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