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Michael Hanke 2 years ago
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+# studyforrest.org Dataset
+
+[![made-with-datalad](https://www.datalad.org/badges/made_with.svg)](https://datalad.org)
+[![PDDL-licensed](https://img.shields.io/badge/license-PDDL-blue.svg)](http://opendatacommons.org/licenses/pddl/summary)
+[![No registration or authentication required](https://img.shields.io/badge/data_access-unrestricted-green.svg)]()
+
+## 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. 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.

+ 0 - 126
README.rst

@@ -1,126 +0,0 @@
-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