2D Manual Segmentation

To allow a simple manual segmentation of muscles, subcutaneous fat and visceral fat at level L3 on a CT, you will find here a simple macro for the software ImageJ

 

Download (https://fiji.sc/) and unzip Fiji

Copy the file « L3Slice_UniqueFile.txt » in the folder « macros » of Fiji.app

Launch Fiji (ImageJ-win.exe)

Install the macro (Plugins>Macros>Install…)

Launch the macro (Plugins>Macros>L3Slice_UniqueFile)

Go to the L3 level and click « OK »

To isolate the visceral adipose tissue (VAT), segment the abdominal cavity on the window L3FAT. The line pass roughly inside the muscles of the abdominal cavity and the vertebra. If needed, adapt the contrast with B&C. Then click « OK ».

To isolate the subcutaneous adipose tissue (SAT), segment the body on the window L3FAT. The line pass outside the skin and inside the arms (if present) and above the table. Then click « OK ».

To isolate the muscles, the first step is to draw a line inside the muscles wall of the abdominal cavity on the image « L3Muscles ». If needed, adapt the contrast with B&C.. Be careful to include the psoas muscle and exclude the vertebra. Then click « OK ».

The second step is to draw a line outside the muscles wall. The line pass inside the SAT, between the muscles and the skin. Then click « OK ».

Finally check the segmentation. Then click « OK ».

Surfaces are given in the log (pixel unit^2)