Data Management, Analysis Workflows and Reports
The new data management tools enable a new way of handling and working with (large) data sets: Instead of isolated documents, data is entered and managed in a hierarchical manner describing projects, subjects, workflows and data sets. The information and relationships between these entities are persistently stored in the BrainVoyager database (see figure below). At the top level, projects are created that refer to the data (e.g. project descriptions, subjects, analyzed data) of an experiment or clinical study. Each project is identified by a unique name as well as optional information including the preferred way to organize the data on disk as well as a descriptive text describing the study. Under each specified project, subjects (participants of a study) as well as workflows are added. Subjects added to a project are identified by a code and optional information such as a name and additional features that can be optionally defined. Workflows define pipelines that process input data of multiple subjects in the same consistent way to create desired output data sets. When workflows are executed, produced data sets will be automatically named in a consistent way and added to appropriate data folders. The BrainVoyager database stores all information about defined projects, specified subjects and workflows, and what data sets have been produced. The actual data files are not stored in the database but are referenced and displayed to the user in tables that hide unnecessary details about the underlying folder structure. From the presented data tables, documents can be opened in BrainVoyager's standard multi-document area.
Data sets created by workflows can itself serve as input for other workflows creating powerful processing pipelines. Since workflows process data in the same way for all available subjects, they implement a batch processing mechanism without the need to write scripts. Furthermore, workfows create detailed reports in HTML and PDF format as a basis for quality assurance and for detailed documentations of performed analysis steps. At present the available workflows support project creation, anatomical and functional preprocersssing, alignment of functional and anatomical data, normalization into Talairach or MNI space and statistical (GLM) analysis at the level of single subjects and groups. Since all entered information is stored in a central database (see below), the information from all defined projects is persistently available. Furthermore the data can be easily moved to other locations, for example, to relocate experiments to another computer or to share the data with colleagues.
The Data Analysis Manager
The Data Analysis Manager window (see snapshot below) provides access to the project, workflow, report and database functionality. The window is initially configured to appear automatically at program start. To turn this off, the Start At Launch option in the right lower section of the window can be unchecked. The Data Analysis Manager window can be invoked at any time using the Data Analysis Manager icon at the left side of the toolbar of the main BrainVoyager window or with the keyboard shortcut CTRL-D (CMD-D on Mac). Note that the data management tools are optional, i.e. BrainVoyager can be used in the same way as in previous versions, and it is also possible (recommended) to mix workflow and conventional (single-document) tools, e.g. by performing basic analysis pipelines with data manager workflows and to continue with more specific tools afterwards.
The Projects pane on the left upper side contains a list of all defined projects. In case that projects are avaialbe, the program automatically selects the last inspected project in the Projects pane. Any available project can be selected by clicking its name. When a project is selected in the Projects pane its associated information is accessed from the BrainVoyager database and shown in the Subjects pane (left lower section), in the Workflows and Data tabs (main middle section) and in the Reports pane that is either docked to the right side but can also be undocked from the main window. If a specific subject is selected, the data of this subject is shown in the subject-level data table in the Data tab (filled with "green" entries in the snapshot above). The entries in the data tables not only show references to data that is already available on disk but also data entries that is not yet stored as files but expected to become available when running a corresponding workflow that has been defined but not yet executed. The different entries are distinguished by different colors. If referenced data is available on disk, its entry in the data table is colored green; a data entry (created by a workflow) without a link to existing data on disk is colored red and the Linked File column will be empty.
The following topics describe the most imporant functions offered by the data analysis manager.
- Create new project
- Add subjects to project
- Define and run Create Document workflows
- Define and run Preprocessing workflows
- Define and run Group-GLM Statistics workflows
- Optional: The Add Document workflow
The BrainVoyager Database
The BrainVoyager database is a standard sqlite database that can be assessed also outside of BrainVoyager. While it might be interesting to see the stored tables in full detail (as compared to the simplified user-oriented display in the data analysis manager window), it is recommended to not change the stored information in order to keep the consistency of the database. The BrainVoyager database is stored at the following default location within the user's home directory:
- Windows: C:\Users\[user]\AppData\Local\Brain Innovation\BrainVoyager\brainvoyager.db
- Mac OS X: ~/Library/Application Support/Brain Innovation/brainvoyager.db
- Linux: ~/Documents/Brain Innovation/brainvoyager.db
Note that the BrainVoyager database does not store the actual data files but only references to the data in the projects root directory. The default data root path is located in the user's "Documents/BrainVoyagerData" folder as default but it can be changed by using the Browse button next to the Default projects root path field at the bottom of the Data Analysis Manager window.
Copyright © 2017 Rainer Goebel. All rights reserved.