1 % MarsBaR batch script to make ROIs
   2 % See http://marsbar.sourceforge.net
   3 %Adapted by J Grahn
   4 
   5  root_dir = '/imaging/jessica/Beat/';
   6 
   7 % Directory to store (and load) ROI files
   8 roi_dir = fullfile(root_dir, 'RFX/ROIs');
   9 
  10 % MarsBaR version check
  11 if isempty(which('marsbar'))
  12   error('Need MarsBaR on the path');
  13 end
  14 v = str2num(marsbar('ver'));
  15 if v < 0.35
  16   error('Batch script only works for MarsBaR >= 0.35');
  17 end
  18 marsbar('on');  % needed to set paths etc
  19 
  20 % Set up the SPM defaults, just in case
  21 spm('defaults', 'fmri');
  22 %Optional: this is a list of coordinates from which Marsbar will make
  23 %sphere ROIs. You can specify details of each ROI separately instead of
  24 %using a list like this (look at commented out script below the for:end
  25 %loop.
  26 sphere_centres = {[-6;6;54]
  27 [6;3;63]
  28 [6;15;48]
  29 [-45;-3;45]
  30 [-42;3;27]
  31 [-39;-24;51]
  32 [-48;-42;21]
  33 [48;6;24]
  34 [54;0;45]
  35 [54;12;15]
  36 [66;-36;15]
  37 [66;-24;3]
  38 [51;-24;3]
  39 [30;24;0]
  40 [30;-57;-27]
  41 [42;-66;-27]
  42 [42;-39;45]
  43 [36;-45;45]
  44 [-24;-69;-51]
  45 [-27;-60;-27]
  46 [33;-87;-6]
  47 [24;-90;-6]
  48 [-24;-93;-3]
  49 [24;-66;-51]
  50 [33;-60;-51]
  51 [39;36;27]
  52 [18;6;-3]
  53 [-54;-21;3]
  54 [-6;-18;-3]
  55 [-36;30;21]
  56 [-36;-60;-9]}
  57 %Make sphere ROIs from list given above.
  58 for x = 1:size(sphere_centres)
  59 area =['roi' ]
  60 sphere_centre = sphere_centres{x}'
  61 sphere_radius = 5
  62 sphere_roi = maroi_sphere(struct('centre', sphere_centre, 'radius', sphere_radius));
  63 % Give it a name
  64 details = [area int2str(sphere_centre) int2str(sphere_radius)]
  65 details = details(details ~= ' ')
  66 roitosave = label(sphere_roi, details)
  67 % save ROI to MarsBaR ROI file, in current directory
  68 detailsmat = [details, '_roi.mat']
  69 saveroi(roitosave, fullfile(roi_dir,detailsmat ));
  70 % also Save as image that can be viewed in MRIcroN
  71 detailsimg = [details, '_roi.nii']
  72 save_as_image(roitosave, detailsimg);
  73 end
  74 %*********************************************
  75 %if instead you need to make a bunch of different types of ROIs, comment
  76 %out the entire for end loop above, and use this part of the script instead.
  77 %%See maroi_box and maroi_img (in marsbar directory) for other types of ROIs
  78 
  79 
  80 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
  81 %%THIS SECTION NAMES ROIS AS THEIR COORDINATES AND RADII
  82 
  83 % %Make sphere ROI
  84 % area = 'SMA_10sph'
  85 % sphere_centre = [-8 2 72];
  86 % sphere_radius = 10
  87 % sphere_roi = maroi_sphere(struct('centre', sphere_centre, 'radius', sphere_radius));
  88 % % Give it a name
  89 % details = [area int2str(sphere_centre) int2str(sphere_radius)]
  90 % details = details(details ~= ' ')
  91 % roitosave = label(sphere_roi, details)
  92 % % save ROI to MarsBaR ROI file, in current directory, just to show how
  93 % detailsmat = [details, '_roi.mat']
  94 % saveroi(roitosave, fullfile(roi_dir,detailsmat ));
  95 % % Save as image
  96 % detailsimg = [details, '_roi.nii']
  97 % save_as_image(roitosave, detailsimg);
  98 % 
  99 % 
 100 % %Make sphere ROI
 101 % area = 'LIFG_5sph'
 102 % sphere_centre = [-52 13 14];
 103 % sphere_radius = 5
 104 % sphere_roi = maroi_sphere(struct('centre', sphere_centre, 'radius', sphere_radius));
 105 % % Give it a name
 106 % details = [area int2str(sphere_centre) int2str(sphere_radius)]
 107 % details = details(details ~= ' ')
 108 % roitosave = label(sphere_roi, details)
 109 % % save ROI to MarsBaR ROI file, in current directory, just to show how
 110 % detailsmat = [details, '_roi.mat']
 111 % saveroi(roitosave, fullfile(roi_dir,detailsmat ));
 112 % % Save as image
 113 % detailsimg = [details, '_roi.nii']
 114 % save_as_image(roitosave, detailsimg);
 115 
 116 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 117 % %THIS SECTION NAMES ROIS BY HAND, AND STORES THEM SO THEY CAN BE COMBINED
 118 % 
 119 % %Make sphere ROI
 120 % sphere_centre = [-6 -4 66];
 121 % sphere_radius = 4
 122 % sphere_roi = maroi_sphere(struct('centre', sphere_centre, 'radius', sphere_radius));;
 123 % % Give it a name
 124 % roitosave = label(sphere_roi, 'LSMAsphere_4mm_highres_-6_-4_66')
 125 % LSMAroi = roitosave
 126 % % save ROI to MarsBaR ROI file, in current directory, just to show how
 127 % saveroi(roitosave, fullfile(roi_dir, 'LSMAsphere_4mm_highres_-6_-4_66_roi.mat'));
 128 % 
 129 % % Save as image
 130 % save_as_image(roitosave, 'LSMAsphere_4mm_highres_-6_-4_66_roi.nii');
 131 % 
 132 % %Make sphere ROI
 133 % sphere_centre = [6 0 66];
 134 % sphere_radius = 4
 135 % sphere_roi = maroi_sphere(struct('centre', sphere_centre, 'radius', sphere_radius));;
 136 % % Give it a name
 137 % roitosave = label(sphere_roi, 'RSMAsphere_4mm_highres_6_0_66')
 138 % RSMAroi = roitosave
 139 % % save ROI to MarsBaR ROI file, in current directory, just to show how
 140 % saveroi(roitosave, fullfile(roi_dir, 'RSMAsphere_4mm_highres_6_0_66_roi.mat'));
 141 % 
 142 % % Save as image
 143 % save_as_image(roitosave, 'RSMAsphere_4mm_highres_6_0_66_roi.nii');
 144 
 145 %THIS COMBINES ALL NAMED ROIS SPECIFIED ABOVE INTO 1 BIG ROI
 146 
 147 % All_rois = RSMAroi + LSMAroi;
 148 % % Give it a name
 149 % All_rois = label(All_rois, 'RSMA+LSMA_4mmhighres_roi');
 150 % 
 151 % % save ROI to MarsBaR ROI file, in current directory
 152 % saveroi(All_rois, fullfile(roi_dir, 'RLSMA_4mmhighres_roi.mat'));
 153 % 
 154 % % Save as image
 155 % save_as_image(All_rois, RLSMA_4mmhighres_roi.nii');