Data management

Processes in this category are to be used to import your data in one of the configured BrainVISA database. The first thing you have to do is to create or configure your BrainVISA databases. Then you can use the import processes (which are in the subcategory import) to put your data into the database. It is not mandatory to use a database to process data with BrainVISA but it is highly recommanded.

What is a BrainVISA database ?

Data organization is an important point in BrainVISA. Indeed, BrainVISA was conceived to allow a simplified use of neuroimagery tools coming from various laboratories and being able to combine data resulting from several acquisition modalities (aMRI, fMRI, dMRI, EEG/MEG, PET, etc). Interactions between these tools and the various data were made possible thanks to a system of data organization. In order to remain compatible with existing software, BrainVISA is mainly based on directories and file organization and naming in order to build a database.

A directory is a BrainVISA database if the structure of its sub-directories and the file names in this directory respect a set of rules. These rules make it possible to BrainVISA to scan the whole directory contents and to identify without ambiguity the database elements. These elements are composed of the following information:

Data type: identify the contents of a data (image, mesh, functional image, anatomical RM, etc). The data types are organized in hierarchy making it possible to decline a generic type in several specialized types. For example, there is a 4D Image type which is specialized in 3D Image (indeed, a three-dimensional image is a particular case of a four-dimensional one); the type 3D Image is itself declined in several types of which T1 MRI and Brain mask.
File format: Represent the format of files used to record a data. BrainVISA is able to recognize several file formats (for example DICOM, Analyse/SPM, GIS, etc). It is possible to add new data formats and to provide converters to make it possible for existing processes to use these new formats.
Files: contains the names of the files used to record the data. It is a list of files because some formats use several files to store the data.
Attributes: an attribute is an association between a name and a value. A set of attributes is associated with each element of BrainVISA database. This set represents all of the characteristics of a data (as the image size, the name of the protocol corresponding to the data or the acquisition parameters). Attributes values are set by BrainVISA during directory scanning.

It is possible to completely define the set of rules used to convert a directory in a BrainVISA database. That allows the use of BrainVISA without having to modify an existing file organization. However, the writing of such a system of rules requires a significant investment in the study of BrainVISA. This is why BrainVISA is provided with a default data organization system that can be used easily.

BrainVISA database organization

By default, data in a BrainVISA database are organized in a hierarchical structure with the following directories :

database directory
protocol : a directory for each protocol
subject : a directory for each subject
modality : for example t1mri, diffusion, pet...
acquisition : raw data. It is possible to have several acquisition for each subject.
analysis : results of an analysis, for example files generated by brainVISA during the segmentation pipeline

Why should I use a BrainVISA database ?

It is not mandatory to use a database to process data with BrainVISA. However, some important features are not available when you are using data which are not in a database. For example, the BrainVISA ability to construct a default output file name when an input data is selected in a process relies on the database system. Moreover, some processes use the database system to find data; for example, the brain mask viewer tries to find the T1 MRI used to build the brain mask in order to superimpose both images in an Anatomist window.

How to create or edit BrainVISA databases ?

You can create several BrainVISA databases and select the ones you want to activate. You just have to use the database edition window accessible via the Preferences->databases menu of the main window.