Processes are always configured in the same way, i.e. they always have the same interface and use the same operating mode. Processes differ in the way that the command lines applied to data are assembled. For example, there is a process for creating a T1 volume mask, another one for creating hemisphere meshes, etc. 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 6.2. Description of process window icons:
| Icon | Description |
|---|---|
 | This icon allows you to open a dialog window and select several values. |
 | This icon allows you to create a new entry (protocol, subject, data_session) in the BrainVISA database. |
 | 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 an input parameter. It provides access to existing data stored in a BrainVISA database, using the old (3.0) filesystem-based system. It shows all the data corresponding to the parameter type and allows selection by attribute value. If you see such an icon, you are probably using BrainVISA in a degraded and suboptimal mode. It still exists for backward compatibility. Moreover you will see it a large number of times in this documentation, just because all snapshots have not been updated in the documentation. |
 | This icon represents an output parameter. It provides access to existing or non existing data in a BrainVISA database, using the old (3.0) filesystem-based system. It shows all the data corresponding to the parameter type and allows selection by attribute value. If you see such an icon, you are probably using BrainVISA in a degraded and suboptimal mode. It still exists for backward compatibility. Moreover you will see it a large number of times in this documentation, just because all snapshots have not been updated in the documentation. |
 | 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 icon exists 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). |
 | This icon provides access an editor to correct manually datas. For instance, the editor for label volume is ROIs toolbox in software Anatomist. |
 | This icon indicates that an occurrence is progressing correctly in iterative mode, execution node ..... |
 | This icon indicates that an error has occurred during an occurrence in iterative mode. |
We will take the following process as an example: Prepare subject for anatomical pipeline. This process is located in anatomy -> T1 Pipeline 2004 -> pipeline. It enables you to locate the following: posterior commissure (PC), anterior commissure (AC), interhemispheric point (IP) and a point on the left hemisphere. In fact, these reference points must be located before running the Ana Do A Lot of Things from T1 MRI process to determine whether or not the orientation is correct (axial, coronal, sagittal and radiologic convention).
NOTE: to do this example, first you must import data if you want use a database as explain with Importing a T1 weighted image paragraph.
Parameters are :
T1mri: Selecting the T1 weighted MRI, either using
(selection from your data base of imported images, input filter
select T1 anatomy), 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 stops the process when needed.
The log file enables the user to monitor all the actions performed by BrainVISA. This type of file is used to store configuration data, information on the processes used during a session, and process parameters. This data may include the specific parameters used for a process, or the errors occurring during a session. You should therefore keep this file if you wish to submit an execution error to the support BrainVISA. In many cases, if this file is not available, the information submitted is not specific enough to enable the error to be understood or reproduced.
The log file can be accessed via the BrainVISA -> Show Log menu. If you open it just after starting the session (i.e. before running a process) you can view the list of analysed processes before they are loaded, and check that all the components required to run them are installed on your workstation. If one of the components is missing, you will receive a warning message. Here is an example of an interface:
Table 6.3. Description of BrainVISA user interface log file
| Icon | Description |
|---|---|
 | This icon represents a BrainVISA process .... in the log interface and in the processes themselves. |
| Icon in the log interface, denoting communication with Anatomist. |
 | Icon in the log file, representing a warning. When BrainVISA is loaded, all the processes are analyzed to make sure that all the external programs required to run them are available. If not, the process is not loaded, and a warning is displayed in the log interface. For example, if you wish to use a process that requires Matlab, and Matlab is not installed on your system or your object program path is not properly configured, a warning will be displayed. |
 | This icon represents a command. |
| images/brainvisa/> | This icon represents an error. |
You can view this interface at all times. In the example below, we can see the list of processes run, and the associated parameter
values. Here, we are looking at the Import T1 MRI process, but we can also see that the Anatomist Show
Volume process has been run, and view the communication between BrainVISA and Anatomist via .
The log file is re-edited each time a new session is opened. So, if you want to save it, you must do so before opening a new session, otherwise the data will be lost.
To save the log file, follow the instructions below:
Exit BrainVISA (and don't start it up again until you have saved the log file).
In Linux, go to the following folder:
/home/user/.brainvisa
In Windows, go to the following folder:
C:\Documents and Settings\user\.brainvisa\
Save the brainvisa.log file of this folder.
NOTE 1: If you started up BrainVISA with a specific toto profile (and there is therefore a specific options-toto.py configuration file), you should save the brainvisa-toto.log file.
NOTE 2:you musn't save it during a BrainVISA session otherwise log file won't be interpretable.
When you work with BrainVISA, it is bound to obtain an error screen. The causes are mentionned below. Error screens are divised in 2 parts : the first (1) which indicates the error cause to user and the secund (2) which indicates an explanation to experts (where is located the error in source files or algorithme).
The error screens generated during the running of a process may be caused by several different things:
Mandatory field not completed -> if a mandatory field (in bold type) has not been completed, the following error is systematically generated:
Problems related to input data -> the data selected are incompatible with the running of the process:
Other errors may be generated during the running of a process (information on these errors will be displayed in the window).
BrainVISA has a Log mode, in which you can view the errors generated during processes. See the paragraph on the log file.
Here is a little advice on what to do if an error occurs while a process is running:
Make sure that the error is not related to the management of the database or the type of data selected (wrong type of data, inexisting data, etc.).
Consult the process log via the BrainVISA -> See log menu (for more information, see the paragraph on the log file ).
Sign up to and consult the forum at http://brainvisa.info.
Report the error to the BrainVISA team by using the automatic log file transfer function (see the paragraph on the log file).
The iterative mode enables you to sequentially run the same process on several input data. This is very similar to a batch mode, with a user-friendly interface. This means that, for each input file selected, you can adjust the parameters as required. For example, if you are converting several DICOM volumes, some can be converted to GIS format (.ima and .dim), and others can be converted to ANALYZE format (.img and .hdr). This very practical mode therefore enables you to repeat the same process using different parameters (or not), on a group of input files. For instance, you can apply exactly the same process to all the brains in a given protocol.
To use the iterative mode, follow the instructions below:
Open the process.
If necessary, modify a parameter, which will remain the same for all the repeated processes.
Press the Iterations button on the bottom right. A new window opens.
In the new window, select the input files with
or .If necessary, modify the process parameters of each iteration using
. Note that the number of iterations with a given parameter should be equal to the number of input files. Once the input files and the parameters have been configured, press Ok.
Via this new interface, you can view each process individually. You can also check or modify parameters.
You can deselect processes if you do not want them to be run.
All you have to do now is press Run to run all the processes. You can monitor the sequence of processes in the bottom part of the window. If an error occurs during a process, the iterative mode will go on to the next process.
Parameters can be modified at 3 levels:
Via the general interface of the process that you wish to iterate: this modification will then be applied to all the iterated processes.
When selecting the input file: use
as mentioned above, the number of iterations for a parameter
must be equal to the number of input files. Each parameter value will be applied to the process, depending on the file
incrementation order. Via the iterative mode interface (when you can see an iteration tree). You can modify the process parameters individually. The modification will only be applied to the process selected.
In this example, we wish to convert 3 GIS images (.ima and .dim) in a database to ANALYZE format (.img and .hdr).
Select the conversion process: converters -> automatic -> Aims Converters (userLevel = Advanced).
Select the preferredFormat parameter (SPM image).
Start up the iterative mode by clicking Iterate.
A new window is displayed:
Select the volumes on which you wish to run the process by clicking
. A database file selector is displayed. Select 3 T1 MRI (filter on the type). To select several files, use the
Ctrl + left click combination.Click the Ok buttons in windows 3 and 2. A new window, containing all the files, comes up.
If you wish, you can still modify the process parameters if necessary.
To start the iteration, click Run
When the iteration is finished, the following window is displayed:
NOTE : to select the value of parameter in relation to an other parameter (i.e. value of preferredFormat in relation to value of read), you can proceed by this way as well :
After the fifth step, click on Ok button to return to window 2 :
Click on
of preferredFormat parameter Select the nth preferredFormat parameter to relation to nth read parameter with the menu:
Click on Add (this selection of preferredFormat parameter corresponds to the first read parameter) :
To start again the 3th and the 4th steps for each parameter.
Click on Ok button in windows 3.5 to return to the 6th steps :
Click on Ok button in windows 3.6 to return to step 6
