There is a plugin for spm_orthviews to do just that. An earlier version is
available via the SPM extensions page, attached is a more recent code with
some additional features.
Just place the m file in a subdirectory called spm_orthviews of your SPM2
distribution and display images using the CheckReg button - then an entry
called ROI tool will appear in the context menu of each displayed section.
The individual options are explained briefly in the help text of the code.
Hope this helps,
Volkmar
On Tue, 14 Dec 2004, Rich Hammett wrote:
> What tools do SPM users use to draw/select anatomical ROIs?
>
> --
> rich hammett SSCC/DIRP/NIMH
> National Institutes of Health
> Building 10, Room 1D80
> 10 Center Drive, MSC1148
> Bethesda, MD 20892-1148
> ph 301-402-8416 fax 301-402-1370
>
--
Volkmar Glauche
-
Department of Neurology E-Mail [log in to unmask]
UKE Hamburg Phone 49(0)40-42803-5781
Martinistr. 52 Fax 49(0)40-42803-9955
20246 Hamburg
function ret = spm_ov_roi(varargin)
% ROI tool - plugin for spm_orthviews
%
% With ROI tool it is possible to create new or modify existing mask images
% interactively. ROI tool can be launched via the spm_orthviews image
% context menu.
% While ROI tool is active, mouse buttons have the following functions:
% left Reposition crosshairs
% middle Perform ROI tool box selection according to selected edit mode at
% crosshair position
% right context menu
% Menu options and prompts explained:
% Launch Initialise ROI tool in current image
% 'Load existing ROI image? (yes/no)'
% If you want to modify an existing mask image (e.g. mask.img from
% a fMRI analysis), press 'yes'. You will then be prompted to
% 'Select ROI image'
% This is the image that will be loaded as initial ROI.
% If you want to create a new ROI image, you will first be
% prompted to
% 'Select image defining ROI space'
% The image dimensions, voxel sizes and slice orientation will
% be read from this image. Thus you can edit a ROI based on a
% image with a resolution and slice orientation different from
% the underlying displayed image.
% Edit mode Operation performed when pressing the middle mouse button.
% 'Set selection'
% The selection made with the following commands will
% be included in your ROI.
% 'Clear selection'
% The selection made with the following commands will
% be excluded from your ROI.
% Box size Set size of box to be (de)selected when pressing the
% middle mouse button.
% Polygon Draw an outline on one of the 3 section images. Voxels
% within the outline will be added to the ROI. The same
% outline can be applied to a user-defined number of
% consecutive slices around the current crosshair position.
% Select connected
% Select only voxels that are connected to the voxel at
% current crosshair position through the ROI.
% Threshold You will be prompted to enter a [min max] threshold. Only
% those voxels in the ROI image where the intensities of the
% underlying image are within the [min max] range will survive
% this operation.
% Invert Invert currently defined ROI
% Clear Clear ROI, but keep ROI space information
% Save Save ROI image
% Save As Save ROI image under a new file name
% Quit Quit ROI tool
%
% This routine is a plugin to spm_orthviews for SPM2. For general help about
% spm_orthviews and plugins type
% help spm_orthviews
% at the matlab prompt.
%_____________________________________________________________________________
% $Id: spm_ov_roi.m,v 1.13 2004/11/09 11:56:53 volkmar Exp $
% Note: This plugin depends on the blobs set by spm_orthviews('addblobs',...)
% They should not be removed while ROI tool is active and no other blobs be
% added. This restriction may be removed when switching to MATLAB 6.x and
% using the 'alpha' property to overlay blobs onto images.
rev = '$Revision: 1.13 $';
global st;
if isempty(st)
error('roi: This routine can only be called as a plugin for spm_orthviews!');
end;
if nargin < 2
error('roi: Wrong number of arguments. Usage: spm_orthviews(''roi'', cmd, volhandle, varargin)');
end;
cmd = lower(varargin{1});
volhandle = varargin{2};
toset = [];
toclear = [];
tochange = [];
update_roi = 0;
switch cmd
case 'init'
spm('pointer','watch');
Vroi = spm_vol(varargin{3});
if varargin{4} % loadasroi
roi = spm_read_vols(Vroi)>0;
[x y z] = ndgrid(1:Vroi.dim(1),1:Vroi.dim(2),1:Vroi.dim(3));
xyz = [x(roi(:))'; y(roi(:))'; z(roi(:))'];
else
roi = zeros(Vroi.dim(1:3));
Vroi.fname = fileparts(Vroi.fname); % save path
Vroi.dim(4) = 4;
xyz = [];
end;
clear x y z
% draw a frame only if ROI volume different from underlying GM volume
if any(Vroi.dim(1:3)-st.vols{volhandle}.dim(1:3))| ...
any(Vroi.mat(:)-st.vols{volhandle}.mat(:))
[xx1 yx1 zx1] = ndgrid(1 , 1:Vroi.dim(2), 1:Vroi.dim(3));
[xx2 yx2 zx2] = ndgrid(Vroi.dim(1) , 1:Vroi.dim(2), 1:Vroi.dim(3));
[xy1 yy1 zy1] = ndgrid(1:Vroi.dim(1), 1 , 1:Vroi.dim(3));
[xy2 yy2 zy2] = ndgrid(1:Vroi.dim(1), Vroi.dim(2) , 1:Vroi.dim(3));
[xz1 yz1 zz1] = ndgrid(1:Vroi.dim(1), 1:Vroi.dim(2), 1);
[xz2 yz2 zz2] = ndgrid(1:Vroi.dim(1), 1:Vroi.dim(2), Vroi.dim(3));
fxyz = [xx1(:)' xx2(:)' xy1(:)' xy2(:)' xz1(:)' xz2(:)'; ...
yx1(:)' yx2(:)' yy1(:)' yy2(:)' yz1(:)' yz2(:)'; ...
zx1(:)' zx2(:)' zy1(:)' zy2(:)' zz1(:)' zz2(:)'];
clear xx1 yx1 zx1 xx2 yx2 zx2 xy1 yy1 zy1 xy2 yy2 zy2 xz1 yz1 zz1 xz2 yz2 zz2
hframe = 1;
else
hframe = [];
fxyz = [];
end;
for k=1:3
cb{k}=get(st.vols{volhandle}.ax{k}.ax,'ButtonDownFcn');
set(st.vols{volhandle}.ax{k}.ax,...
'ButtonDownFcn',...
['switch get(gcf,''SelectionType'')',...
'case ''normal'', spm_orthviews(''Reposition'');',...
'case ''extend'', spm_orthviews(''roi'',''edit'',', ...
num2str(volhandle), ');',...
'case ''alt'', spm_orthviews(''context_menu'',''ts'',1);',...
'end;']);
end;
st.vols{volhandle}.roi = struct('Vroi',Vroi, 'xyz',xyz, 'roi',roi,...
'hroi',1, 'fxyz',fxyz,...
'hframe',hframe, 'mode','set',...
'thresh',[60 140], 'box',[4 4 4],...
'cb',[], 'polyslices',1);
st.vols{volhandle}.roi.cb = cb;
if ~isempty(st.vols{volhandle}.roi.fxyz)
if isfield(st.vols{volhandle}, 'blobs')
st.vols{volhandle}.roi.hframe = prod(size(st.vols{volhandle}.blobs))+1;
end;
spm_orthviews('addcolouredblobs',volhandle, ...
st.vols{volhandle}.roi.fxyz,...
ones(size(st.vols{volhandle}.roi.fxyz,2),1), ...
st.vols{volhandle}.roi.Vroi.mat,[1 .5 .5]);
st.vols{volhandle}.blobs{st.vols{volhandle}.roi.hframe}.max=1.3;
end;
update_roi=1;
case 'edit'
spm('pointer','watch');
pos = round(inv(st.vols{volhandle}.roi.Vroi.mat)* ...
[spm_orthviews('pos'); 1]);
tmp = round((st.vols{volhandle}.roi.box-1)/2);
[sx sy sz] = meshgrid(-tmp(1):tmp(1), -tmp(2):tmp(2), -tmp(3):tmp(3));
sel = [sx(:)';sy(:)';sz(:)']+repmat(pos(1:3), 1,prod(2*tmp+1));
tochange = sel(:, (all(sel>0) &...
sel(1,:)<=st.vols{volhandle}.roi.Vroi.dim(1) & ...
sel(2,:)<=st.vols{volhandle}.roi.Vroi.dim(2) & ...
sel(3,:)<=st.vols{volhandle}.roi.Vroi.dim(3)));
update_roi = 1;
case 'poly'
% @COPYRIGHT :
% Copyright 1993,1994 Mark Wolforth and Greg Ward, McConnell
% Brain Imaging Centre, Montreal Neurological Institute, McGill
% University.
% Permission to use, copy, modify, and distribute this software
% and its documentation for any purpose and without fee is
% hereby granted, provided that the above copyright notice
% appear in all copies. The authors and McGill University make
% no representations about the suitability of this software for
% any purpose. It is provided "as is" without express or
% implied warranty.
axhandle = varargin{3};
line_color = [1 1 0];
axes(st.vols{volhandle}.ax{axhandle}.ax);
hold on;
Xlimits = get (st.vols{volhandle}.ax{axhandle}.ax,'XLim');
Ylimits = get (st.vols{volhandle}.ax{axhandle}.ax,'YLim');
XLimMode = get(st.vols{volhandle}.ax{axhandle}.ax,'XLimMode');
set(st.vols{volhandle}.ax{axhandle}.ax,'XLimMode','manual');
YLimMode = get(st.vols{volhandle}.ax{axhandle}.ax,'YLimMode');
set(st.vols{volhandle}.ax{axhandle}.ax,'YLimMode','manual');
ButtonDownFcn = get(st.vols{volhandle}.ax{axhandle}.ax,'ButtonDownFcn');
set(st.vols{volhandle}.ax{axhandle}.ax,'ButtonDownFcn','');
UIContextMenu = get(st.vols{volhandle}.ax{axhandle}.ax,'UIContextMenu');
set(st.vols{volhandle}.ax{axhandle}.ax,'UIContextMenu',[]);
set(st.vols{volhandle}.ax{axhandle}.ax,'Selected','on');
disp (['Please mark the ROI outline in the highlighted image' ...
' display.']);
disp ('Points outside the ROI image area will be clipped to');
disp ('the image boundaries.');
disp ('Left-Click on the vertices of the ROI...');
disp ('Middle-Click to finish ROI selection...');
disp ('Right-Click to cancel...');
x=Xlimits(1);
y=Ylimits(1);
i=1;
lineHandle = [];
xc = 0; yc = 0; bc = 0;
while ~isempty(bc)
[xc,yc,bc] = ginput(1);
if isempty(xc) | bc > 1
if bc == 3
x = []; y=[];
end;
if bc == 2 | bc == 3
bc = [];
break;
end;
else
if xc > Xlimits(2)
xc = Xlimits(2);
elseif xc < Xlimits(1)
xc = Xlimits(1);
end;
if yc > Ylimits(2)
yc = Ylimits(2);
elseif yc < Ylimits(1)
yc = Ylimits(1);
end;
x(i) = xc;
y(i) = yc;
i=i+1;
if ishandle(lineHandle)
delete(lineHandle);
end;
lineHandle = line (x,y,ones(1,length(x)), ...
'Color',line_color,...
'parent',st.vols{volhandle}.ax{axhandle}.ax,...
'HitTest','off');
end;
end
if ishandle(lineHandle)
delete(lineHandle);
end;
if ~isempty(x)
spm('pointer','watch');
x(i)=x(1);
y(i)=y(1);
prms=spm_imatrix(st.vols{volhandle}.roi.Vroi.mat);
% Code from spm_orthviews('redraw') for determining image
% positions
is = inv(st.Space);
cent = is(1:3,1:3)*st.centre(:) + is(1:3,4);
polyoff = [0 0 0];
switch axhandle
case 1,
M0 = [ 1 0 0 -st.bb(1,1)+1
0 1 0 -st.bb(1,2)+1
0 0 1 -cent(3)
0 0 0 1];
polyoff(3) = st.vols{volhandle}.roi.polyslices/2;
polythick = prms(9);
case 2,
M0 = [ 1 0 0 -st.bb(1,1)+1
0 0 1 -st.bb(1,3)+1
0 1 0 -cent(2)
0 0 0 1];
polyoff(2) = st.vols{volhandle}.roi.polyslices/2;
polythick = prms(8);
case 3,
if st.mode ==0,
M0 = [ 0 0 1 -st.bb(1,3)+1
0 1 0 -st.bb(1,2)+1
1 0 0 -cent(1)
0 0 0 1];
else,
M0 = [ 0 -1 0 +st.bb(2,2)+1
0 0 1 -st.bb(1,3)+1
1 0 0 -cent(1)
0 0 0 1];
end;
polyoff(1) = st.vols{volhandle}.roi.polyslices/2;
polythick = abs(prms(7));
end;
polvx = inv(st.vols{volhandle}.roi.Vroi.mat)*st.Space*inv(M0)*...
[x(:)';y(:)'; zeros(size(x(:)')); ones(size(x(:)'))];
% Bounding volume for polygon in ROI voxel space
[xbox ybox zbox] = ndgrid(max(min(floor(polvx(1,:)))-polyoff(1),1):...
min(max(ceil(polvx(1,:)))+polyoff(1),...
st.vols{volhandle}.roi.Vroi.dim(1)),...
max(min(floor(polvx(2,:)))-polyoff(2),1):...
min(max(ceil(polvx(2,:)))+polyoff(2),...
st.vols{volhandle}.roi.Vroi.dim(2)),...
max(min(floor(polvx(3,:)))-polyoff(3),1):...
min(max(ceil(polvx(3,:)))+polyoff(3),...
st.vols{volhandle}.roi.Vroi.dim(3)));
% re-transform in polygon plane
xyzbox = M0*is*st.vols{volhandle}.roi.Vroi.mat*[xbox(:)';ybox(:)';zbox(:)';...
ones(size(xbox(:)'))];
xyzbox = xyzbox(:,abs(xyzbox(3,:))<=.6*polythick*...
st.vols{volhandle}.roi.polyslices); % nearest neighbour to polygon
sel = logical(inpolygon(xyzbox(1,:),xyzbox(2,:),x,y));
xyz = inv(st.vols{volhandle}.roi.Vroi.mat)*st.Space*inv(M0)*xyzbox(:,sel);
if ~isempty(xyz)
tochange = round(xyz(1:3,:));
update_roi = 1;
end;
end;
set(st.vols{volhandle}.ax{axhandle}.ax,...
'Selected','off', 'XLimMode',XLimMode, 'YLimMode',YLimMode,...
'ButtonDownFcn',ButtonDownFcn, 'UIContextMenu',UIContextMenu);
case 'thresh'
spm('pointer','watch');
rind = find(st.vols{volhandle}.roi.roi);
[x y z]=ind2sub(st.vols{volhandle}.roi.Vroi.dim(1:3),rind);
tmp = round(inv(st.vols{volhandle}.mat) * ...
st.vols{volhandle}.roi.Vroi.mat*[x'; y'; z'; ones(size(x'))]);
dat = spm_sample_vol(st.vols{volhandle}, ...
tmp(1,:), tmp(2,:), tmp(3,:), 0);
sel = ~((st.vols{volhandle}.roi.thresh(1) < dat) & ...
(dat < st.vols{volhandle}.roi.thresh(2)));
toclear = [x(sel)'; y(sel)'; z(sel)'];
update_roi = 1;
case 'connect'
spm('pointer','watch');
pos = round(inv(st.vols{volhandle}.roi.Vroi.mat)* ...
[spm_orthviews('pos'); 1]);
pos = pos(1:3);
noconn = st.vols{volhandle}.roi.xyz;
conn = zeros(size(st.vols{volhandle}.roi.xyz));
curset = 1;
vis = zeros(size(st.vols{volhandle}.roi.roi));
pstck = stack('init',size(st.vols{volhandle}.roi.xyz,2));
nbhood = [ -1 1 0 0 0 0; ...
0 0 -1 1 0 0; ...
0 0 0 0 -1 1];
if st.vols{volhandle}.roi.roi(pos(1),pos(2),pos(3))
conn(:,curset) = pos;
curset = curset+1;
vis(pos(1),pos(2),pos(3)) = 1;
for k = 1:size(nbhood,2)
cpos = pos + nbhood(:,k);
if st.vols{volhandle}.roi.roi(cpos(1), cpos(2), cpos(3)) & ...
~vis(cpos(1), cpos(2), cpos(3)) & all(cpos>0) & all(cpos<=st.vols{volhandle}.dim(1:3)')
pstck=stack('push',pstck,cpos);
vis(cpos(1), cpos(2), cpos(3)) = 1;
end;
end;
while ~stack('isempty',pstck)
[pstck pos] = stack('pop', pstck);
conn(:,curset) = pos;
curset = curset+1;
vis(pos(1),pos(2),pos(3)) = 1;
for k = 1:size(nbhood,2)
cpos = pos + nbhood(:,k);
if all(cpos>0) & all(cpos<=st.vols{volhandle}.dim(1:3)') & ...
st.vols{volhandle}.roi.roi(cpos(1), cpos(2), cpos(3)) & ...
~vis(cpos(1), cpos(2), cpos(3))
pstck = stack('push',pstck,cpos);
vis(cpos(1), cpos(2), cpos(3)) = 1;
end;
end;
end;
end;
conn = conn(:,1:curset-1);
if strcmp(st.vols{volhandle}.roi.mode,'set')
toset = conn;
toclear = noconn;
else
toclear = conn;
end;
update_roi = 1;
case 'invert'
spm('pointer','watch');
toclear = st.vols{volhandle}.roi.xyz;
[x y z] = ndgrid(1:st.vols{volhandle}.roi.Vroi.dim(1),...
1:st.vols{volhandle}.roi.Vroi.dim(2),...
1:st.vols{volhandle}.roi.Vroi.dim(3));
if ~isempty(toclear)
toset = setdiff([x(:)'; y(:)'; z(:)']', toclear', 'rows')';
else
toset = [x(:)'; y(:)'; z(:)'];
end;
update_roi = 1;
clear x y z;
case 'clear'
spm('pointer','watch');
st.vols{volhandle}.roi.roi = zeros(size(st.vols{volhandle}.roi.roi));
st.vols{volhandle}.roi.xyz=[];
update_roi = 1;
case {'save','saveas'}
if strcmp(cmd,'saveas') | ...
exist(st.vols{volhandle}.roi.Vroi.fname)==7
st.vols{volhandle}.roi.Vroi.fname = spm_input(...
'ROI filename','!+1','s', ...
st.vols{volhandle}.roi.Vroi.fname);
end;
spm('pointer','watch');
spm_write_vol(st.vols{volhandle}.roi.Vroi, ...
st.vols{volhandle}.roi.roi);
spm('pointer','arrow');
return;
case 'redraw'
% do nothing
return;
%-------------------------------------------------------------------------
% Context menu and callbacks
case 'context_menu'
item0 = uimenu(varargin{3}, 'Label', 'ROI tool');
item1 = uimenu(item0, 'Label', 'Launch', 'Callback', ...
['feval(''spm_ov_roi'',''context_init'', ', ...
num2str(volhandle), ');'], 'Tag', ['ROI_0_', num2str(volhandle)]);
item2 = uimenu(item0, 'Label', 'Edit mode', ...
'Visible', 'off', 'Tag', ['ROI_1_', num2str(volhandle)]);
item2_1a = uimenu(item2, 'Label', 'Set selection', 'Callback', ...
['feval(''spm_ov_roi'',''context_edit'',', ...
num2str(volhandle), ',''set'');'], ...
'Tag', ['ROI_EDIT_', num2str(volhandle)], 'Checked','on');
item2_1b = uimenu(item2, 'Label', 'Clear selection', 'Callback', ...
['feval(''spm_ov_roi'',''context_edit'',', ...
num2str(volhandle), ',''clear'');'], ...
'Tag', ['ROI_EDIT_', num2str(volhandle)]);
item3 = uimenu(item0, 'Label', 'Box size', 'Callback', ...
['feval(''spm_ov_roi'',''context_box'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
item3 = uimenu(item0, 'Label', 'Polygon', 'Callback', ...
['feval(''spm_ov_roi'',''context_poly'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
item4 = uimenu(item0, 'Label', 'Threshold', 'Callback', ...
['feval(''spm_ov_roi'',''context_thresh'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
item5 = uimenu(item0, 'Label', 'Connected cluster', 'Callback', ...
['feval(''spm_ov_roi'',''connect'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
item6 = uimenu(item0, 'Label', 'Invert', 'Callback', ...
['feval(''spm_ov_roi'',''invert'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
item7 = uimenu(item0, 'Label', 'Clear', 'Callback', ...
['feval(''spm_ov_roi'',''clear'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
item8 = uimenu(item0, 'Label', 'Save', 'Callback', ...
['feval(''spm_ov_roi'',''save'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
item8 = uimenu(item0, 'Label', 'Save As', 'Callback', ...
['feval(''spm_ov_roi'',''saveas'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
item9 = uimenu(item0, 'Label', 'Quit', 'Callback', ...
['feval(''spm_ov_roi'',''context_quit'', ', ...
num2str(volhandle), ');'], 'Visible', 'off', ...
'Tag', ['ROI_1_', num2str(volhandle)]);
return;
case 'context_init'
Finter = spm_figure('FindWin', 'Interactive');
spm_input('!DeleteInputObj',Finter);
usefile = spm_input('Load existing ROI image?','!+1','b','yes|no',[1 0],1);
if usefile
imfname = spm_get(1, '*IMAGE', 'Select ROI image');
loadasroi = 1;
else
imfname = spm_get(1, '*IMAGE', 'Select image defining ROI space');
[p n e v] = fileparts(imfname);
loadasroi = 0;
end;
feval('spm_ov_roi','init',volhandle,imfname,loadasroi);
obj = findobj(0, 'Tag', ['ROI_1_', num2str(volhandle)]);
set(obj, 'Visible', 'on');
obj = findobj(0, 'Tag', ['ROI_0_', num2str(volhandle)]);
set(obj, 'Visible', 'off');
spm_input('!DeleteInputObj',Finter);
return;
case 'context_edit'
st.vols{volhandle}.roi.mode = varargin{3};
obj = findobj(0, 'Tag', ['ROI_EDIT_', num2str(volhandle)]);
set(obj, 'Checked', 'off');
set(gcbo, 'Checked', 'on');
return;
case 'context_box'
Finter = spm_figure('FindWin', 'Interactive');
spm_input('!DeleteInputObj',Finter);
box = spm_input('Selection size {vx vy vz}','!+1','e', ...
num2str(st.vols{volhandle}.roi.box), [1 3]);
spm_input('!DeleteInputObj',Finter);
st.vols{volhandle}.roi.box = box;
return;
case 'context_poly',
for k = 1:3
if st.vols{volhandle}.ax{k}.ax == gca
axhandle = k;
break;
end;
end;
Finter = spm_figure('FindWin', 'Interactive');
spm_input('!DeleteInputObj',Finter);
st.vols{volhandle}.roi.polyslices = spm_input('#slices around current slice','!+1','e', ...
num2str(st.vols{volhandle}.roi.polyslices));
spm_input('!DeleteInputObj',Finter);
feval('spm_ov_roi', 'poly', volhandle, axhandle);
return;
case 'context_thresh'
Finter = spm_figure('FindWin', 'Interactive');
spm_input('!DeleteInputObj',Finter);
thresh = spm_input('Threshold {min max}','!+1','e', ...
num2str(st.vols{volhandle}.roi.thresh), [1 2]);
spm_input('!DeleteInputObj',Finter);
st.vols{volhandle}.roi.thresh = thresh;
feval('spm_ov_roi', 'thresh', volhandle);
return;
case 'context_quit'
obj = findobj(0, 'Tag', ['ROI_1_', num2str(volhandle)]);
set(obj, 'Visible', 'off');
obj = findobj(0, 'Tag', ['ROI_0_', num2str(volhandle)]);
set(obj, 'Visible', 'on');
spm_orthviews('rmblobs', volhandle);
for k=1:3
set(st.vols{volhandle}.ax{k}.ax,'ButtonDownFcn', st.vols{volhandle}.roi.cb{k});
end;
st.vols{volhandle} = rmfield(st.vols{volhandle}, 'roi');
spm_orthviews('redraw');
return;
otherwise
fprintf('spm_orthviews(''roi'', ...): Unknown action %s', cmd);
return;
end;
if update_roi
if ~isempty(tochange) % change state according to mode
if strcmp(st.vols{volhandle}.roi.mode,'set')
toset = tochange;
else
toclear = tochange;
end;
end;
% clear first, then set (needed for connect operation)
if ~isempty(toclear)
itoclear = sub2ind(st.vols{volhandle}.roi.Vroi.dim(1:3), ...
toclear(1,:), toclear(2,:), toclear(3,:));
st.vols{volhandle}.roi.roi(itoclear) = 0;
if ~isempty(st.vols{volhandle}.roi.xyz)
st.vols{volhandle}.roi.xyz = setdiff(st.vols{volhandle}.roi.xyz',toclear','rows')';
else
st.vols{volhandle}.roi.xyz = [];
end;
end;
if ~isempty(toset)
% why do we need this round()?? I don't know, but Matlab thinks
% it is necessary
itoset = round(sub2ind(st.vols{volhandle}.roi.Vroi.dim(1:3), ...
toset(1,:), toset(2,:), toset(3,:)));
st.vols{volhandle}.roi.roi(itoset) = 1;
if ~isempty(st.vols{volhandle}.roi.xyz)
st.vols{volhandle}.roi.xyz = union(st.vols{volhandle}.roi.xyz',toset','rows')';
else
st.vols{volhandle}.roi.xyz = toset;
end;
end;
if isfield(st.vols{volhandle}, 'blobs')
nblobs=length(st.vols{volhandle}.blobs);
if nblobs>1
blobstmp(1:st.vols{volhandle}.roi.hroi-1) = st.vols{volhandle}.blobs(1:st.vols{volhandle}.roi.hroi-1);
blobstmp(st.vols{volhandle}.roi.hroi:nblobs-1) = st.vols{volhandle}.blobs(st.vols{volhandle}.roi.hroi+1:nblobs);
st.vols{volhandle}.blobs=blobstmp;
else
if isempty(st.vols{volhandle}.roi.hframe) % save frame
st.vols{volhandle}=rmfield(st.vols{volhandle},'blobs');
end;
end;
end;
if isfield(st.vols{volhandle}, 'blobs')
st.vols{volhandle}.roi.hroi = prod(size(st.vols{volhandle}.blobs))+1;
else
st.vols{volhandle}.roi.hroi = 1;
end;
if isempty(st.vols{volhandle}.roi.xyz) % initialised with empty roi
spm_orthviews('addcolouredblobs', volhandle, ...
[1; 1; 1], 0, st.vols{volhandle}.roi.Vroi.mat,[1 3 1]);
else
spm_orthviews('addcolouredblobs', volhandle, ...
st.vols{volhandle}.roi.xyz, ones(size(st.vols{volhandle}.roi.xyz,2),1), ...
st.vols{volhandle}.roi.Vroi.mat,[1 3 1]); % use color that is more intense than standard rgb range
end;
st.vols{volhandle}.blobs{st.vols{volhandle}.roi.hroi}.max=2;
spm_orthviews('redraw');
end;
spm('pointer','arrow');
function varargout = stack(cmd, varargin)
switch cmd
case 'init'
varargout{1}.st = cell(varargin{1},1);
varargout{1}.top= 0;
case 'isempty'
varargout{1} = (varargin{1}.top==0);
case 'push'
stck = varargin{1};
if (stck.top < size(stck.st,1))
stck.top = stck.top + 1;
stck.st{stck.top} = varargin{2};
varargout{1}=stck;
else
error('Stack overflow\n');
end;
case 'pop'
if stack('isempty',varargin{1})
error('Stack underflow\n');
else
varargout{2} = varargin{1}.st{varargin{1}.top};
varargin{1}.top = varargin{1}.top - 1;
varargout{1} = varargin{1};
end;
end;
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