The Preferences menu allows to customize user settings in several aspects of BrainVISA. Depending on the installed toolboxes, the preferences window may show a variable number of items. It is not necessary to complete all the fields to use BrainVISA, however they do allow you to optimally configure your user profile. The mandatory fields, such as user level or language contain a default value. Some fields become mandatory when you want to use processes that start up external programs such as Matlab (matlabExecutable field).
The general BrainVISA sub-panel is used to configure several options for customizing your BrainVISA platform (see figure above).
userLevel: this field can contain any one of 3 values: Basic for a standard user (access to top-level processes) or Advanced/Expert for more experienced users (access to lower level processes or processes undergoing validation/implementation).
language: this field can contain any one of 3 values: System default which is the default language in your operating system, English or French.
- textEditor is the external editor program used to show or edit text files when needed. It is used by several viewer or editor processes.
HTMLBrowser: list of browsers available on your workstation. you can specify the browser you wish to use.
The following parameters are for an advanced use of BrainVISA:
processesPath: this optional field is used to configure the path to BrainVISA processes program files. It is for experienced users.
temporaryDirectory : parameter is used to configure a path to temporary files.
removeTemporary determines if temporary files created within BrainVISA should be deleted immediately to free disk space, or only when exiting BrainVISA. Such deletion delay is useful for processes developers when debugging processes.
gui_style enables choosing the preferred style for the graphical interface.
databasesWarning: unselect this option to disable the warning that is shown at startup when you have not created any database.
databaseVersionSync: Management of the database synchronization through BrainVISA versions. Possible options are:
- Ask User : BrainVISA will ask what to do when a database need to be updated.
- Automatic : BrainVISA will automatically update your database if you switch from one BrainVISA version to another.
- Manual : If you modify a database and then switch from one BrainVISA version to another, you will have to update the database if you want BrainVISA take into account the modifications.
SPM99_compatibility tells AIMS applications and Anatomist if it should read/write SPM/Analyze format images like SPM99 did, or rather like SPM2 does. See AIMS and SPM documentations for more details.
radiological_orientation: for SPM format images, tells wheter they are considered to be in radiological (right to left) or neurological (left to right) convention when no further information is available in the image files.
The Support settings section is used to configure the automatic electronic mail system for sending bug reports. This configuration is only relevant if you have access to the internet, and if you are familiar with all the mail transfer parameters. If in doubt, contact your network administrator.
userEmail: e-mail address of the sender, i.e. the user who sends the bug report.
supportEmail: destination, i.e. the address to which the bug report is sent. The default destination address is:
support@brainvisa.infoSMTP_server_name: address/name of the server that manages the SMTP (Simple Mail Transfer Protocol).
The Databases configuration item is used to configure one or more databases. Each database is associated with a directory and a database organization description (ontology).
The database configuration window provides several functions (cf. figure below):
Edit: Provides access to the parameters of a database, and allows the user to modify them.
Add: Used to configure a new database.
Remove: This removes the database entry in BrainVISA, but does not delete the database file and directory (no data is lost).
We are now going to create a database. Please follow the instructions below:
Open the Preferences window.
and select the Databases item.Click the Add button.
Complete the following fields (only directory is mandatory) :
directory: mandatory field. Enter the path of the folder that will contain your database.
- Expert settings
ontology: The ontology describes the database organization. The default organization, brainvisa-3.1.0, should be OK for most usage. However, custom organizations may be defined and used.
sqliteFileName: The database indexation is stored in a SQLite file. With this option, it is possible to choose the name of this file.
activate_history: When this option is checked history information will be recorded in the database directory: the log of the processes and brainvisa session which have been run to write data in the specified database. It is possible to view the history of data thanks to the Database browser.
Click Ok when you have finished entering your parameters.
executable: this parameter is used to configure the command for starting up Anatomist.
executable: command used for starting up the R program.
options: R software options passed to the R commandline.
executable: this parameter is used to configure the command for starting up MatLab.
- version: Matlab release version, used to assume a specific version and avoid the automatic detection which may take a few seconds.
options: used to configure options for MatLab.
path: used to configure the path from which matlab files will be loaded.
startup: run this matlab command when starting up matlab.
It is possible to set the paths to 3 versions of SPM: SPM 5, SPM 8 (Matlab) and SPM 8 standalone.
spm8_path: Path to SPM 8 installation (Matlab version)
spm8_standalone_command: Location of the standalone version of SPM 8 run command (run_spm8.sh on linux).
spm8_standalone_mcr_path: Path to the Matlab Compiler Runtime (MCR) needed for a standalone version of SPM 8.
spm8_standalone_path: Path to SPM 8 files (where the templates for example are installed) in the standalone version.
spm5_path: Path to SPM 5 installation (Matlab version).
An Auto detect button is available at the bottom of the panel. It enables to try and find the spm paths automatically. Only one the 3 versions is needed to use the processes that need SPM (SPM normalization in Morphologist for example).
fsl_commands_prefix: Needed if the fsl commands in your installation starts with a prefix, for example fsl4.1-flirt.
freesurfer_home_path: Location of Freesurfer installation directory.
subjects_dir_path: Value of SUBJECTS_DIR variable.
check_spam_models: Enable or Disable the checking of SPAM identification models installation for the automatic recognition of sulci.
When configuration is done, the configuration data is stored in the user .brainvisa folder. There are actually 2 profile types: a general one (options.minf) and named profiles that can be used to store or use alternative configurations (options-<userprofile>.minf)
These different profiles are particularly useful when you must use a shared user connection.
If your user name is user, for instance the general configuration file will be placed in:
Unix / MacOS: $(HOME)/.brainvisa/options.minf, typically /home/user/.brainvisa/options.minf
Windows: generally something like C:\Documents and Settings\user\.brainvisa\options.minf
Customized configuration files for named profiles are placed in the same directory.
The general profile is automatically used when BrainVISA is launched.
To use and configure a specific profile, for example toto, follow the instructions below:
Start BrainVISA with a profile name (even if it does not exist yet), for instance
brainvisa -u toto
Customize this profile with the configuration interface: Preferences menu.
Validate them with the OK button
Exit BrainVISA.
To start BrainVISA with this profile:
brainvisa -u toto
