ’Cluster’ ); end handles.data_loaded.number_of_ROI = 0 ; handles.data_loaded.number_of_Cluster = 0 ; for i = 1 :numel(data_selected) if ~exist(fullfilename(handles, data_selected(i), ’.nii’ ), ’file’ ) && exist(fullfilename(handles, data_selected(i), ’.nii.gz’ ), ’file’ ) gunzip(fullfilename(handles, data_selected(i), ’.nii.gz’ )); assert(exist(fullfilename(handles, data_selected(i), ’.nii’ ), ’file’ )== 2 ) delete(fullfilename(handles, data_selected(i), ’.nii.gz’ )) end fid_nii=fopen(fullfilename(handles, data_selected(i), ’.nii’ ), ’r’ ); if fid_nii> 0 fclose(fid_nii); % scan_of_reference = get(handles.MP3_orientation_space_popupmenu, ’Value’ ); if strcmp(char(handles.database(data_selected(i),:).Type), ’ROI’ ) %% read and load the nii file handles.data_loaded.number_of_ROI = handles.data_loaded.number_of_ROI+ 1 ; handles.data_loaded.ROI(handles.data_loaded.number_of_ROI).V = spm_vol(char(fullfilename(handles, data_selected(i), ’.nii’ ))); % handles.data_loaded.ROI(i).nii = read_volume(handles.data_loaded.ROI(i).V, handles.data_loaded.Scan(scan_of_reference).V, 3 , handles.view_mode); % handles.data_loaded.ROI(i).nii(handles.data_loaded.ROI(i).nii> 0 ) = 1 ; handles.data_loaded.info_data_loaded = [handles.data_loaded.info_data_loaded; handles.database(data_selected(i),:)]; elseif strcmp(char(handles.database(data_selected(i),:).Type), ’Cluster’ ) set(handles.MP3_PRM_slider_trans, ’Visible’ , ’on’ ); %% read and load the nii file handles.data_loaded.number_of_Cluster = handles.data_loaded.number_of_Cluster+ 1 ; handles.data_loaded.Cluster(handles.data_loaded.number_of_Cluster).V = spm_vol(char(fullfilename(handles, data_selected(i), ’.nii’ ))); % handles.data_loaded.ROI(i).nii = read_volume(handles.data_loaded.ROI(i).V, handles.data_loaded.Scan(scan_of_reference).V, 3 , handles.view_mode); % handles.data_loaded.ROI(i).nii(handles.data_loaded.ROI(i).nii> 0 ) = 1 ; handles.data_loaded.info_data_loaded = [handles.data_loaded.info_data_loaded; handles.database(data_selected(i),:)]; end else warndlg( ’something wrong with the data. Nii or json file is missing’ , ’Warning’ ); return end guidata(hObject, handles); end function handles = MP3_load_axes_single(hObject, ~, handles) data_selected = finddata_selected(handles); if numel(data_selected) > 4 % select only the 4 first scan data_selected = data_selected( 1 : 4 ); end for i = 1 :numel(data_selected) if ~exist(fullfilename(handles, data_selected(i), ’.nii’ ), ’file’ ) && exist(fullfilename(handles, data_selected(i), ’.nii.gz’ ), ’file’ ) gunzip(fullfilename(handles, data_selected(i), ’.nii.gz’ )); assert(exist(fullfilename(handles, data_selected(i), ’.nii’ ), ’file’ )== 2 ) delete(fullfilename(handles, data_selected(i), ’.nii.gz’ )) end fid_nii=fopen(fullfilename(handles, data_selected(i), ’.nii’ ), ’r’ ); fid_json=fopen(fullfilename(handles, data_selected(i), ’.json’ ), ’r’ ); if fid_nii> 0 && fid_json> 0 fclose(fid_nii); fclose(fid_json); %% read and load the json file handles.data_loaded.Scan(i).json = spm_jsonread(fullfilename(handles, data_selected(i), ’.json’ )); %% read and load the nii file handles.data_loaded.Scan(i).V =spm_vol(fullfilename(handles, data_selected(i), ’.nii’ )); else warndlg( ’something wrong with the data. Nii of json file is missing’ , ’Warning’ ); return end clear new end set(handles.MP3_patient_information_title, ’String’ , [char(unique(handles.database.Patient(data_selected))) ’_’ char(unique(handles.database.Tp(data_selected)))]); set(handles.MP3_orientation_space_popupmenu, ’String’ , char(unique(handles.database.SequenceName(data_selected), ’stable’ )), ’Value’ , 1 ); if numel(data_selected) > 1 set(handles.MP3_orientation_space_popupmenu, ’Visible’ , ’on’ ); set(handles.MP3_orientation_space_text, ’Visible’ , ’on’ ); else set(handles.MP3_orientation_space_popupmenu, ’Visible’ , ’off’ ); set(handles.MP3_orientation_space_text, ’Visible’ , ’off’ ); end handles.data_loaded.number_of_scan = numel(data_selected); handles.data_loaded.info_data_loaded = handles.database(data_selected,:); guidata(hObject, handles); if ~isempty(findobj( ’type’ , ’figure’ , ’name’ , ’FileHistory’ )) && length(handles.data_loaded.Scan) == 1 % Get the hObject of MP3_pipeline h = findobj( ’type’ , ’figure’ , ’name’ , ’FileHistory’ ); % Get the handles of MP3_pipeline data = guidata(h); % Update the handles of MP3_pipeline by stocking the latest version of % MP3 handles. data.MP3_data = handles; % Don ’t touch the original eventdata, just in case. %Update the MP3_pipeline tmp_database data.FileHistory_JobsListbox.Value = 1; [h,data] = FileHistory(’ UpdateJobsList ’, h, data); %[~, ~, data] = MP3_pipeline(’ MP3_pipeline_UpdateTables ’, h, eventdata2, data); guidata(h, data) elseif ~isempty(findobj(’ type ’, ’ figure ’, ’ name ’, ’ FileHistory ’)) close(findobj(’ type ’, ’ figure ’, ’ name ’, ’ FileHistory ’)) end function handles = MP3_load_axes_PRM(hObject, ~, handles) % PRM mode i.e. need to open the one parameter (diffusion % or perfusion or...) for every time point data_selected = finddata_selected(handles); if numel(data_selected) ~= 1 warndlg(’ In longitudinal view mode you can open only on scan!! ’, ’ Warning ’); return end % find indice of the same scan name across each time point to the selected % patient data_to_load = find(handles.database.Patient == handles.database.Patient(data_selected) &... handles.database.SequenceName == handles.database.SequenceName(data_selected)); [~, idx] =sort(handles.database.Tp(data_to_load)); data_to_load = data_to_load(idx); if numel(data_to_load) <2 warndlg(strcat({’ Need more than one ’}, char(handles.database.SequenceName(data_selected)), ’ scan to run the longitudinal view mode ’) ,’ Warning ’); return end