0001 function o = mars_build_roi
0002
0003
0004
0005
0006 o = [];
0007 [Finter,Fgraph,CmdLine] = spm('FnUIsetup','Build ROI', 0);
0008
0009
0010 optfields = {'image','voxel', 'sphere', 'box_cw', 'box_lims'};
0011 optlabs = {'Image', 'Voxel', 'Sphere',...
0012 'Box (centre,widths)', 'Box (ranges XYZ)'};
0013
0014 roitype = char(...
0015 spm_input('Type of ROI', '+1', 'm',{optlabs{:} 'Quit'},...
0016 {optfields{:} 'quit'},length(optfields)+1));
0017
0018
0019 img_flt = mars_veropts('get_img_ext');
0020
0021 d = [];
0022 switch roitype
0023 case 'image'
0024 imgname = spm_get(1, img_flt, 'Image defining ROI');
0025 [p f e] = fileparts(imgname);
0026 binf = spm_input('Maintain as binary image', '+1','b',...
0027 ['Yes|No'], [1 0],1);
0028 func = '';
0029 if spm_input('Apply function to image', '+1','b',...
0030 ['Yes|No'], [1 0],1);
0031 spm_input('img < 30',1,'d','Example function:');
0032 func = spm_input('Function to apply to image', '+1', 's', 'img');
0033 end
0034 d = f; l = f;
0035 if ~isempty(func)
0036 d = [d ' func: ' func];
0037 l = [l '_f_' func];
0038 end
0039 if binf
0040 d = [d ' - binarized'];
0041 l = [l '_bin'];
0042 end
0043 o = maroi_image(struct('vol', spm_vol(imgname), 'binarize',binf,...
0044 'func', func));
0045
0046
0047 o = maroi_matrix(o);
0048
0049 case 'voxel'
0050 not_donef = 1;
0051 while not_donef
0052 XYZ = spm_input('Coordinate(s)', '+1', 'e', []);
0053 if size(XYZ,1) == 1, XYZ = XYZ'; end
0054 if size(XYZ,1) ~= 3, warning('Need 3xN or Nx3 matrix');
0055 else not_donef = 0; end
0056 end
0057 v = char(spm_input('Coordinate(s) in','+1','b','mm|voxels',{'mm','vox'}, 1));
0058 spopts = {'spacebase','image'};
0059 splabs = {'Base space for ROIs','From image'};
0060 spo = spm_input('Space for voxel ROI', '+1', 'm',splabs,...
0061 spopts, 1);
0062 switch char(spo)
0063 case 'spacebase'
0064 sp = maroi('classdata', 'spacebase');
0065 case 'image'
0066 img = spm_get([0 1], img_flt, 'Image defining space');
0067 if isempty(img),return,end
0068 sp = mars_space(img);
0069 end
0070 o = maroi_pointlist(struct('XYZ', XYZ, 'mat', sp.mat), v);
0071 if size(XYZ, 2) > 1
0072 pos = c_o_m(o); coord_lbl = 'C.o.M.';
0073 else
0074 pos = XYZ; coord_lbl = 'coordinate';
0075 end
0076 d = sprintf('points; %s (%s) [%0.1f %0.1f %0.1f]',coord_lbl,v,pos);
0077 l = sprintf('points_%s_%s_%0.0f_%0.0f_%0.0f',coord_lbl,v,pos);
0078 case 'sphere'
0079 c = spm_input('Centre of sphere (mm)', '+1', 'e', [], 3);
0080 r = spm_input('Sphere radius (mm)', '+1', 'r', 10, 1);
0081 d = sprintf('%0.1fmm radius sphere at [%0.1f %0.1f %0.1f]',r,c);
0082 l = sprintf('sphere_%0.0f-%0.0f_%0.0f_%0.0f',r,c);
0083 o = maroi_sphere(struct('centre',c,'radius',r));
0084 case 'box_cw'
0085 c = spm_input('Centre of box (mm)', '+1', 'e', [], 3);
0086 w = spm_input('Widths in XYZ (mm)', '+1', 'e', [], 3);
0087 d = sprintf('[%0.1f %0.1f %0.1f] box at [%0.1f %0.1f %0.1f]',w,c);
0088 l = sprintf('box_w-%0.0f_%0.0f_%0.0f-%0.0f_%0.0f_%0.0f',w,c);
0089 o = maroi_box(struct('centre',c,'widths',w));
0090 case 'box_lims'
0091 X = sort(spm_input('Range in X (mm)', '+1', 'e', [], 2));
0092 Y = sort(spm_input('Range in Y (mm)', '+1', 'e', [], 2));
0093 Z = sort(spm_input('Range in Z (mm)', '+1', 'e', [], 2));
0094 A = [X Y Z];
0095 c = mean(A);
0096 w = diff(A);
0097 d = sprintf('box at %0.1f>X<%0.1f %0.1f>Y<%0.1f %0.1f>Z<%0.1f',A);
0098 l = sprintf('box_x_%0.0f:%0.0f_y_%0.0f:%0.0f_z_%0.0f:%0.0f',A);
0099 o = maroi_box(struct('centre',c,'widths',w));
0100 case 'quit'
0101 o = [];
0102 return
0103 otherwise
0104 error(['Strange ROI type: ' roitype]);
0105 end
0106 o = descrip(o,d);
0107 o = label(o,l);
