nii.rar_.n_MATLAB NII_nii_nii mat_nii.

% VIEW_NII: Create or update a 3-View (Front, Top, Side) of the % brain data that is specified by nii structure % % Usage: status = view_nii([h], nii, [option]) or % status = view_nii(h, [option]) % % Where, h is the figure on which the 3-View will be plotted; % nii is the brain data in NIFTI format; % option is a struct that configures the view plotted, can be: % % option.command = 'init' % option.command = 'update' % option.command = 'clearnii' % option.command = 'updatenii' % option.command = 'updateimg' (nii is nii.img here) % % option.usecolorbar = 0 | [1] % option.usepanel = 0 | [1] % option.usecrosshair = 0 | [1] % option.usestretch = 0 | [1] % option.useimagesc = 0 | [1] % option.useinterp = [0] | 1 % % option.setarea = [x y w h] | [0.05 0.05 0.9 0.9] % option.setunit = ['vox'] | 'mm' % option.setviewpoint = [x y z] | [origin] % option.setscanid = [t] | [1] % option.setcrosshaircolor = [r g b] | [1 0 0] % option.setcolorindex = From 1 to 9 (default is 2 or 3) % option.setcolormap = (Mx3 matrix, 0 <= val <= 1) % option.setcolorlevel = No more than 256 (default 256) % option.sethighcolor = [] % option.setcbarminmax = [] % option.setvalue = [] % option.glblocminmax = [] % option.setbuttondown = '' % option.setcomplex = [0] | 1 | 2 % % Options description in detail: % ============================== % % 1. command: A char string that can control program. % % init: If option.command='init', the program will display % a 3-View plot on the figure specified by figure h % or on a new figure. If there is already a 3-View % plot on the figure, please use option.command = % 'updatenii' (see detail below); otherwise, the % new 3-View plot will superimpose on the old one. % If there is no option provided, the program will % assume that this is an initial plot. If the figure % handle is omitted, the program knows that it is % an initial plot. % % update: If there is no command specified, and a figure % handle of the existing 3-View plot is provided, % the program will choose option.command='update' % to update the 3-View plot with some new option % items. % % clearnii: Clear 3-View plot on specific figure % % updatenii: If a new nii is going to be loaded on a fig % that has already 3-View plot on it, use this % command to clear existing 3-View plot, and then % display with new nii. So, the new nii will not % superimpose on the existing one. All options % for 'init' can be used for 'updatenii'. % % updateimg: If a new 3D matrix with the same dimension % is going to be loaded, option.command='updateimg' % can be used as a light-weighted 'updatenii, since % it only updates the 3 slices with new values. % inputing argument nii should be a 3D matrix % (nii.img) instead of nii struct. No other option % should be used together with 'updateimg' to keep % this command as simple as possible. % % % 2. usecolorbar: If specified and usecolorbar=0, the program % will not include the colorbar in plot area; otherwise, % a colorbar will be included in plot area. % % 3. usepanel: If specified and usepanel=0, the control panel % at lower right cornor will be invisible; otherwise, % it will be visible. % % 4. usecrosshair: If specified and usecrosshair=0, the crosshair % will be invisible; otherwise, it will be visible. % % 5. usestretch: If specified and usestretch=0, the 3 slices will % not be stretched, and will be displayed according to % the actual voxel size; otherwise, the 3 slices will be % stretched to the edge. % % 6. useimagesc: If specified and useimagesc=0, images data will % be used directly to match the colormap (like 'image' % command); otherwise, image data will be scaled to full % colormap with 'imagesc' command in Matlab. % % 7. useinterp: If specified and useinterp=1, the image will be % displayed using interpolation. Otherwise, it will be % displayed like mosaic, and each tile stands for a % pixel. This option does not apply to 'setvalue' option % is set. % % % 8. setarea: 3-View plot will be displayed on this specific % region. If it is not specified, program will set the % plot area to [0.05 0.05 0.9 0.9]. % % 9. setunit: It can be specified to setunit='voxel' or 'mm' % and the view will change the axes unit of [X Y Z] % accordingly. % % 10. setviewpoint: If specified, [X Y Z] values will be used % to set the viewpoint of 3-View plot. % % 11. setscanid: If specified, [t] value will be used to display % the specified image scan in NIFTI data. % % 12. setcrosshaircolor: If specified, [r g b] value will be used % for Crosshair Color. Otherwise, red will be the default. % % 13. setcolorindex: If specified, the 3-View will choose the % following colormap: 2 - Bipolar; 3 - Gray; 4 - Jet; % 5 - Cool; 6 - Bone; 7 - Hot; 8 - Copper; 9 - Pink; % If not specified, it will choose 3 - Gray if all data % values are not less than 0; otherwise, it will choose % 2 - Bipolar if there is value less than 0. (Contrast % control can only apply to 3 - Gray colormap. % % 14. setcolormap: 3-View plot will use it as a customized colormap. % It is a 3-column matrix with value between 0 and 1. If % using MS-Windows version of Matlab, the number of rows % can not be more than 256, because of Matlab limitation. % When colormap is used, setcolorlevel option will be % disabled automatically. % % 15. setcolorlevel: If specified (must be no more than 256, and % cannot be used for customized colormap), row number of % colormap will be squeezed down to this level; otherwise, % it will assume that setcolorlevel=256. % % 16. sethighcolor: If specified, program will squeeze down the % colormap, and allocate sethighcolor (an Mx3 matrix) % to high-end portion of the colormap. The sum of M and % setcolorlevel should be less than 256. If setcolormap % option is used, sethighcolor will be inserted on top % of the setcolormap, and the setcolorlevel option will % be disabled automatically. % % 17. setcbarminmax: if specified, the [min max] will be used to % set the min and max of the colorbar, which does not % include any data for highcolor. % % 18. setvalue: If specified, setvalue.val (with the same size as % the source data on solution points) in the source area % setvalue.idx will be superimposed on the current nii % image. So, the size of setvalue.val should be equal to % the size of setvalue.idx. To use this feature, it needs % single or double nii structure for background image. % % 19. glblocminmax: If specified, pgm will use glblocminmax to % calculate the colormap, instead of minmax of image. % % 20. setbuttondown: If specified, pgm will evaluate the command % after a click or slide action is invoked to the new % view point. % % 21. setcomplex: This option will decide how complex data to be % displayed: 0 - Real part of complex data; 1 - Imaginary % part of complex data; 2 - Modulus (magnitude) of complex % data; If not specified, it will be set to 0 (Real part % of complex data as default option. This option only apply % when option.command is set to 'init or 'updatenii'. % % % Additional Options for 'update' command: % ======================================= % % option.enablecursormove = [1] | 0 % option.enableviewpoint = 0 | [1] % option.enableorigin = 0 | [1] % option.enableunit = 0 | [1] % option.enablecrosshair = 0 | [1] % option.enablehistogram = 0 | [1] % option.enablecolormap = 0 | [1] % option.enablecontrast = 0 | [1] % option.enablebrightness = 0 | [1] % option.enableslider = 0 | [1] % option.enabledirlabel = 0 | [1] % % % e.g.: % nii = load_nii('T1'); % T1.img/hdr % view_nii(nii); % % or % % h = figure('unit','normal','pos', [0.18 0.08 0.64 0.85]); % opt.setarea = [0.05 0.05 0.9 0.9]; % view_nii(h, nii, opt); % % %