In this step you will use the "Snake" mode to isolate the Sub-cutaneous Adipose Tissue (SAT).
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Without SAT |
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With SAT |
/segment_goal_3a.png)
/segment_goal_3b.png)
What the script did for you:
The pixel of value TAG_1 have been changed to TAG_3.
The "Mode ALL" is enabled, showing all the slices.
The Mixer class "Fat" bypass has been activated.
The TAG labels have been modified:
The "TAG 1" is renamed "SAT".
The "TAG 2" is renamed "IMAT".
The "TAG 3" is renamed "Muscle".
The "TAG 4" is renamed "Bone".
The "Snake" mode interface is open.
The 4th brush size is pre-selected.
The TAG_1 (SAT) is made the current TAG value.
The polarity is set to "Polarity +"
The "Color Scheme" tool is open.
The color scheme is set to "Mix".
The "TAG Lock" tool is open.
The TAG 0 (none) is locked.
The TAG 3 (Muscle) is locked.
The TAG 4 (Bone) is locked.
The "Automation" tool is open. (All parameters of this tool have been set to do 10 "Snake: Propagate Up" at once.)
What to do:
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The SAT
We will re-use the snake interface, but this time we will create a conter-clockwise snake on the border between the SAT and the muscle.
•Select the first slice from the series and press the "Space Bar" to toggle in "Mode One" and display only one slice.
•Blow up the slice ("+" key) until it fit the screen .
The 4th brush is selected, the TAG_1 ("SAT") is selected and the polarity should be "Polarity +".
•Press on the "Create New Snake" button.
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/snake_create_b.png)
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•Left click on a first position on the interface between the SAT and the muscle.
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/snake_sat_1.png)
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•Continue placing points around the circomference of the muscle. The points must be placed in conterclockwhise order. Leave a gap between the last point and the first point.
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/snake_sat_2.png)
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•Click on the "Minimize Energy" button.
A snake is now created around your muscle.
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/snake_but_minimize.png){kind=small}
/snake_sat_3.png)
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•Do the same thing on the other leg on the image, using the same sequence and placing counterclockwhise points.
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/snake_sat_4.png)
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Propagate:
We can now propagate the 2 "SAT" snakes we have on the first image on the other images.
•Propagate the snake all the way up to the last frame in the series, correcting any errors in the snakes if they did not follow the oputside of the muscle. |
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/snake_propagate_1.png)
Note:
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Be careful, if there are large fat regions betwen muscle groups, the snake will have a tendency to creep inside these. You may need to manually push the snake out between propagation steps. |
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Snake to TAG:
And now we will fill the interior of these snakes with the matching TAGs. Since only the SAT and IMAT TAGs are unlocked, only the Fat content will be affected.
•Change the display mode to see all the images (Press the "spacebar"). This will select all the images, so that the next action is applied to all the slices in the series.
•Press the "Snake to TAG" button.
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/snake_but_to_tag.png)
The Interface:
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The Snakes
We already gave a description of the snake interface in "Step 4". We will re-use the snake interface, but this time we will create a conter-clockwise snake on the border between the SAT and the muscle. When you then press the "Snake to TAG" button, only the region between the clockwise and conterclockwise snake will be tagged.
You may noticed that the new snake sometime overlap the muscle, but since we protected the "Muscle" TAG, the "Bone" TAG and the "None" TAG, only the fat tissue will be affected by the snake. So even if your snake cut over the muscle, none of the segmented muscle tissue will be lost.
The "Snake to TAG" button cause the interior of the snake to be filled with the snake's TAG value. If no lock where applied, then the old TAG values outside the snakes (SAT and Bone) would revert to "none". Since we did protect "none", the old TAG values are not modified. Also, having protected the "TAG "Muscle" ensure that the muscle tissu is not afftected either.
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