Pre-aligned MRI data
This repository contains data derived from the raw data releases of the
studyforrest.org project. In particular these are:
For more information about the project visit: http://studyforrest.org
File name conventions
Each directory in the subject directories corresponds to one template image
space. Data in
sub* directories are participant-specific (not aligned
across participants). However, templates with
the same name have corresponding input data.
Each directory contains one or more image files with more-or-less
self-explanatory names, identifying the corresponding participant and scan.
code/ directory contains the source code for computing all
files contained, as well as a number of validation analyses.
How to obtain the dataset
This repository is a DataLad dataset. It provides
fine-grained data access down to the level of individual files, and allows for
tracking future updates. In order to use this repository for data retrieval,
DataLad is required. It is a free and
open source command line tool, available for all major operating
systems, and builds up on Git and git-annex
to allow sharing, synchronizing, and version controlling collections of
large files. You can find information on how to install DataLad at
Get the dataset
A DataLad dataset can be
cloned by running
datalad clone <url>
Once a dataset is cloned, it is a light-weight directory on your local machine.
At this point, it contains only small metadata and information on the
identity of the files in the dataset, but not actual content of the
(sometimes large) data files.
Retrieve dataset content
After cloning a dataset, you can retrieve file contents by running
datalad get <path/to/directory/or/file>`
This command will trigger a download of the files, directories, or
subdatasets you have specified.
DataLad datasets can contain other datasets, so called subdatasets.
If you clone the top-level dataset, subdatasets do not yet contain
metadata and information on the identity of files, but appear to be
empty directories. In order to retrieve file availability metadata in
datalad get -n <path/to/subdataset>
Afterwards, you can browse the retrieved metadata to find out about
subdataset contents, and retrieve individual files with
If you use
datalad get <path/to/subdataset>, all contents of the
subdataset will be downloaded at once.
Keep data up-to-date
DataLad datasets can be updated. The command
datalad update will
fetch updates and store them on a different branch (by default
datalad update --merge
will pull available updates and integrate them in one go.
Find out what has been done
DataLad datasets contain their history in the
git log. By running
log (or a tool that displays Git history) in the dataset or on specific files,
you can find out what has been done to the dataset or to individual files by
whom, and when.
More information on DataLad and how to use it can be found in the DataLad Handbook at
handbook.datalad.org. The chapter
"DataLad datasets" can help you to familiarize yourself with the concept of a dataset.