Since the 4.2 release of BrainVISA, we propose a new toolbox which allows making some bridges with the FreeSurfer software. The toolbox will contain two separate parts:



This toolbox is a little bit unusual because you need to use database with an ontology for FreeSurfer. If you work with FreeSurfer, you know that data are organised with a specific order, looking like the following:

In order to use FreeSurfer within BrainVISA, the above description of files has written in the freesurfer ontology.

In the same way, BrainVISA has a specific organization to manage data which is described by an ontology, the "brainvisa-3.1.0" ontology. By default, datasets are always organized with it. But in the case of an interface between FreeSurfer/BrainVISA, you need to know the organization both software. For this, if you use the import process, you will need to set two databases with distinct ontologies one with a specific ontology for FreeSurfer and the other one for the Morphologist pipeline.

For more details about databases, please refer to data management section.

Configure databases

Now, please follow the instructions to properly setup the databases:

Configure the freesurfer database:

Now you have a freesurfer database in our brainvisa settings. Data will be directly available by using via a process. Note that the directory could correspond to the value of $SUBJECTS_DIR freesurfer environment variable.

Configure the brainvisa database:

If you don't have any brainvisa database, please create one like this:


Environment variables

To use FreeSufer, you have to set 2 environment variables:

If these variables are not set, you can use the specific panel in BrainVISA -> Preferences -> FREESURFER.

In order to run FreeSurfer, BrainVISA tries to launch this program in the following order:

If, in spite of the above trials, you still cannot use FreeSurfer, please try a last thing: launch your FreeSurfer environnment in a shell, then launch BrainVISA from within the same shell.