Table of Contents
This chapter describes the various windows that can be found in BrainVISA graphical user interface.
The general user interface is BrainVISA main window that shows up when starting BrainVISA. It consists of four parts (cf. the figure below):
A menu (1)
A window providing access to processes (2) including a toolboxes/bookmarks panel (2.a) and a processes list (2.b)
A window providing documentation about the selected item (3)
A search box to search a process by name (4)
The BrainVISA menu gives you the following choices:
Help: Opens the help page in a web browser, which provides access to a manual, a tutorial, etc.
About: Opens a window that shows the version of BrainVISA and the institutes and laboratories that contributes to the project.
Preferences: Opens the configuration window which is used to choose options and to configure BrainVISA databases.
Show log: Opens a window providing information about the current session of BrainVISA: configuration, loaded processes, run processes, errors...
Open process: Opens a process which have been previously saved in a .bvproc file.
Reload toolboxes: Reloads toolboxes, processes, ontologies, databases. It is useful for people who develop their own toolboxes to take into account new files without having to quit and start again Brainvisa.
Start shell: Opens in a console a IPython shell.
Quit: Closes the application.
The Support menu gives you the following choices:
Bug report: Send a bug report, either with or without the log file.
When you click on Bug report:, a new window opens to send the email. Here are some details about the parameters of this window:
From: mandatory, sender e-mail address, i.e. the user who sends the bug report.
To: mandatory, destination address, i.e. the address to which the bug report is sent. The default destination address is: support@brainvisa.info.
Cc: optional, to send a carbon copy to someone.
Bcc: optional, to send a blind carbon copy to someone.
Attach log file: use this option to attach the log file.
Send: to validate the sending of the e-mail.
Cancel: to cancel the sending of the e-mail.
The View menu can be used to hide/show optional panels in the main window:
Documentation: Hides/Shows the documentation panel (3).
Workflow execution: Shows/hides a panel that shows the workflows that have been run via Soma-workflow on available computing resources. This panel is hidden by default and the parallel computing features are available only if you select a Advanced or higher user level in BrainVISA preferences. See the chapter about parallel computing with Soma-Workflow for more information about this feature.
Close all viewers: Closes all windows opened by Brainvisa viewers whichever way they have been run: through an eye button, directly running the viewer process, or using the contextual menu of the Database browser.
The left panel of the main window contains the list of available toolboxes. A toolbox contains a set of processes related to a common theme. When you select a toolbox, its list of processes appear on the next panel.
Several toolboxes are included in BrainVISA package but some other toolboxes are available for download separately and have to be installed in addition to BrainVISA main package. More information about existing toolboxes on http://brainvisa.info/toolboxes.html.
It is possible to create a custom toolbox by adding your own processes in .brainvisa/processes directory in your personal folder. If this directory contains processes, they will be available in BrainVISA interface in a toolbox named My Processes.
It is also possible to define new toolbox containing links to existing processes, it can a sort of bookmarks toolbox. It can be useful to group in such a toolbox the processes you mostly use.
To create such a toolbox, select New in the contextual menu. The name of the new toolbox is editable, type whatever you want. The name will be modifiable later by double-click on the toolbox. Then you can open the empty toolbox in another window via the contextual menu then drag and drop in it the processes you want to put as shortcut in this toolbox. The shortcuts can be moved, renamed and deleted in the personal toolbox. You can also create category directories to sort the shortcuts.
The custom toolboxes are automatically saved in a file .brainvisa/userProcessTrees.minf in your personal folder. They will be reloaded from this file next time you start BrainVISA.
On the image below, a toolbox My Processes is visible, it means that there are valid processes defined in .brainvisa/processes in the user's personal folder. A custom toolbox named Bookmarks is also visible : it contains shortcuts to processes from various toolboxes (T1 MRI, Tools, Data Management). New directories (tools, data) have been created and some shortcuts have been moved in it. The T1 MRI toolbox is opened in a new window : this enables to drag and drop items from this toolbox to the custom toolbox.
A custom toolbox is editable, so several actions are available on the content of such a toolbox:
Renaming the toolbox: Double-click on the name of the toolbox, type the new name and press enter key.
Adding a shortcut: Drag an element of another toolbox and drop it in the custom toolbox.
Renaming a shortcut: Double-click on the shortcut, type the new name and press enter key.
Moving a shortcut: Drag and drop the shortcut at its new place.
Creating a new category directory: Use contextual menu New.
The contextual menu available in toolboxes panel contains the following options:
New: creates a new custom toolbox to store shortcuts to processes you often use.
Delete: deletes the current selected toolbox if it is a custom toolbox. Of course, BrainVISA toolboxes cannot be removed.
Open: Opens the current toolbox in a new window, this enables to drag and drop elements from one toolbox to another. However only custom toolboxes are editable, you cannot drop elements in a BrainVISA toolbox.
Set as default list: Sets the current selected toolbox as the default toolbox, that is to say the toolbox that is selected at BrainVISA startup. Indeed, it is practical to have the toolbox you use most of the time already selected when BrainVISA starts.
The processes panel contains the list of available processes, which are organized into toolboxes and categories. The list of available processes changes according to the user level selected in the preferences. In basic level, some advanced processes are hidden. The user level of a process is shown on its icon. Remember that level 1 and level 2 processes are either for advanced users (level 1) or evaluation purposes (level 2, for which no help is available).
For example, the T1 MRI -> import category provides access to the Import T1 MRI process. To open the process, either double click on the process name, or right-click on it and select Open in the contextual menu.
The contextual menu available in processes panel when you right click on a process item contains the following options:
Open: Opens the process window in order to run it.
Edit documentation: Opens the documentation edition window that enables to write the documentation of the process. This feature is useful for users who develop their own processes.
Iterate: Opens the iteration dialog window in order to run this process on a set of data. It is equivalent to clicking on the Iterate button in the process window.
There isn't any contextual menu available for categories directories.
This panel displays information to help you using BrainVISA in general, or a specific process. When BrainVISA is opened, this window automatically displays the main BrainVISA help page. When a process is selected, the related documentation is shown.
This panel is now a dock window so it can be hidden using the menu View -> Documentation or by clicking on the close button (cross) at the top right corner of the panel. It is also possible to get this panel out of the main window by clicking on the float button (squares) at the top right corner of the panel.
It is possible to edit and modify the documentation of your processes in BrainVISA interface. Click on the edit button or select Edit in the contextual menu of the process. The following window appears:
See the Process documentation in BrainVISA Programming manual for more information about this documentation edition interface.
Table 3.1. Description of BrainVISA user interface icons
| Icon | Description |
|---|---|
 | This button takes you back to the first documentation page of BrainVISA, i.e. to the main BrainVISA help page. |
 | This button takes you back to the previous documentation page. |
 | This button takes you to the next documentation page (and, in iterative mode, it also indicates the process that is currently underway). |
 | This button reloads the current documentation page. |
 | This icon represents user level 0 processes. Basic processes accessible to all users. |
 | This icon represents user level 1 processes. Advanced processes accessible to advanced users. |
 | This icon represents user level 2 processes. Expert processes accessible to expert users. In fact, these processes consist of internal BrainVISA processes (started up via level 0 or level 1 processes) or processes that are still being developed and do not, therefore, give reliable results. |
 | This icon represents a viewer, that is to say a process dedicated to the visualization of certain type of data. This type of processes is automatically run when you click on the eye button next a parameter data in a process. |
 | This icon represents an editor, that is to say a process dedicated to edition of certain type of data, for example the manual correction of a mask. This type of processes is automatically run when you click on the editor button next a parameter data in a process. |