Step 4: Exporting the L3 results

 

In this step, you will save the segmentation results and export to a file the surface of the different tissues you segmented in the previous step.

 

 

The Interface:
 

In this step, sliceOmatic is placed in Mode "Display 2D".

Only one image window is displayed and it is in "Mode One".

The "2D Results" tool is open

 

 

What to do:

 

Exporting the surfaces

 

 

The installation script for this protocol has already placed a "Result_2D.scp" file in the sliceOmatic's installation directory.  This script has define some defaults cells for the Excel result file.

 

But, of course, you can modify this.

 

By clicking on the "Config" button in the 2D Results interface, you open the configuration menu.  This menu has 2 tabs:

The "Cell selection" tab enable to select the content and order of the Excel result file.

The "General" tab enable you to select where the result files will be stored by default and few more parameters.

 

The "Cell Selection" tab is split in 2 vertical columns.  The left one contain all the information that is available for export in sliceOmatic.  These are presented in a tree.  You can expand/collapse a branch of that tree with the "+" and "-" icons. If all the items in a tree are selected for export, they have a green check-mark. If some of the items are selected, a yellow check-mark.

 

The right column is the list of all the cells that will be created in each line of the result file.  You can change the order of these cells with the arrow buttons at the button of the column.

 

Once you are satisfied with the cell configuration, you can click "Save & Exit".  This will create a "Result_2D.scp" file in your personal directory.  that file will be used next time you use sliceOmatic instead of the one in the installation directory.

 

By default both the surface (in cm2) and the mean value (in Hounsfield) of the pixels under the different tags will be saved.

 

 

Simply click on the "Save 2D Results" button of the 2D Results tool's interface to save your results.
 

The first time you do this, a new "Result_2D.csv" file will be created in the default directory (c:\Temp).
 

 

 

Subsequent saves will cause the following pop-up window to appear.  If you select "Append", then a new result line will be appended at the end of the file.

 

Note

You can make the "Append" option the default choice from the "Config" menu, "General" tab.  If you do, then the pop-up will not be displayed.

 

 

 

Saving the segmentation (TAG) data

 

 

From the "File" menu, click on the "Save TAG Files" button.

 

This will create a file containing the segmentation (TAG) results.  By default this file will be in the same directory as the file of the analyzed CT image.  The created file will have the same name as the analyzed CT but with the ".tag" extension appended to it.

 

If you do not explicitly save the TAG file, you will be reminded that this file has not been saved when either you exit the program or close the analyzed image.



 

Note:

 

The script for this step place sliceOmatic in display Mode One.  This mean that only one slice is displayed, and only one slice is selected (the displayed one).  When you save your results, the 2D Results tool will create one excel line per selected slices.  so, if you want to save results for multiple slices at the same time, you need to switch to the display Mode All (press the "space bar" key) and select only the slices you want to see in the excle file.

 

Note:

 

By default, sliceOmatic will use a period (.) to separate the fraction in a real value.  You can change this to a comma (,) in the "Config" menu, "General" tab.