how can cropped subvolume containing all voxels that have intensity in the interval [-100,200]HU from 3D ct images

how can crooped subvolume containing all voxels that have intensity in the interval [-100,200]HU from 3D ct images

Answer 1

[Walter Roberson]

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 );

[alaa shamasneh]

can you send to me the whole code from beggining cause i try to apply same code on the image above but its not working

[Walter Roberson]

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()