Table of Contents
What is the file format for ROI ?
Regions of interest are stored in a graph where each node is a ROI. Some attributes are associated to the graph and its nodes : the voxels size, name of each region... The file format is a couple .arg/.data. The .data is a directory and contains data of each region. The .arg is a file and contains the graph's structure, that is to say nodes organisation.
It is also possible to export a ROI as a mask (a binary volume) using the option Region => Export as mask in ROI toolbox menu.
Accepted file formats to draw ROIs
You can draw ROI on 2D, 3D and 4D volumes.
How to open ROI toolbox ?
You can either click on icon 
in a window containing a volume, or press F1 key (obviously it will work only if there is a window containing a volume).
Some rules ...
A voxel cannot be in more than one region.
You shouldn't draw on a volume whose voxels size is different from the one of the graph. If it occurs, Anatomist will show a warning message.
- Be careful to draw in a window which is in the same referential than the volume. Indeed, the voxels are drawn in the referential of the view, so if it is not the referential of the volume, the voxels of the ROI and the voxels of the volume won't be in the same orientation.
Here is the graphical user interface to manage ROIs :
A session is actually a ROI graph. This menu enables to create a new graph, open an existing one, closing current graph...
Table 9.1. Menu Session
| Option | Description |
|---|---|
|
New |
Creates a new ROI graph. The default name is created according to the name of the selected volume in Image panel. You can change the name of the graph using Save as option. |
|
Open |
Loads a graph. |
|
Close |
Closes the selected graph. |
|
Save |
Saves the selected graph. |
|
Save as |
Saves and eventually renames the selected graph. |
|
Clean |
Deletes all isolated voxels. If you have drawn voxels by mistake, you can delete them using this option. |
This menu enables to manage the regions of the selected graph.
Table 9.2. Region menu
| Option | Description |
|---|---|
|
New |
Creates a new region in the graph. The set of allowed names depends on the selected framework in FrameWork option. If you want to choose your own names, use the Free framework (default). You can also load your own framework using FrameWork => Personal => Load menu. |
|
Delete |
Deletes selected region. |
|
Fusion |
Merges several regions. The following window opens and you can select the regions that have to be merged and the name of the final region among selected regions names.  |
|
Export as a mask |
Saves selected region as a binary mask (label volume). |
|
Morphos Stats |
Displays the volume in mm3 of the selected region in the console used to run Anatomist. |
This menu manages nomenclatures used to name the regions.
This menu manages custom nomenclatures.
Table 9.4. Personal sub-menu
| Option | Description |
|---|---|
|
New |
Creates a new nomenclature for ROI graphs. You first enter a name for the new nomenclature in a pop-up window. Then, a new object is created and shown in Anatomist main window. New sub-menus are available in Personal menu : Define new region, Modify region name and Modify region color. You cannot define two nomenclatures at the same time. If you define a second nomenclature, you can save the first, else it will be deleted. |
|
Load |
Loads an existing nomenclature. |
|
Save |
The nomenclature is saved in Anatomist config directory of the current user : user_home_directory/.anatomist/frameworks. You cannot choose the place to save the nomenclature. |
|
Define new region |
Sub-menu available on creating a new nomenclature. Enables to define a new region by giving its name and color. |
|
Modify region name |
Sub-menu available on creating a new nomenclature. Enables to modify the name of the current region. |
|
Modify region color |
Sub-menu available on creating a new nomenclature. Enable to modify the color of the current region. |
|
Delete region name |
This option enables to remove the current region from the nomenclature. |
Table 9.5. Windows menu
| Option | Description |
|---|---|
|
Axial |
Opens an axial window containing the volume and the ROI graph selected in image and session panels of the ROI toolbox window. |
|
Sagittal |
Opens a sagittal window containing the volume and the ROI graph selected in image and session panels of the ROI toolbox window. |
|
Coronal |
Opens a coronal window containing the volume and the ROI graph selected in image and session panels of the ROI toolbox window. |
|
3D |
Opens an 3D window containing the volume and the ROI graph selected in image and session panels of the ROI toolbox window. |