From a stack of segmented slices

To a 3D reconstructed geometry

Creating a 3D model

•Make sure all 4 TAGs are enabled

•Click on the "Create Geometry" button.

Exporting the 3D resultsl

The "3D Results" tool has only 2 buttons: "Config" and "Save 3D Results". 

The first time you use this protocol, you will want to open the "Config" interface to configurate the cells that will be created in your Excel result file.

We suggest you use the following values saved in the following cell order:

From the "System Info" section:

•User name

•Current Date

•Current Time

From the "Slice Info" section:

•Study ID

•Image Date

•Slice Thickness

•Pixel Width

•Pixel Height

From the "Surface 3D" section:

•TAG ID

•Volume

Once this is done, click the "Save & Exit" button.  Your selection is now saved in a "Result_3D.scp" file in the user's directory.  This file is read back automatically when you get back in sliceOmatic.

•Once you have selected the configuration of your file, you just need to click the "Save 3D Results" button.

Depending opf the settings in the "General" page of the configuration, you may already have a result file with the same name.  If this is the case, then the program will ask you if you want to overwrite that file or just append your new results to the file.

We actually have 2 ways of getting the volumes of the 4 tissues (Muscle, SAT, IMAT and bone) we segmented.

The simplest would probably have been to open the "TAG Surface/Volume" tool while we where in the "Step 7" and export the computed volumes from that tool.

But the "3D Results" tool give you more control over the cells in the created Excel compatible file.  However, the "3d Results" work with geometries not slices.  So we first have to create the geometries for the 4 tissues before we can export their corresponding volumes.

Please note that the "3D results" can actually export 2 sets of volumes for each geometry.  The values available in "Geometry Info" are the volumes of the polygonal objects, while the values available in "Surface 3D" are computed directly from the tagged pixels of the slices.  These are the same values as the ones given by the "TAG Surface/Volume" tool.  For big volumes (such as muscle) they are similar, but for geometries composed of many small regions, the "Geometry Info" may have a tendency to undervalue the volumes.

Sine we will craete 3D geometries of the tissues, this will enable you to see what your models look like, and, if you want, you can use the "3D Shading Control" tool to enable/disable the display of any of the 4 tissues.

In the 3D window, the left mouse button is used to rotate the geometries, the middle mouse button to scale them and the right mouse button to translate them.