editOverlay(varargin) -- edit an ROI ("Overlay" was used early-on for "ROI")
Usage: editOverlay('-base', 'path_to_base_volume_with_stem', '-inmask', ...
'path_to_roi_with_stem', '-savedir', 'path_to_default_save_directory', ...
<'-overlay'>, <'path_to_overlay_roi'>)
editOverlay provides a graphical way for users to create ROIs. The first
step in creating an ROI is to threshold a statistical map; this is
accomplished by either thresholdByFDR.m or thresholdStatMap.m; the output
of these programs is an ROI that contains all voxels that pass a certain
statistical threshold. However, one commonly wants only a subset of these
voxels and this is where editOverlay comes in. editOverlay displays the
input ROI on top of a base functional image. On startup, all voxels
in the input ROI are selected and colored as red. You can clear all the
voxels which will then color the voxels in the input ROI yellow. Thus,
selected voxels = red, deselected but in original ROI = yellow. This
is done so that you can create additional ROIs that are a subset of the
input ROI.
To name the functionals on which to display the ROI, use the '-base' option;
this the path+stem to the set of functiona slices (in bshort format).
The parameter '-inmask' is the path to the input ROI, again with path+stem.
To setup the default output save path, give the '-savedir' option; by
default, "edit_roi" and "make_roi" use the path to the ROI as the default
save directory. Finally, you can choose to have one ROI be an overlay on
top of another ROI; the overlay voxels will be colored in red, while the
other, underlying ROI will be colored in yellow. To do this, give the
'-overlay' option with path+stem.
Modified from "editmask.m" in the Freesurfer/FS-FAST distribution
Original version by Doug Greve can be found in fsfast/toolbox/editmask.m
$Id: editOverlay.m,v 1.19 2003/09/18 16:58:53 nknouf Exp $This function calls:
This function is called by:
0001 function r = editOverlay(varargin) 0002 % editOverlay(varargin) -- edit an ROI ("Overlay" was used early-on for "ROI") 0003 % 0004 % Usage: editOverlay('-base', 'path_to_base_volume_with_stem', '-inmask', ... 0005 % 'path_to_roi_with_stem', '-savedir', 'path_to_default_save_directory', ... 0006 % <'-overlay'>, <'path_to_overlay_roi'>) 0007 % 0008 % editOverlay provides a graphical way for users to create ROIs. The first 0009 % step in creating an ROI is to threshold a statistical map; this is 0010 % accomplished by either thresholdByFDR.m or thresholdStatMap.m; the output 0011 % of these programs is an ROI that contains all voxels that pass a certain 0012 % statistical threshold. However, one commonly wants only a subset of these 0013 % voxels and this is where editOverlay comes in. editOverlay displays the 0014 % input ROI on top of a base functional image. On startup, all voxels 0015 % in the input ROI are selected and colored as red. You can clear all the 0016 % voxels which will then color the voxels in the input ROI yellow. Thus, 0017 % selected voxels = red, deselected but in original ROI = yellow. This 0018 % is done so that you can create additional ROIs that are a subset of the 0019 % input ROI. 0020 % 0021 % To name the functionals on which to display the ROI, use the '-base' option; 0022 % this the path+stem to the set of functiona slices (in bshort format). 0023 % The parameter '-inmask' is the path to the input ROI, again with path+stem. 0024 % To setup the default output save path, give the '-savedir' option; by 0025 % default, "edit_roi" and "make_roi" use the path to the ROI as the default 0026 % save directory. Finally, you can choose to have one ROI be an overlay on 0027 % top of another ROI; the overlay voxels will be colored in red, while the 0028 % other, underlying ROI will be colored in yellow. To do this, give the 0029 % '-overlay' option with path+stem. 0030 % 0031 % Modified from "editmask.m" in the Freesurfer/FS-FAST distribution 0032 % Original version by Doug Greve can be found in fsfast/toolbox/editmask.m 0033 % 0034 % $Id: editOverlay.m,v 1.19 2003/09/18 16:58:53 nknouf Exp $ 0035 0036 version = '$Id: editOverlay.m,v 1.19 2003/09/18 16:58:53 nknouf Exp $'; 0037 r = 1; 0038 0039 %% Print usage if there are no arguments %% 0040 if(nargin == 0) 0041 print_usage; 0042 return; 0043 end 0044 0045 hcurrentfig = get(0,'CurrentFigure'); 0046 0047 %--------------- Initialize if needed -----------------% 0048 init = 0; 0049 flag = deblank(varargin{1}); 0050 if(~isempty(strmatch(flag,'-init')) | isempty(hcurrentfig)) 0051 init = 1; 0052 s = parse_args(varargin); 0053 if(isempty(s)) return; end 0054 s = check_params(s); 0055 if(isempty(s)) return; end 0056 0057 %% define a value 0058 s.sliceNum = 0; 0059 0060 % Load the base % 0061 fprintf('Loading base %s\n',s.baseid); 0062 s.base = fmri_ldbvolume(s.baseid); 0063 s.base = s.base(:,:,:,s.baseframe+1); 0064 if(isempty(s.base)) 0065 fprintf('ERROR: cannot load %s\n',s.baseid); 0066 return; 0067 end 0068 s.volsize = size(s.base); 0069 0070 % Convert to mosaic % 0071 s.base = vol2mos(permute(s.base,[2 3 1])); 0072 s.mossize = size(s.base); 0073 0074 % Load the input mask (if specificied) or segment the base % 0075 if(~isempty(s.inmaskid)) 0076 s.mask = textread([s.inmaskid '.roi']); 0077 s.mask = expandROI(s.mask, s.volsize); 0078 %%s.mask = fmri_ldbvolume(s.inmaskid); 0079 if(isempty(s.mask)) 0080 fprintf('ERROR: could not load input mask %s\n',s.inmaskid); 0081 return; 0082 end 0083 s.mask = s.mask(:,:,:,1); 0084 s.mask = vol2mos(permute(s.mask,[2 3 1])); 0085 if(s.invertinmask) s.mask = ~s.mask; end 0086 else 0087 s.mask = zeros(size(s.base)); 0088 if(s.segbase) 0089 meanbase = mean(reshape1d(s.base)); 0090 ind = find(s.base > s.segthresh*meanbase); 0091 s.mask(ind) = 1; 0092 fprintf('Segmenting base %g %d\n',meanbase,length(ind)); 0093 end 0094 if(s.invertinmask) s.mask = ~s.mask; end 0095 s.saveneeded = 1; 0096 end 0097 0098 %% initialize the overlay 0099 if (~isempty(s.overlayid)) 0100 s.overlay = textread([s.overlayid '.roi']); 0101 s.overlay = expandROI(s.overlay, s.volsize); 0102 %%s.overlay = fmri_ldbvolume(s.overlayid); 0103 if(isempty(s.overlay)) 0104 fprintf('ERROR: could not load overlay %s\n',s.overlayid); 0105 return; 0106 end 0107 s.overlay = s.overlay(:,:,:,1); 0108 s.overlay = vol2mos(permute(s.overlay,[2 3 1])); 0109 else 0110 s.overlay = s.mask; 0111 end 0112 0113 if(s.heqbase) 0114 fprintf('Equalizing Base Intesity Values\n'); 0115 [histbase valbase] = hist(reshape1d(s.base),100); 0116 pbase = histbase/sum(histbase); 0117 pdfbase = cumsum(pbase); 0118 x = max(find(pdfbase < .98)); 0119 x = valbase(ix); 0120 ind = find(s.base > x); 0121 s.base(ind) = x; 0122 end 0123 0124 % Rescale Base to be between 1 and (s.ncmap-2) % 0125 minbase = min(reshape1d(s.base)); 0126 maxbase = max(reshape1d(s.base)); 0127 s.base = floor((s.ncmap-2)*(s.base-minbase)/(maxbase-minbase)) + 1; 0128 % Create the color map 0129 s.cmap = gray(s.ncmap); % Start with gray 0130 % Set the last entry to be color; 0131 s.cmap(end-1,:) = [.99 .99 0]; % raises a figure window here (why?) 0132 s.cmap(end,:) = [0.99 0 0]; % raises a figure window here (why?) 0133 0134 s.displayimg = s.base .* (~s.mask) + ((s.ncmap-1)*s.mask); 0135 0136 s.oldbase = s.base; 0137 s.base = s.base .* (~s.mask) + (s.ncmap-1)*s.mask; 0138 s.displayimg = s.base .* (~s.overlay); 0139 s.displayimg = s.displayimg + (s.ncmap) * s.overlay; 0140 0141 s.overlay = squeeze(s.overlay); 0142 0143 % Image the display image % 0144 s.himage = image(s.displayimg); 0145 set(s.himage,'EraseMode','none'); 0146 axis image; 0147 s.hfig = gcf; 0148 s.haxis = gca; 0149 colormap(s.cmap); 0150 set(gcf,'pointer','crosshair'); 0151 0152 % Set up the call-back functions % 0153 set(gcf,'KeyPressFcn', 'editOverlay(''kbd'');'); 0154 set(gcf,'WindowButtonDownFcn', 'editOverlay(''wbd'');'); 0155 set(gcf,'WindowButtonUpFcn', 'editOverlay(''wbu'');'); 0156 set(gcf,'WindowButtonMotionFcn','editOverlay(''wbm'');'); 0157 s.nmarked = length(find(s.overlay==1)); 0158 0159 set(gcf,'UserData',s); 0160 0161 fprintf('\n'); 0162 fprintf(' ----------------------------------\n'); 0163 fprintf(' For help press "h"\n'); 0164 fprintf(' ------------ Help ----------------\n'); 0165 printhelp; 0166 fprintf('\n'); 0167 fprintf(' ------ Current State -------------\n'); 0168 printstate(s); 0169 fprintf('\n'); 0170 0171 return; 0172 end 0173 %---------------------------------------------------------% 0174 %---------------------------------------------------------% 0175 %---------------------------------------------------------% 0176 0177 %----------- Parse the call-back function ----------% 0178 s = get(gcf,'UserData'); 0179 redraw = 0; 0180 switch(flag) 0181 0182 case {'wbd','wbm'} % -------Window Button Down ------------ % 0183 if(strcmp(flag,'wbm') & ~s.mousedown) return; end 0184 if(s.editmode == 0) return; end 0185 0186 xyz = get(gca,'CurrentPoint'); 0187 c = round(xyz(1,1)); 0188 r = round(xyz(1,2)); 0189 if(r < 1 | r > size(s.base,1) | c < 1 | c > size(s.base,2)) 0190 return; 0191 end 0192 s.cp = round([r c]); 0193 rlist = r-(s.brushsize-1):r+(s.brushsize-1); 0194 ind = find(rlist < s.mossize(1)); 0195 rlist = rlist(ind); 0196 0197 clist = c-(s.brushsize-1):c+(s.brushsize-1); 0198 ind = find(clist < s.mossize(2)); 0199 clist = clist(ind); 0200 0201 %fprintf('%d %d %g %d\n',r,c,s.base(r,c),s.mask(r,c)); 0202 0203 for r = rlist, 0204 for c = clist, 0205 switch(s.editmode) 0206 case 1, s.overlay(r,c) = 1; 0207 case 2, s.overlay(r,c) = 0; 0208 case 3, s.overlay(r,c) = ~s.overlay(r,c); 0209 end 0210 end 0211 end 0212 0213 %% so the overlay is a matrix of ones and zeros, ones where the 0214 %% there is an selected voxel. The first line sets all of the 0215 %% selected voxels in the base to zero. The second line 0216 %% then adds the overlay, multiplied by a scaling factor, so that 0217 %% the colormap works out. 0218 s.displayimg = s.base .* (~s.overlay); 0219 s.displayimg = s.displayimg + (s.ncmap) * s.overlay; 0220 0221 s.nmarked = length(find(s.overlay==1)); 0222 0223 s.saveneeded = 1; 0224 s.mousedown = 1; 0225 redraw = 1; 0226 0227 case {'wbu'} % -------Window Button Up ------------ % 0228 %fprintf('Button Up\n'); 0229 s.mousedown = 0; 0230 0231 case {'kbd'} %----------- Keyboard -------------% 0232 c = get(s.hfig,'CurrentCharacter'); 0233 switch(c) 0234 case {'b'}, 0235 s.brushsize = s.brushsize + 1; 0236 if(s.brushsize > 8) s.brushsize = 1; end 0237 tmp = 2*(s.brushsize-1) + 1; 0238 fprintf('Brush Size: %d x %d\n',tmp,tmp); 0239 fprintf('\n'); 0240 set(gcf,'UserData',s); 0241 return; 0242 case {'h'}, 0243 fprintf('\n'); 0244 printhelp; 0245 fprintf('\n'); 0246 printstate(s); 0247 fprintf('\n'); 0248 case {'a'}, 0249 s.overlay = s.mask; 0250 s.displayimg = s.base .* (~s.overlay); 0251 s.displayimg = s.displayimg + (s.ncmap) * s.overlay; 0252 fprintf('All voxels marked\n'); 0253 fprintf('\n'); 0254 redraw = 1; 0255 case {'i'}, 0256 s.overlay = computeIntersection(s.overlay, s.mask); 0257 s.displayimg = s.base .* (~s.overlay); 0258 s.displayimg = s.displayimg + (s.ncmap) * s.overlay; 0259 fprintf('Computed intersection of overlay and mask\n'); 0260 fprintf('\n'); 0261 redraw = 1; 0262 case {'c'}, 0263 s.overlay = zeros(size(s.base)); 0264 s.displayimg = s.base .* (~s.overlay); 0265 s.displayimg = s.displayimg + (s.ncmap) * s.overlay; 0266 fprintf('All voxels cleared\n'); 0267 fprintf('\n'); 0268 redraw = 1; 0269 case {'e'}, 0270 title = 'Examine a particular slice'; 0271 prompt = {'Slice number:'}; 0272 lines = 1; 0273 def = {'1'}; 0274 answer = inputdlg(prompt,title,lines,def); 0275 0276 %% if we actually have a slice number 0277 if (~isempty(answer)) 0278 s.sliceNum = sscanf(answer{1},'%d'); 0279 if ((s.sliceNum <= 0) | (s.sliceNum > s.volsize(:,1))) 0280 msg = sprintf('Please enter a valid slice'); 0281 errordlg(msg); 0282 end 0283 0284 %% save mosaics 0285 s.originalbase = s.base; 0286 s.originaloverlay = s.overlay; 0287 s.originalmask = s.mask; 0288 fprintf('setting display to slice %d\n',s.sliceNum); 0289 fprintf('\n'); 0290 0291 %% convert to volumes 0292 tmpbase = mos2vol(s.originalbase,[s.volsize(2) s.volsize(3) s.volsize(1)]); 0293 tmpoverlay = mos2vol(s.originaloverlay,[s.volsize(2) s.volsize(3) s.volsize(1)]); 0294 tmpmask = mos2vol(s.originalmask,[s.volsize(2) s.volsize(3) s.volsize(1)]); 0295 tmpbase = permute(tmpbase,[3 1 2]); 0296 tmpoverlay = permute(tmpoverlay,[3 1 2]); 0297 tmpmask = permute(tmpmask,[3 1 2]); 0298 0299 %% get the current slice 0300 s.base = squeeze(tmpbase(s.sliceNum,:,:)); 0301 s.overlay = squeeze(tmpoverlay(s.sliceNum,:,:)); 0302 s.mask = squeeze(tmpmask(s.sliceNum,:,:)); 0303 0304 %% setup the new display image 0305 s.displayimg = s.base .* (~s.overlay); 0306 s.displayimg = s.displayimg + (s.ncmap) * s.overlay; 0307 0308 %% display the new image 0309 s.himage = image(s.displayimg); 0310 set(s.himage,'EraseMode','none'); 0311 axis image; 0312 s.hfig = gcf; 0313 s.haxis = gca; 0314 colormap(s.cmap); 0315 set(s.himage,'CData',s.displayimg); 0316 set(gcf,'UserData',s); 0317 redraw = 1; 0318 return; 0319 end 0320 case {'r'}, 0321 fprintf('returning to mosaic view...\n'); 0322 0323 %% return to a mosaic view 0324 s.base = s.originalbase; 0325 s.mask = s.originalmask; 0326 0327 %% mosaic to volume trickery 0328 tmpoverlay = mos2vol(s.originaloverlay,[s.volsize(2) s.volsize(3) s.volsize(1)]); 0329 tmpoverlay = permute(tmpoverlay,[3 1 2]); 0330 tmpoverlay(s.sliceNum,:,:) = s.overlay; 0331 s.overlay = vol2mos(permute(tmpoverlay,[2 3 1])); 0332 0333 %% setup the mosaic display image 0334 s.displayimg = s.base .* (~s.overlay); 0335 s.displayimg = s.displayimg + (s.ncmap) * s.overlay; 0336 0337 %% display the new image 0338 s.himage = image(s.displayimg); 0339 set(s.himage,'EraseMode','none'); 0340 axis image; 0341 s.hfig = gcf; 0342 s.haxis = gca; 0343 colormap(s.cmap); 0344 set(s.himage,'CData',s.displayimg); 0345 set(gcf,'UserData',s); 0346 s.sliceNum = 0; 0347 redraw = 1; 0348 return; 0349 case {'m'}, 0350 s.editmode = s.editmode + 1; 0351 if(s.editmode > 3) s.editmode = 0; end 0352 fprintf('Mode: %s\n',modename(s.editmode)); 0353 fprintf('\n'); 0354 case {'q'}, 0355 if(s.saveneeded) 0356 resp = questdlg('Changes pending. Do you want to quit?',... 0357 'Quit?','Quit','No','No'); 0358 if(strcmp(resp,'No')) return; end 0359 end 0360 close(s.hfig); 0361 r = 0; 0362 return; 0363 case {'s'}, 0364 %% we only can save when in mosaic view; probably could remove this 0365 %% restriction, but right now, more important things to do 0366 %%if (s.sliceNum) 0367 %% fprintf('Must switch to mosaic view (\"r\") in order to save your ROI.\n'); 0368 %% return; 0369 %%end 0370 0371 if(isempty(s.outmaskid)) 0372 curdir = pwd; 0373 cd(s.savedir); 0374 [fname pname] = uiputfile('*.roi', 'Save Mask'); 0375 cd(curdir); 0376 if(fname ~= 0) 0377 if(isempty(pname)) ud.savedir = '.'; 0378 else ud.savedir = pname; 0379 end 0380 if (~isempty(findstr('.roi',fname))) 0381 fname = fname(1:(end-4)); 0382 end 0383 s.outmaskid = strcat(pname,fname); 0384 else return; 0385 end 0386 end 0387 tmp = mos2vol(s.overlay,[s.volsize(2) s.volsize(3) s.volsize(1)]); 0388 tmp = permute(tmp,[3 1 2]); 0389 fprintf('Saving to %s\n',[s.outmaskid '.roi']); 0390 roimtx = compactROI(tmp); 0391 output = sprintf('save %s.roi roimtx -ASCII', s.outmaskid); 0392 eval(output); 0393 fprintf('Done\n'); 0394 clear tmp; 0395 s.saveneeded = 0; 0396 s.outmaskid = ''; 0397 set(gcf,'UserData',s); 0398 return; 0399 case {'t'}, 0400 s.showbaseonly = ~ s.showbaseonly; 0401 if(s.showbaseonly) 0402 s.displayimg = s.base; 0403 else 0404 s.displayimg = s.base .* (~s.overlay); 0405 s.displayimg = s.base .* (~s.overlay) + (s.ncmap)*s.overlay; 0406 end 0407 redraw = 1; 0408 figure(s.hfig); 0409 axes(s.haxis); 0410 fprintf('\n'); 0411 case {'o'}, 0412 fprintf('finding marked overlay voxels\n'); 0413 fprintf('\n'); 0414 case {'v'}, 0415 fprintf('\n'); 0416 fprintf('\n'); 0417 printstate(s); 0418 fprintf('\n'); 0419 fprintf('\n'); 0420 case {'z'}, 0421 zoom; 0422 s.zoomstate = ~ s.zoomstate; 0423 set(gcf,'UserData',s); 0424 if(s.zoomstate) 0425 fprintf('Zoom is on\n'); 0426 else 0427 fprintf('Zoom is off\n'); 0428 end 0429 fprintf('\n'); 0430 return; 0431 end 0432 0433 end % --- switch(flag) ----- % 0434 0435 if(redraw) 0436 set(s.himage,'CData',s.displayimg); 0437 end 0438 0439 set(gcf,'UserData',s); 0440 0441 return; 0442 %--------------------------------------------------% 0443 %--------------------------------------------------% 0444 %--------------------------------------------------% 0445 0446 %% compute the matrix intersection 0447 function intersection = computeIntersection(A, B) 0448 if (size(A) ~= size(B)) 0449 oops(252); 0450 end 0451 0452 [numRows, numCols] = size(A); 0453 intersection = zeros(numRows, numCols); 0454 0455 for i=1:numRows 0456 for j=1:numCols 0457 if (A(i,j) == B(i,j)) 0458 intersection(i,j) = A(i,j); 0459 end 0460 end 0461 end 0462 return; 0463 0464 %--------------------------------------------------% 0465 %% Print Usage 0466 function print_usage(dummy) 0467 0468 fprintf(1,'USAGE:\n'); 0469 fprintf(1,' editmask\n'); 0470 fprintf(1,' -base base volume \n'); 0471 fprintf(1,' -inmask load this roi\n'); 0472 fprintf(1,' -overlay path to an overlay ROI to load on top of inmask\n'); 0473 fprintf(1,' -savedir set the default save directory\n'); 0474 return 0475 %--------------------------------------------------% 0476 0477 %--------------------------------------------------% 0478 %% Default data structure 0479 function s = editmask_struct 0480 s.volsize = []; 0481 s.mossize = []; 0482 s.baseid = ''; 0483 s.base = []; 0484 s.heqbase = 0; 0485 s.inmaskid = ''; 0486 s.invertinmask = 0; 0487 s.outmaskid = ''; 0488 s.savedir = ''; 0489 s.overlayid = ''; 0490 s.overlay = []; 0491 s.mask = []; 0492 s.overlay = []; 0493 s.baseframe = 0; 0494 s.hfig = []; 0495 s.haxis = []; 0496 s.himage = []; 0497 s.ncmap = 64; 0498 s.displayimg = []; 0499 s.segbase = 0; 0500 s.segthresh = .75; 0501 s.cp = [1 1]; % current point [r c] 0502 s.zoomstate = 0; 0503 s.brushsize = 2; 0504 s.mousedown = 0; 0505 s.showbaseonly = 0; 0506 s.savedir = '.'; 0507 s.editmode = 0; 0508 s.nmarked = 0; 0509 s.saveneeded = 0; 0510 return; 0511 0512 %--------------------------------------------------% 0513 % ----------- Parse Input Arguments ---------------% 0514 function s = parse_args(varargin) 0515 0516 fprintf(1,'Parsing Arguments \n'); 0517 s = editmask_struct; 0518 0519 inputargs = varargin{1}; 0520 ninputargs = length(inputargs); 0521 0522 narg = 1; 0523 while(narg <= ninputargs) 0524 0525 flag = deblank(inputargs{narg}); 0526 narg = narg + 1; 0527 %fprintf(1,'Argument: %s\n',flag); 0528 if(~isstr(flag)) 0529 flag 0530 fprintf(1,'ERROR: All Arguments must be a string\n'); 0531 %%error; 0532 oops(150); 0533 end 0534 0535 switch(flag) 0536 0537 case {'-b','-base'}, 0538 arg1check(flag,narg,ninputargs); 0539 s.baseid = inputargs{narg}; 0540 narg = narg + 1; 0541 0542 case {'-inmask'}, 0543 arg1check(flag,narg,ninputargs); 0544 s.inmaskid = inputargs{narg}; 0545 narg = narg + 1; 0546 0547 case {'-savedir'}, 0548 arg1check(flag,narg,ninputargs); 0549 s.savedir = inputargs{narg}; 0550 narg = narg + 1; 0551 0552 case {'-overlay'}, 0553 arg1check(flag, narg, ninputargs); 0554 s.overlayid = inputargs{narg}; 0555 narg = narg + 1; 0556 0557 case '-verbose', 0558 s.verbose = 1; 0559 0560 case {'-debug','-echo','-init'}, % ignore 0561 0562 otherwise 0563 fprintf(2,'ERROR: Flag %s unrecognized\n',flag); 0564 s = []; 0565 return; 0566 0567 end % --- switch(flag) ----- % 0568 0569 end % while(narg <= ninputargs) 0570 0571 return; 0572 %--------------------------------------------------% 0573 0574 %--------------------------------------------------% 0575 %% Check that there is at least one more argument %% 0576 function arg1check(flag,nflag,nmax) 0577 if(nflag>nmax) 0578 fprintf(1,'ERROR: Flag %s needs one argument',flag); 0579 oops(151); 0580 end 0581 return; 0582 0583 %--------------------------------------------------% 0584 %% Check argument consistency, etc %%% 0585 function s = check_params(s) 0586 %fprintf(1,'Checking Parameters\n'); 0587 0588 if( isempty(s.baseid) ) 0589 fprintf(2,'ERROR: No base volumes specified\n'); 0590 s=[]; return; 0591 end 0592 return; 0593 0594 %--------------------------------------------------% 0595 function name = modename(modeno) 0596 switch(modeno) 0597 case 0, name = 'No Edit'; 0598 case 1, name = 'Set'; 0599 case 2, name = 'Unset'; 0600 case 3, name = 'Toggle'; 0601 end 0602 return 0603 0604 %--------------------------------------------------% 0605 function printstate(s) 0606 s.nmarked = length(find(s.overlay==1)); 0607 tmp = 2*(s.brushsize-1) + 1; 0608 fprintf('Base Volume: %s\n',s.baseid); 0609 fprintf('Input Mask Volume: %s\n',s.inmaskid); 0610 fprintf('Output Mask Volume: %s\n',s.outmaskid); 0611 fprintf('Total number of voxels: %d\n',prod(s.volsize)); 0612 fprintf('Number of voxels marked: %d\n',s.nmarked); 0613 fprintf('Brush Size: %d x %d\n',tmp,tmp); 0614 fprintf('Edit Mode: %s\n',modename(s.editmode)); 0615 if(s.saveneeded) 0616 fprintf('Changes Pending\n'); 0617 else 0618 fprintf('No Changes Pending\n'); 0619 end 0620 return; 0621 0622 %--------------------------------------------------% 0623 function printhelp 0624 fprintf('a - select all voxels\n'); 0625 fprintf('c - clear all voxels\n'); 0626 fprintf('e - examine a particular slice\n'); 0627 fprintf('r - return to mosaic view\n'); 0628 fprintf('i - compute the intersection of the underlying mask and the overlay\n'); 0629 fprintf('b - change brush size (1x1,3x3,5x5,7x7,9x9,11x11,13x13,...)\n'); 0630 fprintf('h - print help (this message)\n'); 0631 fprintf('m - change edit mode\n'); 0632 fprintf(' No Edit - button down does nothing\n'); 0633 fprintf(' Set - button down turns on mask at voxel\n'); 0634 fprintf(' Unset - button down turns off mask at voxel\n'); 0635 fprintf(' Toggle - button down toggels mask at voxel\n'); 0636 fprintf('q - quit/exit\n'); 0637 fprintf('s - save mask\n'); 0638 fprintf('t - toggle mask on and off\n'); 0639 fprintf('v - print the current state\n'); 0640 fprintf('z - toggle zoom state. When zoom is on, use left\n'); 0641 fprintf(' button to zoom in and right to zoom out\n'); 0642 return;