The graphical interface of the processes is generally automatically generated, that's why this interface is very similar from one process to the other. We shall call the values that the user must enter to run a process "parameters". There are mandatory parameters (shown in bold type) and optional parameters. The parameters are entered in various ways: selection of a file or a list item, entry of a value, etc.
The table below describes process interface icons:
Table 3.3. Description of process window icons:
| Icon | Description |
|---|---|
 | This icon allows you to open a dialog window and select several values. |
 | This icon provides access to your files. It enables you to select an input or output file without using the BrainVISA database system. |
 | This icon represents an input parameter. It provides access to existing data stored in a BrainVISA database. It shows all the data corresponding to the parameter type and allows selection by attribute value. |
 | This icon represents an output parameter. It provides access to existing or non existing data in a BrainVISA database. It shows all the data corresponding to the parameter type and allows selection by attribute value. |
 | This icon represents a link with Anatomist. It is mainly used for parameters that are, in fact, 3D points. When this icon is clicked, the current location of the 3D cursor (i.e. the red cross) in Anatomist is taken as the parameter value. It allows the user to select a value by clicking it in Anatomist. |
 | This icon tells you whether a data item can be visualized or not. If the button is enabled it means that BrainVISA has a viewer capable of displaying that type of data. If the icon is disabled (i.e. not clickable), it means that the corresponding file is not readable (usually because the file does not exist). If this button is not displayed, it means that BrainVISA doesn't have any viewer for this type of data. |
 | This icon provides access an editor to manually correct data. For instance, the editor for label volume is ROIs toolbox in Anatomist. |
 | This icon appears next to a parameter name to indicate that this parameter has been modified, it doesn't have its default value anymore. |
 | This icon indicates if the data is locked. Only output files are concerned (files with ). It is not possible to execute a process when it has a locked file in its output parameters. |
 | This icon indicates that a step has finished correctly in an iteration or a pipeline. |
 | This icon indicates that an error has occurred during a step of an iteration or a pipeline. |
By right-click on a parameter, one or two options are available:
default value: Always available. Some parameters have a default value (not null) and so there are already filled in when you open the process. Other parameters are automatically filled in by BrainVISA when you fill in another parameter. Indeed, it is possible to define links between parameters in a process to indicate that the value of one parameter can be guessed from the value of another parameter. A lot of processes use this feature to speed up the parameters capture.
lock: This option is available if the data is an output file and if the file exists. So that, the parameter can be locked. In fact, sometimes you would like to preserve the output file because you set/changed specific options. Once a file is locked, then a process can't rewrite this parameter. A message will be displayed to indicate that you must unlock data if you want to run the process. To unlock a parameter, just click on lock option in the menu to unselect this option. When a parameter is locked, a <filename>.lock file is created. There is no link with the database or .minf file.
We will take the following process as an example: Prepare subject for anatomical pipeline. This process is located in T1 MRI -> Segmentation Pipeline -> components. It enables to locate the following points in a brain image: the posterior commissure (PC), the anterior commissure (AC), an interhemispheric point (IP) and a point on the left hemisphere. In fact, these reference points must be located before running the Morphologist pipeline to determine whether or not the orientation is correct (axial, coronal, sagittal and radiologic convention) and to compute a common referential.
Note
To do this example, first you must import data if you want to use a database as explained in Data importation paragraph.Parameters are :
T1mri: Selecting the T1 weighted MRI, either using
(selection from your database of imported images), or via (selection from all the files on your disk).Commissure_coordinates: selecting the output file. This field is automatically completed when you select a T1 weighted image using
. Otherwise, you must select the output file with .Normalized: you need to know if your image has already been normalized. If it has, choose the procedure used to normalize it, and the AC, PC and IP will not have to be selected from an anatomical volume. You will however have to run the process so that the type of normalization is taken into account and .APC file is created. On the other hand, if your volume has not been normalized, you will have to select the AC, PC and IP from the anatomical volume proposed by Anatomist.
Anterior_Commissure: click
to access your anatomical image via and to select the coordinates. When you click the first time, a new Anatomist session is
opened. Then, if the cursor is correctly located on the volume, click again to display the coordinates in the field.
Posterior_Commissure: cf. Anterior_Commissure
Interhemispheric_Point: cf. Anterior_Commissure
Left_Hemisphere_Point: cf. Anterior_Commissure
Allow_flip_initial_MRI: two values are listed, True or False. This option authorizes or forbids the user to rewrite the volume so that the orientations (axial, coronal and sagittal) and the convention (radiological) are correct.
After running the process, you will be able to view the .APC file by clicking the in Commissure_coordinates.
When you have completed all the fields required by the process (all fields in bold), you can launch the process by clicking the Run button halfway up the left-hand side of the process window. You can then watch the progress of the process in the lower half of the process window. You will be told explicitly when the process starts and ends. While the process is running, the following icon (in the top right and corner) will be constantly animated. The duration of a process varies according to the algorithms used by the process and performances of your workstation. In fact, a process such as a conversion is almost instantaneous, whereas a process such as the sulci recognition process may take anything from 1 to 2 hours depending on your workstation.
When the process begins, the Run button is replaced by an Interrupt button, which enables to stop the process when needed.
It is possible to save the state of a process (input and output parameters) in a file in order to reload it later. To do so, click on the Process -> Save menu and choose the place and name of the file which will store the state of the process. The file will have the extension .bvproc.
To reload a saved process, use the BrainVISA -> Open process menu and select the .bvproc file previously saved.