how can cropped subvolume containing all voxels that have intensity in the interval [-100,200]HU from 3D ct images
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alaa shamasneh
on 4 Aug 2016
Commented: Walter Roberson
on 4 Aug 2016
how can crooped subvolume containing all voxels that have intensity in the interval [-100,200]HU from 3D ct images
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Accepted Answer
Walter Roberson
on 4 Aug 2016
mask = YourVoxels >= -100 & YourVoxels <= 200;
any1 = any(mask,1);
any12 = any(any1, 2);
start_pane = find( any12, 1, 'first');
end_pane = find( any12, 1, 'last');
any13 = any(any1, 3);
start_col = find( any13, 1, 'first');
end_col = find( any13, 1, 'last');
any23 = any(any( mask, 2), 3);
start_row = find( any23, 1, 'first');
end_row = find( any23, 1, 'last');
sub_volume = YourVoxels(start_row : end_row, start_col : end_col, start_pane : end_pane );
Alternately,
mask = YourVoxels >= -100 & YourVoxels <= 200;
rinfo = regionprops( double(mask), 'BoundingBox');
bb = rinfo.BoundingBox;
sub_volume = YourVoxels(bb(1) : bb(1) + bb(4) - 1, bb(2) : bb(2) + bb(5) - 1, bb(3) : bb(3) + bb(6) - 1);
Or if you want that more verbosely:
mask = YourVoxels >= -100 & YourVoxels <= 200;
rinfo = regionprops( double(mask), 'BoundingBox');
bb = rinfo.BoundingBox;
start_row = bb(1);
end_row = bb(1) + bb(4) - 1;
start_col = bb(2);
end_col = bb(2) + bb(5) - 1;
start_pane = bb(3);
end_pane = bb(3) + bb(6) - 1;
sub_volume = YourVoxels(start_row : end_row, start_col : end_col, start_pane : end_pane );
2 Comments
Walter Roberson
on 4 Aug 2016
My first version works without changes.
The second version should be
mask = YourVoxels >= -100 & YourVoxels <= 200;
rinfo = regionprops( double(mask), 'BoundingBox');
bb = ceil(rinfo.BoundingBox);
sub_volume = YourVoxels(bb(2) : bb(2) + bb(5) - 1, bb(1) : bb(1) + bb(4) - 1, bb(3) : bb(3) + bb(6) - 1);
The image you posted is not a 3D CT image: it is a 2D slice of a CT image that has had its values shifted and scaled, and then it has been blurred (by saving as JPEG.) The YourVoxels array that you should be using is the data that you get from dicomread()
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