Mode TAG: ABACS+

 

This mode is used to automatically segment axial CT images at any anatomic level between T1 and the Sacrum.

 

This tool has been developped by Voronoy Health Analytics Inc. and is available as a plug-in in sliceOmatic.

 

License:

 

This user mode require a special license.  Please contact TomoVision for more information.

 

Encryption:

 

At the request of Voronoy Health Analytics:

•The TAG files associated with any slices that have been analyzed with ABACS+ will be encrypted. SliceOmatic will automatically encrypt the files when they are saved and decrypt them when they are read back.  So inside sliceOmatic, the user will not even noticed. But if you used to read the TAG files directly for your research or to import in another application, you will no longuer be able to do that.

•Any slices analyzed with ABACS+ can no longuer be displayed in the color scheme modes "Over" or "TAG".

 

 

From the Graphic Interface

 

 

 

Anatomic Level

This selection tool is used to assign a vertebral label to the axial slices that are to be analysed by ABACS+.

 

The tool display the label of the "current" slice.  Changing the label in the tool will change the label of the current slice.

 

If you work with a 3D dataset, you will want to also open the "2D Side View" and "2D Vertebral Label" tools to help simplify the labeling of the slices.

 

Config

Activating this button will open the "ABACS+ Configuration" window.  This window allow you to select the tissues segmented by the ABACS+ module.  This window is described in more details further down.

 

License

Activating this button will open the "ABACS+ License" window, displaying the status of your ABACS+ license.  This window is described in more details further down.

 

Compute

Start the computation on all the selected frames.

 

The ABACS+ module can segment any CT axial slice between the the level of T1 to the sacrum. But, the module need to have a rough idea of the anatomical level of each slices in order to do its job. So you need to manually assign a "label" to each slice you want the module to segment.

 

When you start the computation, sliceOmatic will make sure that all the selected slices have valid labels.  If some of the slices are labeled "Undefine" or "Outside", the program will pop a warning window.  Selecting "Continue" will send the remaining slices to the ABACS+ for computation.

 

 

Once the copmputation is started, the interafce will pop a progress window, showing the feedbacks from the ABACS+ module.

 

You can click on the "Cancel" button to stop the computation at any time.

 

 

 

The Configuration window

 

 

 

Tissue

In this interface, you can activate/de-activate the different tissues that the mode can segment.  You can also assign a different TAG value to each tissue and fix the minimum and maximum hounsfield associated with the tissu.

 

Note:

It is recommanded that you do not change the Min/Max values and leave them to the complete range a "short" integer can have (-32768 to 32767).

 

Restore

Restore the default values to tissue interface: All tissues on, sequential tags, min = $ABACS_THRESHOLD_MIN and max = $ABACS_THRESHOLD_MAX

 

Save & Exit

Apply the changes, save them to a script file and exit the window.  The current configuration will be saved to a "ABACS+.scp" in the user's directory (c:\Users\user_name\AppData\Roaming\TomoVision).  The changes will be read back the next time you start sliceOamtic.

 

Exit

Apply the changes and exit the window without saving to a script.  the changes will only persist during this session of sliceOmatic.

 

Cancel

Exit the window without applying the changes.

 

 

The License window

 

 

 

License status

This box display the current expiration date and number of tokens left in your ABACS+ license.  It will also display some status messages such as "License valid", License Expired", "No token left" or messages if the last ABACS+ computation failed.

 

Help

If the computation failed, or if the license is invalid, you will also be presented with a "Help" button that will bring you to a TomoVision support web pages offering more information on how to solve your problem.

•Expired license or no tokens: https://tomovision.com/ordering/order_ABACS+.html

•Problems with the HASP envelope: https://tomovision.com/support/sup_abacs_hasp.html

•Problems with Matlab: https://tomovision.com/support/sup_abacs_matlab.html

 

Refresh

Ask ABACS+ to refresh the status of the license.

 

License web pages

Open a TomoVision support web page explaining how to generate and install new ABACS+ licenses.  The page is: https://tomovision.com/support/sup_abacs_license.html

 

Exit

Exit the license window.

 

 

From the Display Area

 

There is no Display Area interaction specific to this tool.

 

 

From the Keyboard

 

There is no keyboard interface specific to this tool.

 

 

From the Command Line

 

System Variables defined in this tool:

 

 

$ABACS_THRESHOLD_MIN

(I16)

The default minimum HS value for all the tissues (def: -32768)

 

$ABACS_THRESHOLD_MAX

(I16)

The default maximum HS value for all the tissues (def: 32767)

 

 

Text commands defined in this tool:

 

ABACS: tissue (on|off)

Select whether the tissue will be computed by ABACS.

 

ABACS: tissue tag min max

Associate a tag value, a minimum and a maximum  HS value to the tissue.