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
am 4 Aug. 2016
Kommentiert: Walter Roberson
am 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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Walter Roberson
am 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 Kommentare
Walter Roberson
am 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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