Description of avw_view

0001 function [ varargout ] = avw_view_ras(avw,parent,command),
0002 
0003 % avw_view - create and navigate ortho views of Analyze 7.5 volume
0004 %
0005 % [ avw ] = avw_view_ras([avw], [parent], [command])
0006 %
0007 % avw - a struct, created by avw_read; if omitted, a gui file locator will
0008 % prompt for a .hdr file.
0009 %
0010 % parent  - an optional handle to the gui that calls this gui, useful for
0011 % updating the UserData field of the parent. The avw structure may be
0012 % returned to the parent, if possible.
0013 %
0014 % command - an optional string, such as 'init' or various callback
0015 % commands, 'init' is the default.
0016 %
0017 % The navigation is by sliders, mouse clicks and arrow keys.  Right mouse
0018 % clicks on any ortho-view will show a command menu, for simple block
0019 % region of interest (ROI) calculations, image zoom, and save image.  The
0020 % ROI calculations are returned into avw.stats.
0021 %
0022 % Fiducial points can be selected, which are returned into 'avw.fiducials'
0023 % in the base workspace. These points are given in several coordinate
0024 % frameworks (voxels, mm, and meters), with values given relative to an
0025 % origin located at the "center" of the MRI volume (see avw_center, which
0026 % returns abs and corner values, abs used here).
0027 %
0028 % The AC location can be selected and the values are returned into 'avw.ac'
0029 % in the base workspace. These points are given in voxels, mm & meters; for
0030 % the latter, the values are given as offsets from the "center" of the MRI
0031 % volume (see avw_center).
0032 %
0033 % +X is right (R), +Y is anterior (A), +Z is superior (S), the default RAS
0034 % orientation of the Analyze 7.5 format.  The coordinate system is right
0035 % handed.
0036 %
0037 % Example of loading and viewing the SPM T1 template:
0038 % avw = avw_read('T1')
0039 % avw = avw_view_ras(avw);
0040 %
0041 % Similarly, just 'avw_view_ras' can be typed at the command prompt and you can
0042 % use the gui file locator to select any .hdr file.
0043 %
0044 % See also, avw_read, avw_img_read, avw_hdr_read
0045 %
0046 
0047 % $Revision: 2025 $ $Date:: 2021-09-01 11:56:46 +0900#$
0048 
0049 % Licence:  GNU GPL, no express or implied warranties
0050 % History:  change display coordinate from radiological(LAS) to neurological.
0051 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0052 
0053 if ~isempty(gcbf),
0054     AVWVIEW = get(gcbf,'Userdata');
0055 end
0056 
0057 if ~exist('command','var'), command = 'init'; end
0058 
0059 command = lower(command);
0060 
0061 % Check for specific keys and assign command
0062 if strcmp(command, 'keypress'),
0063   
0064   cc = get(AVWVIEW.gui,'CurrentCharacter');
0065   cc = double(cc);
0066   if cc,
0067     switch cc,
0068 %      case 27, command = 'quit';  % ESC
0069       case 28, command = 'left';  % left
0070       case 29, command = 'right'; % right
0071       case 30, command = 'up';    % up
0072       case 31, command = 'down';  % down
0073       case 127, command = 'left'; 
0074       otherwise, return;  % all other keys
0075     end
0076   end
0077 end
0078 
0079 switch command,
0080     
0081   case 'init',
0082     
0083     if ~exist('avw','var'),
0084       avw = avw_read_ras;% modified by Masa-aki Sato
0085     end
0086     
0087     if nargin == 0,
0088       AVWVIEW = init(avw);
0089     elseif isempty(inputname(1)),
0090       AVWVIEW = init(avw);
0091     else
0092       AVWVIEW = init(avw,inputname(1));
0093     end
0094     
0095     AVWVIEW = set_coordinates(AVWVIEW);
0096     AVWVIEW = set_crosshairs(AVWVIEW);
0097 
0098 
0099     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0100     
0101   case 'coordinates',
0102     
0103     AVWVIEW = set_coordinates(AVWVIEW);
0104     
0105     
0106     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0107     
0108   case 'crosshairs',
0109     
0110     AVWVIEW = set_crosshairs(AVWVIEW);
0111     
0112     
0113   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0114   
0115   case {'axial_image','coronal_image','sagittal_image'},
0116     
0117     switch command,
0118       case 'axial_image',    AVWVIEW.view = 'axi'; axi_update = 0; cor_update = 1; sag_update = 1;
0119       case 'coronal_image',  AVWVIEW.view = 'cor'; axi_update = 1; cor_update = 0; sag_update = 1;
0120       case 'sagittal_image', AVWVIEW.view = 'sag'; axi_update = 1; cor_update = 1; sag_update = 0;
0121     end
0122     
0123     AVWVIEW = get_current_position(AVWVIEW);
0124     
0125     if axi_update,
0126         axial_update(AVWVIEW);
0127     end
0128     if cor_update,
0129         coronal_update(AVWVIEW);
0130     end;
0131     if sag_update,
0132         sagittal_update(AVWVIEW);
0133     end;
0134     
0135     set_display_values(AVWVIEW);
0136     
0137     AVWVIEW = set_crosshairs(AVWVIEW);
0138     
0139     
0140     
0141     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0142     
0143   case {'axial_slider','coronal_slider','sagittal_slider'},
0144     
0145     switch command,
0146       
0147       case 'axial_slider',
0148         AVWVIEW.view = 'axi';
0149         AVWVIEW = get_slider_position(AVWVIEW);
0150         axial_update(AVWVIEW);
0151         
0152       case 'coronal_slider',
0153         AVWVIEW.view = 'cor';
0154         AVWVIEW = get_slider_position(AVWVIEW);
0155         coronal_update(AVWVIEW);
0156         
0157       case 'sagittal_slider',
0158         AVWVIEW.view = 'sag';
0159         AVWVIEW = get_slider_position(AVWVIEW);
0160         sagittal_update(AVWVIEW);
0161     end
0162     
0163     set_display_values(AVWVIEW);
0164     
0165     AVWVIEW = set_crosshairs(AVWVIEW);
0166     
0167     
0168     
0169     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0170     
0171   case {'left','right','up','down'},
0172     
0173     AVWVIEW = get_slider_position(AVWVIEW);
0174     
0175     % what axes are we in?
0176     if isequal(gca, AVWVIEW.handles.axial_axes),
0177       switch command,
0178         case 'left',
0179           % decrease sagittal slice
0180           if AVWVIEW.slices.sag > 1,
0181             AVWVIEW.slices.sag = AVWVIEW.slices.sag - 1;
0182           end
0183         case 'right',
0184           % increase sagittal slice
0185           if AVWVIEW.slices.sag < AVWVIEW.xdim,
0186             AVWVIEW.slices.sag = AVWVIEW.slices.sag + 1;
0187           end
0188         case 'up',
0189           % increase coronal slice
0190           if AVWVIEW.slices.cor < AVWVIEW.ydim,
0191             AVWVIEW.slices.cor = AVWVIEW.slices.cor + 1;
0192           end
0193         case 'down',
0194           % decrease coronal slice
0195           if AVWVIEW.slices.cor > 1,
0196             AVWVIEW.slices.cor = AVWVIEW.slices.cor - 1;
0197           end
0198       end
0199       switch command,
0200         case {'left','right'}
0201           set(AVWVIEW.handles.sagittal_slider,'Value',AVWVIEW.slices.sag);
0202           Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
0203           set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
0204           set(AVWVIEW.handles.sagittal_sliderN,'String',num2str(AVWVIEW.slices.sag));
0205           set(AVWVIEW.handles.sagittal_sliderN,'Value',AVWVIEW.slices.sag);
0206         case {'up','down'},
0207           set(AVWVIEW.handles.coronal_slider,'Value',AVWVIEW.slices.cor);
0208           Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
0209           set(AVWVIEW.handles.coronal_image,'CData',Scor');
0210           set(AVWVIEW.handles.coronal_sliderN,'String',num2str(AVWVIEW.slices.cor));
0211           set(AVWVIEW.handles.coronal_sliderN,'Value',AVWVIEW.slices.cor);
0212       end
0213     end
0214     
0215     if isequal(gca, AVWVIEW.handles.coronal_axes),
0216       switch command,
0217         case 'left',
0218           % decrease sagittal slice
0219           if AVWVIEW.slices.sag > 1,
0220             AVWVIEW.slices.sag = AVWVIEW.slices.sag - 1;
0221           end
0222         case 'right',
0223           % increase sagittal slice
0224           if AVWVIEW.slices.sag < AVWVIEW.xdim,
0225             AVWVIEW.slices.sag = AVWVIEW.slices.sag + 1;
0226           end
0227         case 'up',
0228           % increase axial slice
0229           if AVWVIEW.slices.axi < AVWVIEW.zdim,
0230             AVWVIEW.slices.axi = AVWVIEW.slices.axi + 1;
0231           end
0232         case 'down',
0233           % decrease axial slice
0234           if AVWVIEW.slices.axi > 1,
0235             AVWVIEW.slices.axi = AVWVIEW.slices.axi - 1;
0236           end
0237       end
0238       switch command,
0239         case {'left','right'}
0240           set(AVWVIEW.handles.sagittal_slider,'Value',AVWVIEW.slices.sag);
0241           Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
0242           set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
0243           set(AVWVIEW.handles.sagittal_sliderN,'String',num2str(AVWVIEW.slices.sag));
0244           set(AVWVIEW.handles.sagittal_sliderN,'Value',AVWVIEW.slices.sag);
0245         case {'up','down'},
0246           set(AVWVIEW.handles.axial_slider,'Value',AVWVIEW.slices.axi);
0247           Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
0248           set(AVWVIEW.handles.axial_image,'CData',Saxi');
0249           set(AVWVIEW.handles.axial_sliderN,'String',num2str(AVWVIEW.slices.axi));
0250           set(AVWVIEW.handles.axial_sliderN,'Value',AVWVIEW.slices.axi);
0251       end
0252     end
0253     
0254     if isequal(gca, AVWVIEW.handles.sagittal_axes),
0255       switch command,
0256         case 'left',
0257           % decrease sagittal slice
0258           if AVWVIEW.slices.cor > 1,
0259             AVWVIEW.slices.cor = AVWVIEW.slices.cor - 1;
0260           end
0261         case 'right',
0262           % increase sagittal slice
0263           if AVWVIEW.slices.cor < AVWVIEW.ydim,
0264             AVWVIEW.slices.cor = AVWVIEW.slices.cor + 1;
0265           end
0266         case 'up',
0267           % increase axial slice
0268           if AVWVIEW.slices.axi < AVWVIEW.zdim,
0269             AVWVIEW.slices.axi = AVWVIEW.slices.axi + 1;
0270           end
0271         case 'down',
0272           % decrease axial slice
0273           if AVWVIEW.slices.axi > 1,
0274             AVWVIEW.slices.axi = AVWVIEW.slices.axi - 1;
0275           end
0276       end
0277       switch command,
0278         case {'left','right'}
0279           set(AVWVIEW.handles.coronal_slider,'Value',AVWVIEW.slices.cor);
0280           Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
0281           set(AVWVIEW.handles.coronal_image,'CData',Scor');
0282           set(AVWVIEW.handles.coronal_sliderN,'String',num2str(AVWVIEW.slices.cor));
0283           set(AVWVIEW.handles.coronal_sliderN,'Value',AVWVIEW.slices.cor);
0284         case {'up','down'},
0285           set(AVWVIEW.handles.axial_slider,'Value',AVWVIEW.slices.axi);
0286           Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
0287           set(AVWVIEW.handles.axial_image,'CData',Saxi');
0288           set(AVWVIEW.handles.axial_sliderN,'String',num2str(AVWVIEW.slices.axi));
0289           set(AVWVIEW.handles.axial_sliderN,'Value',AVWVIEW.slices.axi);
0290       end
0291     end
0292     
0293     AVWVIEW = set_crosshairs(AVWVIEW);
0294     
0295     
0296     
0297     
0298     
0299     
0300     
0301     
0302     
0303     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0304     
0305   case {'roi_9','roi_7','roi_5','roi_3'},
0306     
0307     position = [ AVWVIEW.slices.sag, AVWVIEW.slices.cor, AVWVIEW.slices.axi ];
0308     
0309     shape.type = 'block';
0310     if findstr(command,'9'), shape.size = [9,9,9]; end
0311     if findstr(command,'7'), shape.size = [7,7,7]; end
0312     if findstr(command,'5'), shape.size = [5,5,5]; end
0313     if findstr(command,'3'), shape.size = [3,3,3]; end
0314     
0315     stats.roi = avw_roi(AVWVIEW.avw,position,shape);
0316     
0317     AVWVIEW.avw.stats = avw_stats(stats);
0318     
0319     
0320     
0321     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0322     
0323   case {'nasion','rpa','lpa','ac'},
0324     
0325     % return voxel coordinates into AVWVIEW.imgXYZ
0326     AVWVIEW = slices2metric(AVWVIEW);
0327     
0328     if get(AVWVIEW.handles.coord,'value') == 2,
0329       format = '%7.3f %7.3f %7.3f';
0330       imgXYZ = AVWVIEW.imgXYZ.mm;
0331       string = sprintf('%7.3f %7.3f %7.3f',imgXYZ);
0332     elseif get(AVWVIEW.handles.coord,'value') == 3,
0333       format = '%7.3f %7.3f %7.3f';
0334       imgXYZ = AVWVIEW.imgXYZ.meters;
0335       string = sprintf('%7.3f %7.3f %7.3f',imgXYZ);
0336     else
0337       imgXYZ = AVWVIEW.imgXYZ.voxels;
0338       string = sprintf('%7.0f %7.0f %7.0f',imgXYZ);
0339     end;
0340     
0341     switch command,
0342       case 'nasion',
0343         set(AVWVIEW.handles.nasion,'String',string);
0344         AVWVIEW.avw.fiducials.nasion.voxels(1,:) = AVWVIEW.imgXYZ.voxels;
0345         AVWVIEW.avw.fiducials.nasion.meters(1,:) = AVWVIEW.imgXYZ.meters;
0346         AVWVIEW.avw.fiducials.nasion.mm(1,:)     = AVWVIEW.imgXYZ.mm;
0347       case 'rpa',
0348         set(AVWVIEW.handles.rpa,'String',string);
0349         AVWVIEW.avw.fiducials.rpa.voxels(1,:) = AVWVIEW.imgXYZ.voxels;
0350         AVWVIEW.avw.fiducials.rpa.meters(1,:) = AVWVIEW.imgXYZ.meters;
0351         AVWVIEW.avw.fiducials.rpa.mm(1,:)     = AVWVIEW.imgXYZ.mm;
0352       case 'lpa',
0353         set(AVWVIEW.handles.lpa,'String',string);
0354         AVWVIEW.avw.fiducials.lpa.voxels(1,:) = AVWVIEW.imgXYZ.voxels;
0355         AVWVIEW.avw.fiducials.lpa.meters(1,:) = AVWVIEW.imgXYZ.meters;
0356         AVWVIEW.avw.fiducials.lpa.mm(1,:)     = AVWVIEW.imgXYZ.mm;
0357       case 'ac',
0358         set(AVWVIEW.handles.ac,'String',string);
0359         AVWVIEW.avw.ac.voxels(1,:) = AVWVIEW.imgXYZ.voxels;
0360         AVWVIEW.avw.ac.meters(1,:) = AVWVIEW.imgXYZ.meters;
0361         AVWVIEW.avw.ac.mm(1,:) = AVWVIEW.imgXYZ.mm;
0362     end
0363     
0364     
0365     
0366     
0367     
0368     
0369     
0370     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0371     
0372   case 'flip',
0373     
0374     % flip X dim here...
0375     AVWVIEW.avw.img = flipdim(AVWVIEW.avw.img,1);
0376     
0377     if isfield(AVWVIEW.handles,'axial_image'),
0378       Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
0379       set(AVWVIEW.handles.axial_image,'CData',Saxi');
0380     end;
0381     if isfield(AVWVIEW.handles,'coronal_image'),
0382       Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
0383       set(AVWVIEW.handles.coronal_image,'CData',Scor');
0384     end;
0385     if isfield(AVWVIEW.handles,'sagittal_image'),
0386       Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
0387       set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
0388     end;
0389     
0390     flipStatus = get(AVWVIEW.handles.flipStatus,'string');
0391     if strmatch(flipStatus,'R>>L (radiological)'),
0392       flipStatus = 'L>>R (neurological)';
0393     else,
0394       flipStatus = 'R>>L (radiological)';
0395     end;
0396     set(AVWVIEW.handles.flipStatus,'string',flipStatus);
0397     
0398     
0399     
0400     
0401     
0402     
0403     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0404     
0405   case {'brighter','dimmer','setclimit'},
0406     
0407     switch command,
0408       case 'brighter',
0409         AVWVIEW.clim = AVWVIEW.clim .* 0.9;
0410       case 'dimmer',
0411         AVWVIEW.clim = AVWVIEW.clim .* 1.1;
0412       case 'setclimit',
0413         clim = get(AVWVIEW.handles.clim,'string');
0414         AVWVIEW.clim(2) = str2num(clim);
0415     end
0416     climString = sprintf('%05.2f',AVWVIEW.clim(2));
0417     set(AVWVIEW.handles.clim,'string',climString);
0418     
0419     if isfield(AVWVIEW.handles,'axial_image'),
0420       set(AVWVIEW.handles.axial_axes,'Clim',AVWVIEW.clim);
0421     end;
0422     if isfield(AVWVIEW.handles,'coronal_image'),
0423       set(AVWVIEW.handles.coronal_axes,'Clim',AVWVIEW.clim);
0424     end;
0425     if isfield(AVWVIEW.handles,'sagittal_image'),
0426       set(AVWVIEW.handles.sagittal_axes,'Clim',AVWVIEW.clim);
0427     end;
0428     
0429     
0430     
0431     
0432     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0433     
0434   case 'contrast'
0435     
0436     if isfield(AVWVIEW.handles,'axial_image'),
0437       X = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
0438       AVWVIEW.cmap = contrast(X);
0439       colormap(AVWVIEW.handles.axial_axes,AVWVIEW.cmap);
0440     end;
0441     if isfield(AVWVIEW.handles,'coronal_image'),
0442       X = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
0443       AVWVIEW.cmap = contrast(X);
0444       colormap(AVWVIEW.handles.axial_axes,AVWVIEW.cmap);
0445     end;
0446     if isfield(AVWVIEW.handles,'sagittal_image'),
0447       X = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
0448       AVWVIEW.cmap = contrast(X);
0449       colormap(AVWVIEW.handles.axial_axes,AVWVIEW.cmap);
0450     end;
0451     
0452     
0453     
0454     
0455     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0456     
0457   case 'setcmap'
0458     
0459     cmapIndex = get(AVWVIEW.handles.cmap,'value');
0460     cmapString = get(AVWVIEW.handles.cmap,'string');
0461     
0462     AVWVIEW.cmapString = cmapString{cmapIndex};
0463     
0464     if isfield(AVWVIEW.handles,'axial_image'),
0465       AVWVIEW.cmap = colormap(AVWVIEW.handles.axial_axes,AVWVIEW.cmapString);
0466     end;
0467     if isfield(AVWVIEW.handles,'coronal_image'),
0468       AVWVIEW.cmap = colormap(AVWVIEW.handles.coronal_axes,AVWVIEW.cmapString);
0469     end;
0470     if isfield(AVWVIEW.handles,'sagittal_image'),
0471       AVWVIEW.cmap = colormap(AVWVIEW.handles.sagittal_axes,AVWVIEW.cmapString);
0472     end;
0473     
0474     
0475     
0476     
0477     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0478     
0479   case 'histogram',
0480     
0481     avw = AVWVIEW.avw;
0482     
0483     % would be nice to use bins that reflect
0484     % the bits per pixel, but it seems to take
0485     % forever for a 16 bit image, otherwise
0486     % use this code:
0487     %     %check the bits per pixel of avw
0488     %     bitpix = avw.hdr.dime.bitpix;
0489     %     % set the bins according to the data type
0490     %     if bitpix <= 8, bins = 0:255; end
0491     %     if bitpix > 8,  bins = 0:65535; end
0492     
0493     %bins = linspace(0,intensity_max,255);
0494     
0495     intensity_min = min(min(min(avw.img)));
0496     intensity_max = max(max(max(avw.img)));
0497     
0498     bins = intensity_min:intensity_max;
0499     
0500     fprintf('...calculating histogram for %d bins.\n',length(bins));
0501     
0502     for i=1:size(avw.img,3),
0503       n = hist(avw.img(:,:,i), bins);
0504       if i == 1,
0505         intensity_volume = sum(n,2);
0506       else
0507         intensity_slice = sum(n,2);
0508         intensity_volume = intensity_volume + intensity_slice;
0509       end
0510     end
0511     figure('name','intensity histogram');
0512     bar(bins,intensity_volume);
0513     
0514     
0515     
0516     
0517     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0518     
0519   case 'zoom'
0520     
0521     x = AVWVIEW.slices.sag;
0522     y = AVWVIEW.slices.cor;
0523     z = AVWVIEW.slices.axi;
0524     
0525     switch AVWVIEW.view,
0526       case 'axi',
0527         slice = rot90(AVWVIEW.avw.img(:,:,z));
0528       case 'cor',
0529         slice = rot90(squeeze(AVWVIEW.avw.img(:,y,:)));
0530       case 'sag',
0531         slice = rot90(squeeze(AVWVIEW.avw.img(x,:,:)));
0532     end
0533     
0534     figure;
0535     imagesc(slice,AVWVIEW.clim); 
0536     colormap(gray); axis off; zoom on;
0537     daspect(AVWVIEW.daspect);
0538     
0539     
0540     
0541     
0542     %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0543     
0544   case 'save_image',
0545     
0546     [filename, pathname] = uiputfile(...
0547       { '*.png','PNG Files (*.png)'; ...
0548         '*.jpg','JPG Files (*.jpg)'; ...
0549         '*.ppm;*.pgm;*.pbm','Portable Anymap (*.ppm,*.pgm,*.pbm)'; ...
0550         '*.*',  'All Files (*.*)'}, ...
0551       'IMWrite to file');
0552     
0553     if filename,
0554       
0555       x = AVWVIEW.slices.sag;
0556       y = AVWVIEW.slices.cor;
0557       z = AVWVIEW.slices.axi;
0558       
0559       pixelsPerMM = 1 ./ double(AVWVIEW.avw.hdr.dime.pixdim(2:4));
0560       pixelsPerMeter = pixelsPerMM .* 1000;
0561       
0562       switch AVWVIEW.view,
0563         case 'axi',
0564           slice = rot90(AVWVIEW.avw.img(:,:,z));
0565           xresolution = pixelsPerMeter(1);
0566           yresolution = pixelsPerMeter(2);
0567         case 'cor',
0568           slice = rot90(squeeze(AVWVIEW.avw.img(:,y,:)));
0569           xresolution = pixelsPerMeter(1);
0570           yresolution = pixelsPerMeter(3);
0571         case 'sag',
0572           slice = rot90(squeeze(AVWVIEW.avw.img(x,:,:)));
0573           xresolution = pixelsPerMeter(2);
0574           yresolution = pixelsPerMeter(3);
0575       end
0576       
0577       % scale the image values to between 0-1 for imwrite
0578       % (initially used max of slice, but actually want to
0579       % use the scaled intensity from the gui).
0580       %maxValue = max(max(slice));
0581       %scaledSlice = slice ./ maxValue;
0582       scaledSlice = slice ./ AVWVIEW.clim(2);
0583       
0584       % RGB = ind2rgb(X,map) converts the matrix X and corresponding
0585       % colormap map to RGB (truecolor)
0586       
0587       file = [pathname,filename];
0588       fprintf('saving to:...%s\n',file);
0589       
0590       %Most of the supported image file formats store uint8 data.
0591       %PNG and TIFF formats additionally support uint16 data. For
0592       %grayscale and RGB images, if the data array is double, the
0593       %assumed dynamic range is [0,1]. The data array is automatically
0594       %scaled by 255 before being written as uint8. If the data array
0595       %is uint8 or uint16, it is written without scaling as uint8 or
0596       %uint16, respectively.
0597       
0598       [pathname,filename,ext] = fileparts([pathname,filename]);
0599       
0600       switch ext,
0601       
0602         case '.png',
0603           %imwrite(uint8(image),colormap,file,format);
0604           %imwrite(slice,colormap(gray),file,format,...
0605           
0606           %     'XResolution'  A scalar indicating the number of
0607           %                    pixels/unit in the horizontal direction
0608           %
0609           %     'YResolution'  A scalar indicating the number of
0610           %                    pixels/unit in the vertical direction
0611           %
0612           %     'ResolutionUnit' Either 'unknown' or 'meter'
0613           format = 'png';
0614           imwrite(scaledSlice,file,format,...
0615             'BitDepth',16,'ResolutionUnit','meter',...
0616             'XResolution',xresolution,...
0617             'YResolution',yresolution);
0618           
0619         case '.jpg',
0620           format = 'jpg';
0621           imwrite(scaledSlice,file,format);
0622         case {'.ppm','.pgm','.pbm'},
0623           format = ext(2:end);
0624           imwrite(scaledSlice,file,format);
0625         otherwise
0626           fprintf('...cannot write %s image files\n',ext);
0627       end
0628     end
0629     
0630     
0631     
0632     
0633     
0634   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0635     
0636   case 'save',
0637     % try to assign back into the input struct
0638     if ~isempty(AVWVIEW.invarname),
0639       fprintf('...returning data to base workspace struct ''%s''\n',AVWVIEW.invarname);
0640       assignin('base',AVWVIEW.invarname,AVWVIEW.avw);
0641     elseif evalin('base','exist(''mri'',''var'')'),
0642       fprintf('...returning data to base workspace struct ''mri''\n');
0643       string = ['AVWVIEW = get(', num2str(AVWVIEW.gui),...
0644           ',''Userdata''); mri.data = AVWVIEW.avw; clear AVWVIEW;'];
0645       evalin('base',string);
0646     else
0647       fprintf('...returning data into base workspace struct ''avw''\n');
0648       assignin('base','avw',AVWVIEW.avw);
0649     end
0650 
0651     [filename, pathname] = uiputfile('*.mat','Save fiducials');
0652     if isequal(filename,0) | isequal(pathname,0)
0653        disp('filename not specified.')
0654     else
0655        fiducials = AVWVIEW.avw.fiducials;
0656        vb_fsave([fullfile(pathname, filename)], 'fiducials');
0657     end
0658     %    close gcbf;
0659     
0660 
0661   %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0662   
0663   case 'close',
0664       fprintf('...returning data into base workspace struct ''avw''\n');
0665       assignin('base','avw',AVWVIEW.avw);
0666       close gcbf;
0667       
0668   otherwise,
0669 end
0670   
0671 switch command,
0672   case 'save',
0673   case 'close',
0674   otherwise,
0675     set(AVWVIEW.gui,'UserData',AVWVIEW);
0676 end
0677 
0678 if nargout > 0,
0679   varargout{1} = AVWVIEW.avw;
0680 end
0681 
0682 return
0683 
0684 
0685 
0686 
0687 
0688 
0689 
0690 
0691 
0692 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0693 % SUBFUNCTIONS
0694 
0695 
0696 
0697 
0698 
0699 
0700 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0701 function axial_update(AVWVIEW)
0702 
0703 if isfield(AVWVIEW.handles,'axial_image'),
0704     Saxi = squeeze(AVWVIEW.avw.img(:,:,AVWVIEW.slices.axi));
0705     set(AVWVIEW.handles.axial_image,'CData',Saxi');
0706 end
0707 if isfield(AVWVIEW.handles,'axial_sliderN'),
0708     set(AVWVIEW.handles.axial_sliderN,'String',num2str(AVWVIEW.slices.axi));
0709     set(AVWVIEW.handles.axial_sliderN,'Value',AVWVIEW.slices.axi);
0710 end
0711 if isfield(AVWVIEW.handles,'axial_slider'),
0712     set(AVWVIEW.handles.axial_slider,'Value',AVWVIEW.slices.axi);
0713 end;
0714 
0715 return
0716 
0717 
0718 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0719 function coronal_update(AVWVIEW)
0720 
0721 if isfield(AVWVIEW.handles,'coronal_image'),
0722     Scor = squeeze(AVWVIEW.avw.img(:,AVWVIEW.slices.cor,:));
0723     set(AVWVIEW.handles.coronal_image,'CData',Scor');
0724 end
0725 if isfield(AVWVIEW.handles,'coronal_sliderN'),
0726     set(AVWVIEW.handles.coronal_sliderN,'String',num2str(AVWVIEW.slices.cor));
0727     set(AVWVIEW.handles.coronal_sliderN,'Value',AVWVIEW.slices.cor);
0728 end
0729 if isfield(AVWVIEW.handles,'coronal_slider'),
0730     set(AVWVIEW.handles.coronal_slider,'Value',AVWVIEW.slices.cor);
0731 end;
0732 
0733 return
0734 
0735 
0736 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0737 function sagittal_update(AVWVIEW)
0738 
0739 if isfield(AVWVIEW.handles,'sagittal_image'),
0740     Ssag = squeeze(AVWVIEW.avw.img(AVWVIEW.slices.sag,:,:));
0741     set(AVWVIEW.handles.sagittal_image,'CData',Ssag');
0742 end
0743 if isfield(AVWVIEW.handles,'sagittal_sliderN'),
0744     set(AVWVIEW.handles.sagittal_sliderN,'String',num2str(AVWVIEW.slices.sag));
0745     set(AVWVIEW.handles.sagittal_sliderN,'Value',AVWVIEW.slices.sag);
0746 end
0747 if isfield(AVWVIEW.handles,'sagittal_slider'),
0748     set(AVWVIEW.handles.sagittal_slider,'Value',AVWVIEW.slices.sag);
0749 end;
0750 
0751 return
0752 
0753 
0754 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0755 function AVWVIEW = set_crosshairs(AVWVIEW)
0756 
0757 fig = figure(AVWVIEW.gui);
0758 current_axes = get(fig, 'CurrentAxes');
0759 
0760 [AVWVIEW, metric] = slices2metric(AVWVIEW);
0761 
0762 if isfield(AVWVIEW.handles,'axial_axes'),
0763   set(fig, 'CurrentAxes', AVWVIEW.handles.axial_axes);
0764   
0765   x_value = [metric.sag metric.sag];
0766   y_value = [metric.cor metric.cor];
0767 
0768   AVWVIEW.handles.axial_xlim = get(AVWVIEW.handles.axial_axes,'Xlim');
0769   AVWVIEW.handles.axial_ylim = get(AVWVIEW.handles.axial_axes,'Ylim');
0770   set(AVWVIEW.handles.axial_xline, 'Xdata', x_value,'Ydata',AVWVIEW.handles.axial_ylim);
0771   set(AVWVIEW.handles.axial_yline, 'Ydata', y_value,'Xdata',AVWVIEW.handles.axial_xlim);
0772   set(AVWVIEW.handles.axial_xline,'Color','y','Tag','XLINE');
0773   set(AVWVIEW.handles.axial_yline,'Color','y','Tag','YLINE');
0774 
0775   if get(AVWVIEW.handles.crosshairs,'value'),
0776     set(AVWVIEW.handles.axial_xline,'visible','on');
0777     set(AVWVIEW.handles.axial_yline,'visible','on');
0778   else
0779     set(AVWVIEW.handles.axial_xline,'visible','off');
0780     set(AVWVIEW.handles.axial_yline,'visible','off');
0781   end
0782   
0783 end
0784 
0785 if isfield(AVWVIEW.handles,'coronal_axes'),
0786   set(fig, 'CurrentAxes', AVWVIEW.handles.coronal_axes);
0787 
0788   x_value = [metric.sag metric.sag];
0789   y_value = [metric.axi metric.axi];
0790 
0791   AVWVIEW.handles.coronal_xlim = get(AVWVIEW.handles.coronal_axes,'Xlim');
0792   AVWVIEW.handles.coronal_ylim = get(AVWVIEW.handles.coronal_axes,'Ylim');
0793   set(AVWVIEW.handles.coronal_xline, 'Xdata',x_value,'Ydata',AVWVIEW.handles.coronal_ylim);
0794   set(AVWVIEW.handles.coronal_yline, 'Ydata',y_value,'Xdata',AVWVIEW.handles.coronal_xlim);
0795   set(AVWVIEW.handles.coronal_xline,'Color','y','Tag','XLINE');
0796   set(AVWVIEW.handles.coronal_yline,'Color','y','Tag','YLINE');
0797   
0798   
0799   if get(AVWVIEW.handles.crosshairs,'value'),
0800     set(AVWVIEW.handles.coronal_xline,'visible','on');
0801     set(AVWVIEW.handles.coronal_yline,'visible','on');
0802   else
0803     set(AVWVIEW.handles.coronal_xline,'visible','off');
0804     set(AVWVIEW.handles.coronal_yline,'visible','off');
0805   end
0806   
0807 end
0808 
0809 if isfield(AVWVIEW.handles,'sagittal_axes'),
0810   set(fig, 'CurrentAxes', AVWVIEW.handles.sagittal_axes);
0811 
0812   x_value = [metric.cor metric.cor];
0813   y_value = [metric.axi metric.axi];
0814   
0815   AVWVIEW.handles.sagittal_xlim = get(AVWVIEW.handles.sagittal_axes,'Xlim');
0816   AVWVIEW.handles.sagittal_ylim = get(AVWVIEW.handles.sagittal_axes,'Ylim');
0817   set(AVWVIEW.handles.sagittal_xline, 'Xdata',x_value,'Ydata',AVWVIEW.handles.sagittal_ylim);
0818   set(AVWVIEW.handles.sagittal_yline, 'Ydata',y_value,'Xdata',AVWVIEW.handles.sagittal_xlim);
0819   set(AVWVIEW.handles.sagittal_xline,'Color','y','Tag','XLINE');
0820   set(AVWVIEW.handles.sagittal_yline,'Color','y','Tag','YLINE');
0821   
0822   if get(AVWVIEW.handles.crosshairs,'value'),
0823     set(AVWVIEW.handles.sagittal_xline,'visible','on');
0824     set(AVWVIEW.handles.sagittal_yline,'visible','on');
0825   else
0826     set(AVWVIEW.handles.sagittal_xline,'visible','off');
0827     set(AVWVIEW.handles.sagittal_yline,'visible','off');
0828   end
0829  
0830 end
0831 
0832 set(fig, 'CurrentAxes', current_axes);
0833 
0834 return
0835 
0836 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0837 function AVWVIEW = set_coordinates(AVWVIEW)
0838 
0839 % set the axis coordinates to voxels, mm or meters
0840 
0841 s = size(AVWVIEW.avw.img);
0842 if length(s) > 0, xdim = s(1); else xdim = 1; end
0843 if length(s) > 1, ydim = s(2); else ydim = 1; end
0844 if length(s) > 2, zdim = s(3); else zdim = 1; end
0845 
0846 % initialise for voxel coordinates
0847 xpixdim = double(AVWVIEW.avw.hdr.dime.pixdim(2));
0848 ypixdim = double(AVWVIEW.avw.hdr.dime.pixdim(3));
0849 zpixdim = double(AVWVIEW.avw.hdr.dime.pixdim(4));
0850 xdata = [0 xdim];
0851 ydata = [0 ydim];
0852 zdata = [0 zdim];
0853 
0854 aspect = 1./AVWVIEW.daspect; %AVWVIEW.avw.hdr.dime.pixdim(2:4);
0855 
0856 
0857 if get(AVWVIEW.handles.coord,'value') == 2,    % mm
0858   xdata = xdata .* xpixdim;
0859   ydata = ydata .* ypixdim;
0860   zdata = zdata .* zpixdim;
0861   aspect = [1 1 1];
0862 end
0863 
0864 if get(AVWVIEW.handles.coord,'value') == 3,    % meters
0865   xpixdim = xpixdim / 1000;
0866   ypixdim = ypixdim / 1000;
0867   zpixdim = zpixdim / 1000;
0868   xdata = xdata .* xpixdim;
0869   ydata = ydata .* ypixdim;
0870   zdata = zdata .* zpixdim;
0871   aspect = [1 1 1];
0872 end
0873 
0874 
0875 if isfield(AVWVIEW.handles,'axial_image'),
0876   set(AVWVIEW.handles.axial_axes,'Xlim',xdata);
0877   set(AVWVIEW.handles.axial_axes,'Ylim',ydata);
0878   set(AVWVIEW.handles.axial_axes,'Zlim',zdata);
0879   set(AVWVIEW.handles.axial_image,'Xdata',xdata);
0880   set(AVWVIEW.handles.axial_image,'Ydata',ydata);
0881   daspect(AVWVIEW.handles.axial_axes,aspect([1 2 3]));
0882 end;
0883 if isfield(AVWVIEW.handles,'coronal_image'),
0884   set(AVWVIEW.handles.coronal_axes,'Xlim',xdata);
0885   set(AVWVIEW.handles.coronal_axes,'Ylim',zdata);
0886   set(AVWVIEW.handles.coronal_axes,'Zlim',ydata);
0887   set(AVWVIEW.handles.coronal_image,'Xdata',xdata);
0888   set(AVWVIEW.handles.coronal_image,'Ydata',zdata);
0889   daspect(AVWVIEW.handles.coronal_axes,aspect([1 3 2]));
0890 end;
0891 if isfield(AVWVIEW.handles,'sagittal_image'),
0892   set(AVWVIEW.handles.sagittal_axes,'Xlim',ydata);
0893   set(AVWVIEW.handles.sagittal_axes,'Ylim',zdata);
0894   set(AVWVIEW.handles.sagittal_axes,'Zlim',xdata);
0895   set(AVWVIEW.handles.sagittal_image,'Xdata',ydata);
0896   set(AVWVIEW.handles.sagittal_image,'Ydata',zdata);
0897   daspect(AVWVIEW.handles.sagittal_axes,aspect([2 3 1]));
0898 end;
0899 
0900 set_display_values(AVWVIEW);
0901 set_crosshairs(AVWVIEW);
0902 
0903 return
0904 
0905 
0906 
0907 
0908 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0909 function AVWVIEW = get_current_position(AVWVIEW),
0910 
0911 %[AVWVIEW, metric] = slices2metric(AVWVIEW);
0912 
0913 if get(AVWVIEW.handles.coord,'value') == 3
0914     devide = 1000;
0915 else
0916     devide = 1;
0917 end
0918 
0919 switch AVWVIEW.view,
0920   case 'sag',
0921     currentpoint = get(get(AVWVIEW.handles.sagittal_image,'Parent'),'CurrentPoint');
0922     metric.cor = currentpoint(1,1);
0923     metric.axi = currentpoint(1,2);
0924     metric.sag = get(AVWVIEW.handles.sagittal_slider,'Value') / devide;
0925   case 'cor',
0926     currentpoint = get(get(AVWVIEW.handles.coronal_image,'Parent'),'CurrentPoint');
0927     metric.sag = currentpoint(2,1);
0928     metric.axi = currentpoint(2,2);
0929     metric.cor = get(AVWVIEW.handles.coronal_slider,'Value') / devide;
0930   case 'axi',
0931     currentpoint = get(get(AVWVIEW.handles.axial_image,'Parent'),'CurrentPoint');
0932     metric.sag = currentpoint(2,1);
0933     metric.cor = currentpoint(2,2);
0934     metric.axi = get(AVWVIEW.handles.axial_slider,'Value') / devide;
0935 end
0936 
0937 AVWVIEW = metric2slices(AVWVIEW,metric);
0938 AVWVIEW = check_slices(AVWVIEW);
0939 
0940 return
0941 
0942 
0943 
0944 
0945 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0946 function AVWVIEW = get_slider_position(AVWVIEW),
0947 
0948 [AVWVIEW.slices.sag,AVWVIEW.slices.cor,AVWVIEW.slices.axi] = deal(0);
0949 
0950 if isfield(AVWVIEW.handles,'sagittal_slider'),
0951   if ishandle(AVWVIEW.handles.sagittal_slider),
0952     AVWVIEW.slices.sag = round(get(AVWVIEW.handles.sagittal_slider,'Value'));
0953   end
0954 end
0955 if AVWVIEW.slices.sag == 0,
0956   if isfield(AVWVIEW.handles,'sagittal_sliderN'),
0957     if ishandle(AVWVIEW.handles.sagittal_sliderN),
0958       AVWVIEW.slices.sag = round(get(AVWVIEW.handles.sagittal_sliderN,'Value'));
0959     end
0960   end
0961 end
0962 
0963 if isfield(AVWVIEW.handles,'coronal_slider'),
0964   if ishandle(AVWVIEW.handles.coronal_slider),
0965     AVWVIEW.slices.cor = round(get(AVWVIEW.handles.coronal_slider,'Value'));
0966   end
0967 end
0968 if AVWVIEW.slices.cor == 0,
0969   if isfield(AVWVIEW.handles,'coronal_sliderN'),
0970     if ishandle(AVWVIEW.handles.coronal_sliderN),
0971       AVWVIEW.slices.cor = round(get(AVWVIEW.handles.coronal_sliderN,'Value'));
0972     end
0973   end
0974 end
0975 
0976 if isfield(AVWVIEW.handles,'axial_slider'),
0977   if ishandle(AVWVIEW.handles.axial_slider),
0978     AVWVIEW.slices.axi = round(get(AVWVIEW.handles.axial_slider,'Value'));
0979   end
0980 end
0981 if AVWVIEW.slices.axi == 0,
0982   if isfield(AVWVIEW.handles,'axial_sliderN'),
0983     if ishandle(AVWVIEW.handles.axial_sliderN),
0984       AVWVIEW.slices.axi = round(get(AVWVIEW.handles.axial_sliderN,'Value'));
0985     end
0986   end
0987 end
0988 
0989 AVWVIEW = check_slices(AVWVIEW);
0990 
0991 return
0992 
0993 
0994 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
0995 function AVWVIEW = check_slices(AVWVIEW),
0996 
0997 adjust = 0;
0998 
0999 [ SagSize, CorSize, AxiSize ] = size(AVWVIEW.avw.img);
1000 
1001 if AVWVIEW.slices.sag > SagSize,
1002     AVWVIEW.slices.sag = SagSize;
1003     adjust = 1;
1004 end;
1005 if AVWVIEW.slices.sag < 1,
1006     AVWVIEW.slices.sag = 1;
1007     adjust = 1;
1008 end;
1009 if AVWVIEW.slices.cor > CorSize,
1010     AVWVIEW.slices.cor = CorSize;
1011     adjust = 1;
1012 end;
1013 if AVWVIEW.slices.cor < 1,
1014     AVWVIEW.slices.cor = 1;
1015     adjust = 1;
1016 end;
1017 if AVWVIEW.slices.axi > AxiSize,
1018     AVWVIEW.slices.axi = AxiSize;
1019     adjust = 1;
1020 end;
1021 if AVWVIEW.slices.axi < 1,
1022     AVWVIEW.slices.axi = 1;
1023     adjust = 1;
1024 end;
1025 
1026 if adjust,
1027     AVWVIEW = slices2metric(AVWVIEW);
1028 end
1029 
1030 return
1031 
1032 
1033 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1034 function set_display_values(AVWVIEW),
1035 
1036 % get coordinates of selected voxel and the image intensity there
1037 
1038 sag = AVWVIEW.slices.sag;
1039 cor = AVWVIEW.slices.cor;
1040 axi = AVWVIEW.slices.axi;
1041 
1042 imgvalue = AVWVIEW.avw.img(sag,cor,axi);
1043 
1044 set(AVWVIEW.handles.imval,'String',sprintf('%7.2f',imgvalue));
1045 set(AVWVIEW.handles.imval,'Value',imgvalue);
1046 
1047 % Now update the image position text for the selected voxel
1048 
1049 [AVWVIEW, metric] = slices2metric(AVWVIEW);
1050 sag = metric.sag;
1051 cor = metric.cor;
1052 axi = metric.axi;
1053 
1054 string = sprintf('%7.3f %7.3f %7.3f',sag,cor,axi);
1055 
1056 set(AVWVIEW.handles.impos,'String',string);
1057 set(AVWVIEW.handles.impos,'Value',[sag,cor,axi]);
1058 
1059 return
1060 
1061 
1062 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1063 function [AVWVIEW,metric] = slices2metric(AVWVIEW),
1064 
1065 AVWVIEW.imgXYZ.voxels = [AVWVIEW.slices.sag,AVWVIEW.slices.cor,AVWVIEW.slices.axi];
1066 AVWVIEW.imgXYZ.meters = AVWVIEW.imgXYZ.voxels .* AVWVIEW.scale2meters;
1067 AVWVIEW.imgXYZ.mm     = AVWVIEW.imgXYZ.voxels .* AVWVIEW.scale2mm;
1068 
1069 coord_value = get(AVWVIEW.handles.coord,'value');
1070 
1071 if coord_value == 2,
1072   % using mm
1073   img_mm = AVWVIEW.imgXYZ.voxels .* AVWVIEW.scale2mm;
1074   metric.axi = img_mm(3);
1075   metric.cor = img_mm(2);
1076   metric.sag = img_mm(1);
1077 elseif coord_value == 3,
1078   % using meters
1079   img_meters = AVWVIEW.imgXYZ.voxels .* AVWVIEW.scale2meters;
1080   metric.axi = img_meters(3);
1081   metric.cor = img_meters(2);
1082   metric.sag = img_meters(1);
1083 else
1084   % voxels
1085   metric.axi = AVWVIEW.slices.axi;
1086   metric.cor = AVWVIEW.slices.cor;
1087   metric.sag = AVWVIEW.slices.sag;
1088 end;
1089 
1090 return
1091 
1092 
1093 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1094 function AVWVIEW = metric2slices(AVWVIEW,metric),
1095 
1096 coord_value = get(AVWVIEW.handles.coord,'value');
1097 
1098 if coord_value == 2,
1099   % using mm
1100   xpix = double(AVWVIEW.avw.hdr.dime.pixdim(2));
1101   ypix = double(AVWVIEW.avw.hdr.dime.pixdim(3));
1102   zpix = double(AVWVIEW.avw.hdr.dime.pixdim(4));
1103   AVWVIEW.slices.axi = round(metric.axi / zpix);
1104   AVWVIEW.slices.cor = round(metric.cor / ypix);
1105   AVWVIEW.slices.sag = round(metric.sag / xpix);
1106 elseif coord_value == 3,
1107   % using meters
1108   xpix = double(AVWVIEW.avw.hdr.dime.pixdim(2)) / 1000;
1109   ypix = double(AVWVIEW.avw.hdr.dime.pixdim(3)) / 1000;
1110   zpix = double(AVWVIEW.avw.hdr.dime.pixdim(4)) / 1000;
1111   AVWVIEW.slices.axi = round(metric.axi / zpix);
1112   AVWVIEW.slices.cor = round(metric.cor / ypix);
1113   AVWVIEW.slices.sag = round(metric.sag / xpix);
1114 else
1115   % voxels
1116   AVWVIEW.slices.axi = round(metric.axi);
1117   AVWVIEW.slices.cor = round(metric.cor);
1118   AVWVIEW.slices.sag = round(metric.sag);
1119 end;
1120 
1121 return
1122 
1123 
1124 
1125 
1126 
1127 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1128 function AVWVIEW = init(avw,invarname),
1129 
1130 % try to keep track of the input struct
1131 if exist('invarname','var'),
1132   if ~isempty(invarname),
1133     AVWVIEW.invarname = invarname;
1134   else
1135     AVWVIEW.invarname = '';
1136   end
1137 else
1138   AVWVIEW.invarname = '';
1139 end
1140 
1141 % GUI General Parameters
1142 GUIwidth  = 1;
1143 GUIheight = 1/3;
1144 
1145 version = '[$Revision: 2025 $]';
1146 name = sprintf('AVW View [v%s]',version(12:16));
1147 
1148 if isfield(avw,'fileprefix'),
1149   if ~isempty(avw.fileprefix),
1150     format = strcat('%+',sprintf('%d',length(avw.fileprefix)+1),'s');
1151     name = strcat(name,' - ',sprintf(format,avw.fileprefix));
1152   end
1153 end
1154 
1155 % The Zbuffer provides smooth slice animations (OpenGL is no good)
1156 GUI = figure('Name',name,'Tag','AVWVIEW','units','Normalized',...
1157   'BackingStore','off',...
1158   'NumberTitle','off','color',[0 0 0],...
1159   'MenuBar','figure','Position',[0 0.1 1.0 0.8],...
1160   'Renderer','zbuffer');
1161 
1162 movegui(GUI,'center');
1163 
1164 set(GUI,'KeyPressFcn','avw_view_ras([],[],''keypress'');');
1165 
1166 AVWVIEW.gui = GUI;
1167 
1168 Font.FontName   = 'Helvetica';
1169 Font.FontUnits  = 'Pixels';
1170 Font.FontSize   = 15;
1171 Font.FontWeight = 'normal';
1172 Font.FontAngle  = 'normal';
1173 
1174 
1175 AVWVIEW.shading = 'flat';
1176 shading(AVWVIEW.shading)
1177 
1178 
1179 
1180 %     % determine the datatype of avw.img
1181 %     switch double(avw.hdr.dime.bitpix),
1182 %     case 1,
1183 %         fprintf('...converting avw.img to uint8 for viewing only.\n\n');
1184 %         avw.img = uint8(avw.img);
1185 %     case 8,
1186 %         fprintf('...converting avw.img to uint8 for viewing only.\n\n');
1187 %         avw.img = uint8(avw.img);
1188 %     case 16,
1189 %         fprintf('...converting avw.img to uint16 for viewing only.\n\n');
1190 %         avw.img = uint16(avw.img);
1191 %     case {32,64},
1192 %         % make sure it is double, not single
1193 %         avw.img = double(avw.img);
1194 %     otherwise,
1195 %         % do nothing, leave it as is
1196 %     end
1197 
1198 
1199 % calculate image stats
1200 intensityMean = mean(mean(mean(avw.img)));
1201 intensityMeanRobust = mean(mean(mean(avw.img(find(avw.img)))));
1202 intensityStdev = std(std(std(avw.img)));
1203 
1204 intensityMax = max(max(max(avw.img)));
1205 
1206 % try to adjust for large intensity extremes
1207 if intensityMax > 255,
1208   % got 16 bit data, at least
1209   adjust = 0.5;
1210 else
1211   adjust = 0.9;
1212 end
1213 %AVWVIEW.clim = [0 (intensityMeanRobust + (10 * intensityStdev)) ];
1214 AVWVIEW.clim = [0 (intensityMax * adjust)];
1215 
1216 
1217 
1218 AVWVIEW.xdim = size(avw.img,1);
1219 AVWVIEW.ydim = size(avw.img,2);
1220 AVWVIEW.zdim = size(avw.img,3);
1221 
1222 AVWVIEW.slices.sag = 1;
1223 AVWVIEW.slices.cor = 1;
1224 AVWVIEW.slices.axi = 1;
1225 if AVWVIEW.xdim > 1, AVWVIEW.slices.sag = floor(AVWVIEW.xdim/2); end
1226 if AVWVIEW.ydim > 1, AVWVIEW.slices.cor = floor(AVWVIEW.ydim/2); end
1227 if AVWVIEW.zdim > 1, AVWVIEW.slices.axi = floor(AVWVIEW.zdim/2); end
1228 
1229 % store the volume center for later reference when
1230 % calculating fiducial locations
1231 center = avw_center(avw);
1232 AVWVIEW.center = center.abs.voxels;
1233 
1234 % set the default origin at the center
1235 AVWVIEW.origin  = AVWVIEW.center;
1236 
1237 AVWVIEW.pixdim = double(avw.hdr.dime.pixdim(2:4));
1238 
1239 AVWVIEW.scale2mm     = AVWVIEW.pixdim;          % vol scale in mm
1240 AVWVIEW.scale2meters = AVWVIEW.pixdim ./ 1000;  % vol scale in meters
1241 AVWVIEW.daspect      = AVWVIEW.pixdim ./ min(AVWVIEW.pixdim);
1242 
1243 xPlotSize = 0.38;
1244 yPlotSize = 0.38;
1245 
1246 AVWVIEW.cmapString = 'gray';
1247 
1248 AVWVIEW.cmap = colormap(AVWVIEW.cmapString);
1249 
1250 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1251 
1252 % Axial Slice
1253 if AVWVIEW.xdim > 1 & AVWVIEW.ydim > 1,
1254   
1255   handles.axial_subplot = subplot('position',[0.075 0.075 xPlotSize yPlotSize]);
1256   
1257   %avw.img = flipdim(avw.img,1);
1258   % add hayashi change default coordinate left handed to right handed.
1259   
1260   Saxial = squeeze(avw.img(:,:,AVWVIEW.slices.axi));
1261   
1262   %handles.axial_image = pcolor(double(Saxial)); colormap(gray); shading interp
1263   %pcolor(Saxial'); colormap(gray); shading flat
1264   
1265   %surf(avw.img(:,:,20)','edgecolor','none'); view(2); axis tight; colormap(flipdim(gray,1)); colorbar
1266   %surf(avw.img(:,:,20)','edgecolor','none'); view(2); axis tight; colormap(gray)
1267   %image(avw.img(:,:,20)'); axis image; colormap(gray)
1268   %imagesc(avw.img(:,:,20)'); axis image; colormap(gray)
1269   
1270   %handles.axial_image = image('Cdata',Saxial','CDataMapping','scaled',...
1271   %    'XData',[0 xdim],'YData',[0 ydim]);
1272   
1273   handles.axial_image = imagesc([0,AVWVIEW.xdim],[0,AVWVIEW.ydim],Saxial',AVWVIEW.clim);
1274   
1275   handles.axial_axes = gca;
1276   set(gca,'YDir','normal','XLimMode','manual','YLimMode','manual',...
1277     'ClimMode','manual','YColor',[1 1 1],'XColor',[1 1 1])
1278   
1279   title('Axial','Color',[1 1 1])
1280   ylabel('Y')
1281   xlabel('Left ----- X ----- Right')
1282 %xlabel('(Right <<) X (>> Left)'); % default radiological orientation for Analyze
1283   %xlabel('(Left <<) X (>> Right)')
1284   
1285   % This callback navigates with mouse button click
1286   set(handles.axial_image,'ButtonDownFcn','avw_view_ras([],[],''axial_image'');');
1287   
1288   GUIheight = 0.46;
1289   
1290   if AVWVIEW.zdim > 1,
1291     slider_step(1) = 1/(AVWVIEW.zdim);
1292     slider_step(2) = 1/(AVWVIEW.zdim);
1293     handles.axial_slider = uicontrol('Parent',GUI,'Style','slider',...
1294       'Units','Normalized', Font, ...
1295       'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'center',...
1296       'BusyAction','queue',...
1297       'TooltipString','Axial slice navigation',...
1298       'Min',1,'Max',AVWVIEW.zdim,'SliderStep',slider_step,'Value',AVWVIEW.slices.axi,...
1299       'Callback','avw_view_ras([],[],''axial_slider'');');
1300   end
1301   handles.axial_sliderN = uicontrol('Parent',GUI,'Style','text',...
1302     'Units','Normalized', Font, ...
1303     'Position',[.65 GUIheight .03 .03], 'HorizontalAlignment', 'center',...
1304     'BackgroundColor',[0 0 0],'ForegroundColor',[1 1 1],...
1305     'BusyAction','queue',...
1306     'TooltipString','Axial slice number',...
1307     'String',num2str(AVWVIEW.slices.axi),'Value',AVWVIEW.slices.axi);
1308   handles.axial_sliderT = uicontrol('Parent',GUI,'Style','text',...
1309     'Units','Normalized', Font, ...
1310     'Position',[.70 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1311     'BackgroundColor',[0 0 0],'ForegroundColor',[1 1 1],...
1312     'BusyAction','queue',...
1313     'TooltipString','Axial slice navigation',...
1314     'String','Axial');
1315   
1316   handles.axial_xlim = get(handles.axial_axes,'Xlim');
1317   handles.axial_ylim = get(handles.axial_axes,'Ylim');
1318   handles.axial_xline = line('Xdata',[AVWVIEW.slices.sag AVWVIEW.slices.sag], ...
1319                              'Ydata',handles.axial_ylim, ...
1320                              'ButtonDownFcn','avw_view_ras([],[],''axial_image'');');
1321   handles.axial_yline = line('Ydata',[AVWVIEW.slices.cor AVWVIEW.slices.cor], ...
1322                              'Xdata',handles.axial_xlim, ...
1323                              'ButtonDownFcn','avw_view_ras([],[],''axial_image'');');
1324   set(handles.axial_xline,'Color','y','Tag','XLINE', 'Visible', 'off');
1325   set(handles.axial_yline,'Color','y','Tag','YLINE', 'Visible', 'off');
1326   
1327 end
1328 
1329 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1330 
1331 % Coronal Slice
1332 if AVWVIEW.xdim > 1 & AVWVIEW.zdim > 1,
1333   
1334   handles.coronal_subplot = subplot('position',[0.075 0.575 xPlotSize yPlotSize]);
1335   
1336   Scor = squeeze(avw.img(:,AVWVIEW.slices.cor,:));
1337   handles.coronal_image = imagesc([0,AVWVIEW.xdim],[0,AVWVIEW.zdim],Scor',AVWVIEW.clim);
1338   handles.coronal_axes = gca;
1339   set(gca,'YDir','normal','XLimMode','manual','YLimMode','manual',...
1340     'ClimMode','manual','YColor',[1 1 1],'XColor',[1 1 1])
1341   
1342   %xlabel('(Left <<) X (>> Right)')
1343   %xlabel('(Right <<) X (>> Left)')
1344   xlabel('Left ----- X ----- Right')
1345   ylabel('Z')
1346   title('Coronal','Color',[1 1 1])
1347   
1348   % This callback navigates with left click
1349   set(handles.coronal_image,'ButtonDownFcn','avw_view_ras([],[],''coronal_image'');');
1350   
1351   GUIheight = GUIheight - 0.04;
1352   
1353   if AVWVIEW.ydim > 1,
1354     slider_step(1) = 1/(AVWVIEW.ydim);
1355     slider_step(2) = 1/(AVWVIEW.ydim);
1356     handles.coronal_slider = uicontrol('Parent',GUI,'Style','slider',...
1357       'Units','Normalized', Font, ...
1358       'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'center',...
1359       'BusyAction','queue',...
1360       'TooltipString','Coronal slice navigation',...
1361       'Min',1,'Max',AVWVIEW.ydim,'SliderStep',slider_step,'Value',AVWVIEW.slices.cor,...
1362       'Callback','avw_view_ras([],[],''coronal_slider'');');
1363   end
1364   handles.coronal_sliderN = uicontrol('Parent',GUI,'Style','text',...
1365     'Units','Normalized', Font, ...
1366     'Position',[.65 GUIheight .03 .03], 'HorizontalAlignment', 'center',...
1367     'BackgroundColor',[0 0 0],'ForegroundColor',[1 1 1],...
1368     'BusyAction','queue',...
1369     'TooltipString','Coronal slice number',...
1370     'String',num2str(AVWVIEW.slices.cor),'Value',AVWVIEW.slices.cor);
1371   handles.coronal_sliderT = uicontrol('Parent',GUI,'Style','text',...
1372     'Units','Normalized', Font, ...
1373     'Position',[.70 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1374     'BackgroundColor',[0 0 0],'ForegroundColor',[1 1 1],...
1375     'BusyAction','queue',...
1376     'TooltipString','Coronal slice navigation',...
1377     'String','Coronal');
1378   
1379   handles.coronal_xlim = get(handles.coronal_axes,'Xlim');
1380   handles.coronal_ylim = get(handles.coronal_axes,'Ylim');
1381   handles.coronal_xline = line('Xdata',[AVWVIEW.slices.sag AVWVIEW.slices.sag],...
1382                                'Ydata',handles.coronal_ylim, ...
1383                                'ButtonDownFcn','avw_view_ras([],[],''coronal_image'');');
1384   handles.coronal_yline = line('Ydata',[AVWVIEW.slices.axi AVWVIEW.slices.axi], ...
1385                                'Xdata',handles.coronal_xlim, ...
1386                                'ButtonDownFcn','avw_view_ras([],[],''coronal_image'');');
1387   set(handles.coronal_xline,'Color','y','Tag','XLINE', 'Visible', 'off');
1388   set(handles.coronal_yline,'Color','y','Tag','YLINE', 'Visible', 'off');
1389   
1390 end
1391 
1392 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1393 
1394 % Sagittal Slice
1395 if AVWVIEW.ydim > 1 & AVWVIEW.zdim > 1,
1396   
1397   handles.sagittal_subplot = subplot('position',[0.575 0.575 xPlotSize yPlotSize]);
1398   
1399   Ssag = squeeze(avw.img(AVWVIEW.slices.sag,:,:));
1400   handles.sagittal_image = imagesc([0,AVWVIEW.ydim],[0,AVWVIEW.zdim],Ssag',AVWVIEW.clim);
1401   
1402   handles.sagittal_axes = gca;
1403   set(gca,'YDir','normal','XLimMode','manual','YLimMode','manual',...
1404     'ClimMode','manual','YColor',[1 1 1],'XColor',[1 1 1])
1405   
1406   xlabel('Y')
1407   ylabel('Z')
1408   title('Sagittal','Color',[1 1 1])
1409   
1410   % This callback navigates with mouse click
1411   set(handles.sagittal_image,'ButtonDownFcn','avw_view_ras([],[],''sagittal_image'');');
1412   
1413   GUIheight = GUIheight - 0.04;
1414   
1415   if AVWVIEW.xdim > 1,
1416     slider_step(1) = 1/(AVWVIEW.xdim);
1417     slider_step(2) = 1/(AVWVIEW.xdim);
1418     handles.sagittal_slider = uicontrol('Parent',GUI,'Style','slider',...
1419       'Units','Normalized', Font, ...
1420       'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'center',...
1421       'BusyAction','queue',...
1422       'TooltipString','Sagittal slice navigation',...
1423       'Min',1,'Max',AVWVIEW.xdim,'SliderStep',slider_step,'Value',AVWVIEW.slices.sag,...
1424       'Callback','avw_view_ras([],[],''sagittal_slider'');');
1425   end
1426   handles.sagittal_sliderN = uicontrol('Parent',GUI,'Style','text',...
1427     'Units','Normalized', Font, ...
1428     'Position',[.65 GUIheight .03 .03], 'HorizontalAlignment', 'center',...
1429     'BackgroundColor',[0 0 0],'ForegroundColor',[1 1 1],...
1430     'BusyAction','queue',...
1431     'TooltipString','Sagittal slice number',...
1432     'String',num2str(AVWVIEW.slices.sag),'Value',AVWVIEW.slices.sag);
1433   handles.sagittal_sliderT = uicontrol('Parent',GUI,'Style','text',...
1434     'Units','Normalized', Font, ...
1435     'Position',[.70 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1436     'BackgroundColor',[0 0 0],'ForegroundColor',[1 1 1],...
1437     'BusyAction','queue',...
1438     'TooltipString','Sagittal slice navigation',...
1439     'String','Sagittal');
1440   
1441   handles.sagittal_xlim = get(handles.sagittal_axes,'Xlim');
1442   handles.sagittal_ylim = get(handles.sagittal_axes,'Ylim');
1443   handles.sagittal_xline = line('Xdata',[AVWVIEW.slices.cor AVWVIEW.slices.cor], ...
1444                                 'Ydata',handles.sagittal_ylim, ...
1445                                 'ButtonDownFcn','avw_view_ras([],[],''sagittal_image'');');
1446   handles.sagittal_yline = line('Ydata',[AVWVIEW.slices.axi AVWVIEW.slices.axi], ...
1447                                 'Xdata',handles.sagittal_xlim, ...
1448                                 'ButtonDownFcn','avw_view_ras([],[],''sagittal_image'');');
1449   set(handles.sagittal_xline,'Color','y','Tag','XLINE', 'Visible', 'off');
1450   set(handles.sagittal_yline,'Color','y','Tag','YLINE', 'Visible', 'off');
1451   
1452 end
1453 
1454 
1455 
1456 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1457 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1458 % Image Contex Menus
1459 
1460 menu=uicontextmenu;
1461 
1462 % enable right click access to ROI tools
1463 roi = uimenu(menu,'Label','ROI');
1464 uimenu(roi,'Label','ROI (9x9x9 block)','Callback','avw_view_ras([],[],''roi_9'');');
1465 uimenu(roi,'Label','ROI (7x7x7 block)','Callback','avw_view_ras([],[],''roi_7'');');
1466 uimenu(roi,'Label','ROI (5x5x5 block)','Callback','avw_view_ras([],[],''roi_5'');');
1467 uimenu(roi,'Label','ROI (3x3x3 block)','Callback','avw_view_ras([],[],''roi_3'');');
1468 
1469 % save image to graphics file
1470 uimenu(menu,'Label','Save Image','Callback','avw_view_ras([],[],''save_image'');');
1471 
1472 % zoom image to new figure
1473 uimenu(menu,'Label','Zoom Image','Callback','avw_view_ras([],[],''zoom'');');
1474 
1475 if isfield(handles,'axial_image'),
1476   if isempty(get(handles.axial_image,'uicontextmenu')),
1477     set(handles.axial_image,'uicontextmenu',menu);
1478   end
1479 end
1480 if isfield(handles,'coronal_image'),
1481   if isempty(get(handles.coronal_image,'uicontextmenu')),
1482     set(handles.coronal_image,'uicontextmenu',menu);
1483   end
1484 end
1485 if isfield(handles,'sagittal_image'),
1486   if isempty(get(handles.sagittal_image,'uicontextmenu')),
1487     set(handles.sagittal_image,'uicontextmenu',menu);
1488   end
1489 end
1490 
1491 
1492 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1493 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1494 
1495 % Image Intensity at Mouse Click
1496 
1497 GUIheight = GUIheight - 0.04;
1498 
1499 handles.Timval = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1500   'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1501   'BackgroundColor', [0 0 0],...
1502   'ForegroundColor', [1 1 1],...
1503   'BusyAction','queue',...
1504   'String','Image Intensity');
1505 handles.imval = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1506   'Position',[.65 GUIheight .15 .03], 'HorizontalAlignment', 'right',...
1507   'BackgroundColor', [0 0 0],...
1508   'ForegroundColor', [1 1 1],...
1509   'BusyAction','queue',...
1510   'String','x','Value',0);
1511 
1512 % Image Position at Mouse Click
1513 
1514 GUIheight = GUIheight - 0.04;
1515 
1516 handles.Timpos = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1517   'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1518   'BackgroundColor', [0 0 0],...
1519   'ForegroundColor', [1 1 1],...
1520   'BusyAction','queue',...
1521   'String','Image Position');
1522 handles.impos = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1523   'Position',[.65 GUIheight .15 .03], 'HorizontalAlignment', 'right',...
1524   'BackgroundColor', [0 0 0],...
1525   'ForegroundColor', [1 1 1],...
1526   'BusyAction','queue',...
1527   'String','xyz','Value',[0 0 0]);
1528 
1529 
1530 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1531 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1532 
1533 GUIheight = GUIheight - 0.04;
1534 
1535 %handles.flip = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1536 %  'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1537 %  'BackgroundColor', [.3 .3 .3],'ForegroundColor', [0 0 0],...
1538 %  'BusyAction','queue',...
1539 %  'TooltipString','Flip Left and Right (viewer only, see also avw_flip).',...
1540 %  'String','Flip L/R',...
1541 %  'Callback','avw_view_ras([],[],''flip'');');
1542 handles.flipStatus = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1543   'Position',[.65 GUIheight .15 .03], 'HorizontalAlignment', 'right',...
1544   'BackgroundColor', [0 0 0],...
1545   'ForegroundColor', [1 1 1],...
1546   'BusyAction','queue',...
1547   'TooltipString','Flipped Status',...
1548   'String','L>>R (neurological)');
1549 
1550 
1551 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1552 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1553 
1554 % % AC Location
1555 %
1556 % GUIheight = GUIheight - 0.04;
1557 %
1558 % handles.Tac = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1559 %   'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1560 %   'BackgroundColor', [.3 .3 .3],...
1561 %   'ForegroundColor', [0 0 0],...
1562 %   'BusyAction','queue',...
1563 %   'TooltipString','AC point in (voxels) or (meter offset from center of volume)',...
1564 %   'String','AC Point',...
1565 %   'Callback','avw_view_ras([],[],''ac'');');
1566 % handles.ac = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1567 %   'Position',[.65 GUIheight .15 .03], 'HorizontalAlignment', 'right',...
1568 %   'BackgroundColor', [0 0 0],...
1569 %   'ForegroundColor', [1 1 1],...
1570 %   'BusyAction','queue',...
1571 %   'TooltipString','These values are offset from volume center.',...
1572 %   'String','x,y,z');
1573 
1574 % Nasion Location
1575 
1576 GUIheight = GUIheight - 0.04;
1577 
1578 handles.Tnasion = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1579   'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1580   'BackgroundColor', [.3 .3 .3],...
1581   'ForegroundColor', [0 0 0],...
1582   'BusyAction','queue',...
1583   'TooltipString','Update Nasion - should be toward +Y',...
1584   'String','Fiducial: Nasion',...
1585   'Callback','avw_view_ras([],[],''nasion'');');
1586 handles.nasion = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1587   'Position',[.65 GUIheight .15 .03], 'HorizontalAlignment', 'right',...
1588   'BackgroundColor', [0 0 0],...
1589   'ForegroundColor', [1 1 1],...
1590   'BusyAction','queue',...
1591   'TooltipString','These values are offset from volume center, should be toward +Y',...
1592   'String','x,y,z');
1593 
1594 % Right Preauricular Location
1595 
1596 GUIheight = GUIheight - 0.04;
1597 
1598 handles.Trpa = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1599   'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1600   'BackgroundColor', [.3 .3 .3],...
1601   'ForegroundColor', [0 0 0],...
1602   'BusyAction','queue',...
1603   'TooltipString','Update Right Preauricular - should be toward +X',...
1604   'String','Fiducial: RPA',...
1605   'Callback','avw_view_ras([],[],''rpa'');');
1606 handles.rpa = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1607   'Position',[.65 GUIheight .15 .03], 'HorizontalAlignment', 'right',...
1608   'BackgroundColor', [0 0 0],...
1609   'ForegroundColor', [1 1 1],...
1610   'BusyAction','queue',...
1611   'TooltipString','These values are offset from volume center, should be toward +X',...
1612   'String','x,y,z');
1613 
1614 % Left Preauricular Location
1615 
1616 GUIheight = GUIheight - 0.04;
1617 
1618 handles.Tlpa = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1619   'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1620   'BackgroundColor', [.3 .3 .3],...
1621   'ForegroundColor', [0 0 0],...
1622   'BusyAction','queue',...
1623   'TooltipString','Update Left Preauricular - should be toward -X',...
1624   'String','Fiducial: LPA',...
1625   'Callback','avw_view_ras([],[],''lpa'');');
1626 handles.lpa = uicontrol('Parent',GUI,'Style','text','Units','Normalized', Font, ...
1627   'Position',[.65 GUIheight .15 .03], 'HorizontalAlignment', 'right',...
1628   'BackgroundColor', [0 0 0],...
1629   'ForegroundColor', [1 1 1],...
1630   'BusyAction','queue',...
1631   'TooltipString','These values are offset from volume center, should be toward -X',...
1632   'String','x,y,z');
1633 
1634 
1635 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1636 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1637 
1638 %GUIheight = GUIheight - 0.04;
1639 
1640 %handles.contrast = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1641 %  'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1642 %  'BackgroundColor', [.3 .3 .3],'ForegroundColor', [0 0 0],...
1643 %  'BusyAction','queue',...
1644 %  'TooltipString','Auto contrast with gray colormap',...
1645 %  'String','Auto Contrast',...
1646 %  'Callback','avw_view_ras([],[],''contrast'');');
1647 
1648 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1649 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1650 
1651 GUIheight = GUIheight - 0.04;
1652 
1653 handles.dimmer = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1654   'Position',[.55 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1655   'BackgroundColor', [.3 .3 .3],'ForegroundColor', [0 0 0],...
1656   'BusyAction','queue',...
1657   'TooltipString','Dim by 1%',...
1658   'String','Dimmer',...
1659   'Callback','avw_view_ras([],[],''dimmer'');');
1660 
1661 handles.brighter = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1662   'Position',[.65 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1663   'BackgroundColor', [.3 .3 .3],'ForegroundColor', [0 0 0],...
1664   'BusyAction','queue',...
1665   'TooltipString','Brighten by 1%',...
1666   'String','Brighter',...
1667   'Callback','avw_view_ras([],[],''brighter'');');
1668 
1669 handles.clim = uicontrol('Parent',GUI,'Style','edit','Units','Normalized', Font, ...
1670   'Position',[.75 GUIheight .06 .03], 'HorizontalAlignment', 'right',...
1671   'BackgroundColor', [0 0 0],...
1672   'ForegroundColor', [1 1 1],...
1673   'BusyAction','queue',...
1674   'TooltipString','Image intensity Climit (inverse brightness)',...
1675   'String',num2str(AVWVIEW.clim(2)),...
1676   'Callback','avw_view_ras([],[],''setClimit'');');
1677 
1678 handles.cmap = uicontrol('Parent',GUI,'Style','popup','Units','Normalized', Font, ...
1679   'Position',[.82 GUIheight .06 .03], 'HorizontalAlignment', 'left',...
1680   'BackgroundColor', [0 0 0],...
1681   'ForegroundColor', [1 1 1],...
1682   'BusyAction','queue',...
1683   'TooltipString','Color Map',...
1684   'String',{'gray','bone','copper','hot','cool','spring','summer','autumn','winter','hsv','jet'},...
1685   'Callback','avw_view_ras([],[],''setCmap'');');
1686 
1687 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1688 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1689 
1690 GUIheight = 0.46;
1691 
1692 handles.crosshairs = uicontrol('Parent',GUI,'Style','checkbox','Units','Normalized', Font, ...
1693   'Position',[.85 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1694   'BackgroundColor', [.3 .3 .3],'ForegroundColor', [0 0 0],...
1695   'BusyAction','queue',...
1696   'TooltipString','Toggle Crosshairs on/off',...
1697   'String','Crosshairs','Value',1,...
1698   'Callback','avw_view_ras([],[],''crosshairs'');');
1699 
1700 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1701 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1702 
1703 GUIheight = GUIheight - 0.04;
1704 
1705 handles.histogram = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1706   'Position',[.85 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1707   'BackgroundColor', [.3 .3 .3],'ForegroundColor', [0 0 0],...
1708   'BusyAction','queue',...
1709   'TooltipString','Histogram of Volume Intensity',...
1710   'String','Histogram',...
1711   'Callback','avw_view_ras([],[],''histogram'');');
1712 
1713 
1714 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1715 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1716 
1717 GUIheight = GUIheight - 0.04;
1718 
1719 handles.coord = uicontrol('Parent',GUI,'Style','popupmenu','Units','Normalized', Font, ...
1720   'Position',[.85 GUIheight .10 .03], 'HorizontalAlignment', 'left',...
1721   'BackgroundColor', [.3 .3 .3],'ForegroundColor', [0 0 0],...
1722   'BusyAction','queue',...
1723   'TooltipString','Voxel or Mensurated Axis Coordinates',...
1724   'String',{'Voxels','mm','meters'},...
1725   'Callback','avw_view_ras([],[],''coordinates'');');
1726 
1727 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1728 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1729 
1730 Font.FontWeight = 'bold';
1731 
1732 % View avw.hdr
1733 % handles.Bhdr = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1734 %   'Position',[.90 .09 .09 .03],...
1735 %   'String','HDR','BusyAction','queue',...
1736 %   'TooltipString','View the .hdr parameters.',...
1737 %   'BackgroundColor',[0.0 0.0 0.5],...
1738 %   'ForegroundColor',[0 0 0], 'HorizontalAlignment', 'center',...
1739 %   'Callback',strcat('AVWVIEW = get(gcbf,''Userdata''); ',...
1740 %   'avw_view_hdr(AVWVIEW.avw,AVWVIEW.gui);',...
1741 %   'clear AVWVIEW;'));
1742 
1743 % Save: Save fiducials
1744 handles.Bquit = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1745   'Position',[.70 .01 .15 .05],...
1746   'String','Save fiducials','BusyAction','queue',...
1747   'BackgroundColor',[0.0 0.5 0.0],...
1748   'ForegroundColor', [0 0 0], 'HorizontalAlignment', 'center',...
1749   'Callback','avw_view_ras([],[],''save'');');
1750 
1751 % Close: application end
1752 handles.Bclose = uicontrol('Parent',GUI,'Style','pushbutton','Units','Normalized', Font, ...
1753   'Position',[.88 .01 .10 .05],...
1754   'String','Close','BusyAction','queue',...
1755   'BackgroundColor',[0.0 0.5 0.0],...
1756   'ForegroundColor', [0 0 0], 'HorizontalAlignment', 'center',...
1757   'Callback','avw_view_ras([],[],''close'');');
1758 
1759 % Update the gui_struct handles for this gui
1760 if exist('parent','var'), AVWVIEW.parent.gui = parent; end
1761 AVWVIEW.avw = avw;
1762 AVWVIEW.handles = handles;
1763 set(AVWVIEW.gui,'Userdata',AVWVIEW);
1764 set(AVWVIEW.gui,'HandleVisibility','callback');
1765 
1766 return
1767 
1768 
1769 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
1770 function slice_img(avw),
1771 
1772 figure
1773 xslice = 128;
1774 slice = squeeze( avw.img(xslice,:,:) );
1775 imagesc(slice); axis image; colormap('gray')
1776 figure
1777 yslice = 128;
1778 slice = squeeze( avw.img(:,yslice,:) );
1779 imagesc(slice); axis image; colormap('gray')
1780 figure
1781 zslice = 128;
1782 slice = squeeze( avw.img(:,:,zslice) );
1783 imagesc(slice); axis image; colormap('gray')
1784 
1785 return
avw_view_ras

PURPOSE

SYNOPSIS

DESCRIPTION

CROSS-REFERENCE INFORMATION

SUBFUNCTIONS

SOURCE CODE
