Neuroimaging data are hard to work with: often large in size, full of noise from all sources under the sun, and usually exclusively available in domain-specific file formats that need to undergo fragile format conversions. These and many other reasons may be responsible for the relatively rare successful (re-)use of neuroimaging data by researchers from other disciplines. Consequently, neuroimaging is most likely seeing less transfer of new technology for analysis and visualization from outside its own bubble than there could be, given the general interest in all things that look like a brain.

One strategy to improve this situation is to provide software that makes it almost trivial for "foreign" researchers to access neuroimaging data in their native formats. The NiBabel project is an excellent example of this approach — a collaborative development effort that aims to support any relevant neuroimaging file format and to offer access to data and meta-data using basic data types, such as numerical arrays, that are universally supported.

Another way is to go one step further and transform neuroimaging data into a form that is both technically and semantically easier to comprehend for a non-neuroimaging audience. That is easier said than done. What is a better unit than a voxel, what is a better format than a binary array? I don't know the answer, but I am pretty confident that there is no single one that fits all cases.

One needs to start somewhere, so we decided to offer the fMRI data for the Forrest Gump audio movie in a format that should strike a chord with people working with time series data — people that may otherwise work with stock market data, or climate data. Most probably, it increases the likelihood of some of these researchers to take a look our fMRI data if we make the data look like any other time series data. Therefore, we need to present it in a familiar format, for example a table, and we have to perform a massive data reduction in order to bring down the number of variable to a comprehensible level.

There is an almost infinite number of possibilities to perform data reduction on fMRI data. We went with a simple one: use definitions of cortical and sub-cortical areas from probabilistic brain atlases (roughly 200 of them from the Harvard-Oxford cortical and sub-cortical atlases, as well as the Juelich brain atlas that are shipped with FSL), and for each area we extracted time series of the mean, median, minimum, maximum, and standard deviation of all voxels in that area for any given time point. More information on the procedure and the selected brain areas is available in the dataset's README (section: "Aggregate BOLD functional MRI for brain atlas parcellations").

So far so good, but "what for?" — a legitimate question. By condensing a fine-grained pattern of several 100k voxels into 200 time series of more-or-less arbitrarily chosen brain regions, we have thrown over board most advantages of high-resolution fMRI. Yet, I would argue that a lot can still be learned about the relatively macroscopic interplay of brain regions, even from this dramatically reduced dataset. Furthermore, I would argue that it takes very little effort with marginal storage costs to provide neuroimaging data in such an additional format — in our case simple tables in text-based CSV format or plain arrays in HDF5 format. A small investment in the potential contribution of a researcher that would have otherwise shied away from this dataset in its original form and complexity. Time will tell whether this investment will pay off.

Here is a quick demo of what kind of data analysis is now easily possible with a few lines of Python code after downloading a few megabytes of data (in contrast to dozens of gigabytes). The interactive demo below uses the powerful D3 javascript library to render a chord plot that shows the correlation of fMRI signal time series for selected brain regions for each minute of the Forrest Gump movie (the associated javascript code was derived from work of Carson Farmer). Each chord indicates a correlation of two brain regions of 0.5 or higher during the respective minute. The angular width of the circle segment for a brain regions indicates the relative magnitude of correlations with all other regions. Hover over the region label to highlight the chords of an individual brain area.

[click on the preview image to enable the demo and the time slider] ROi connectivity demo preview