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-studyforrest.org Dataset
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-************************
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-
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-|license| |access|
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-
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-Template images and image space transformations
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-===============================================
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-
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-This repository contains data derived from the raw data releases of the
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-*studyforrest.org* project. In particular these are:
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-
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-* participant/scan-specific template images
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-* transformation between these respective image spaces
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-
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-For more information about the project visit: http://studyforrest.org
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-
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-File name conventions
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----------------------
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-
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-Each directory in the subject directories and the "templates" directory
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-corresponds to one image template. Templates in ``sub*`` directories are
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-participant-specific (not aligned across participants). However, templates with
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-the same name have corresponding input data. Templates in the ``templates``
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-directory have been derived from all participants, and there are typically
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-transformation from participant specific templates into the group template
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-space provided. Group template images carry a ``grp`` prefix in their label.
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-
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-All transformations are the output if FSL tools: either MAT files with
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-4x4 affine transformation matrices from FLIRT, or FNIRT warp files.
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-
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-Here is an example of how transformations can be located. The transformation
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-of the template image created from all 3T BOLD images of participant ``01``
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-acquired in phase 2 of the project into the group template space for 3T BOLD
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-scans can be found in:
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-
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-``sub-01/bold3Tp2/in_grpbold3Tp2/subj2tmpl_warp.nii.gz``
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-
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-Each template directory contains one or more image files with more-or-less
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-self-explanatory names, such as "head", "brain", or "brain_mask". File with
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-such a name in the one of the ``in_*`` folders represent the image in the parent
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-folder, aligned and resliced to the target space for this transformation.
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-These images can be used to inspect the quality of the transformation.
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-
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-Lastly, the ``code/`` directory contains the source code for computing template
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-images and transformation between them.
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-
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-
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-How to obtain the dataset
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--------------------------
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-
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-This repository is a `DataLad <https://www.datalad.org/>`__ dataset. It provides
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-fine-grained data access down to the level of individual files, and allows for
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-tracking future updates up to the level of single files. In order to use
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-this repository for data retrieval, `DataLad <https://www.datalad.org>`_ is
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-required. It is a free and open source command line tool, available for all
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-major operating systems, and builds up on Git and `git-annex
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-<https://git-annex.branchable.com>`__ to allow sharing, synchronizing, and
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-version controlling collections of large files. You can find information on
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-how to install DataLad at `handbook.datalad.org/en/latest/intro/installation.html
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-<http://handbook.datalad.org/en/latest/intro/installation.html>`_.
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-
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-Get the dataset
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-^^^^^^^^^^^^^^^
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-
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-A DataLad dataset can be ``cloned`` by running::
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-
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- datalad clone <url>
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-
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-Once a dataset is cloned, it is a light-weight directory on your local machine.
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-At this point, it contains only small metadata and information on the
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-identity of the files in the dataset, but not actual *content* of the
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-(sometimes large) data files.
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-
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-Retrieve dataset content
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-^^^^^^^^^^^^^^^^^^^^^^^^
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-
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-After cloning a dataset, you can retrieve file contents by running::
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-
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- datalad get <path/to/directory/or/file>
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-
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-This command will trigger a download of the files, directories, or
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-subdatasets you have specified.
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-
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-DataLad datasets can contain other datasets, so called *subdatasets*. If you
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-clone the top-level dataset, subdatasets do not yet contain metadata and
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-information on the identity of files, but appear to be empty directories. In
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-order to retrieve file availability metadata in subdatasets, run::
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-
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- datalad get -n <path/to/subdataset>
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-
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-Afterwards, you can browse the retrieved metadata to find out about
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-subdataset contents, and retrieve individual files with ``datalad get``. If you
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-use ``datalad get <path/to/subdataset>``, all contents of the subdataset will
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-be downloaded at once.
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-
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-Stay up-to-date
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-^^^^^^^^^^^^^^^
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-
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-DataLad datasets can be updated. The command ``datalad update`` will *fetch*
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-updates and store them on a different branch (by default
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-``remotes/origin/master``). Running::
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-
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- datalad update --merge
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-
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-will *pull* available updates and integrate them in one go.
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-
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-More information
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-^^^^^^^^^^^^^^^^
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-
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-More information on DataLad and how to use it can be found in the DataLad Handbook at
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-`handbook.datalad.org <http://handbook.datalad.org/en/latest/index.html>`_. The
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-chapter "DataLad datasets" can help you to familiarize yourself with the
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-concept of a dataset.
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-
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-.. _Git: http://www.git-scm.com
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-
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-.. _git-annex: http://git-annex.branchable.com/
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-
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-.. |license|
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- image:: https://img.shields.io/badge/license-PDDL-blue.svg
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- :target: http://opendatacommons.org/licenses/pddl/summary
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- :alt: PDDL-licensed
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-
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-.. |access|
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- image:: https://img.shields.io/badge/data_access-unrestricted-green.svg
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- :alt: No registration or authentication required
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