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# studyforrest.org Dataset
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[](https://datalad.org)
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[](http://opendatacommons.org/licenses/pddl/summary)
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[]()
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## Pre-aligned MRI data
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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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* BOLD fMRI timeseries aligned to subject-specific template images
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and using transformations available from
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https://github.com/psychoinformatics-de/studyforrest-data-templatetransforms
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For more information about the project visit: http://studyforrest.org
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## File name conventions
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Each directory in the subject directories corresponds to one template image
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space. Data in ``sub*`` directories are participant-specific (not aligned
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across participants). However, templates with
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the same name have corresponding input data.
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Each directory contains one or more image files with more-or-less
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self-explanatory names, identifying the corresponding participant and scan.
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Lastly, the ``code/`` directory contains the source code for computing all
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files contained, as well as a number of validation analyses.
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## How to obtain the dataset
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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. In order to use this repository for data retrieval,
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[DataLad](https://www.datalad.org/) is required. It is a free and
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open source command line tool, available for all major operating
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systems, and builds up on Git and [git-annex](https://git-annex.branchable.com/)
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to allow sharing, synchronizing, and version controlling collections of
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large files. You can find information on how to install DataLad at
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[handbook.datalad.org/en/latest/intro/installation.html](http://handbook.datalad.org/en/latest/intro/installation.html).
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### Get the dataset
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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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### Retrieve dataset content
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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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DataLad datasets can contain other datasets, so called *subdatasets*.
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If you clone the top-level dataset, subdatasets do not yet contain
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metadata and information on the identity of files, but appear to be
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empty directories. In order to retrieve file availability metadata in
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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`.
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If you use `datalad get <path/to/subdataset>`, all contents of the
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subdataset will be downloaded at once.
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|
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### Keep data up-to-date
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|
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DataLad datasets can be updated. The command `datalad update` will
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*fetch* 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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### Find out what has been done
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DataLad datasets contain their history in the ``git log``. By running ``git
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log`` (or a tool that displays Git history) in the dataset or on specific files,
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you can find out what has been done to the dataset or to individual files by
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whom, and when.
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### More information
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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 chapter
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"DataLad datasets" can help you to familiarize yourself with the concept of a dataset.
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115
README.rst
115
README.rst
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@ -1,115 +0,0 @@
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studyforrest.org Dataset
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************************
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|license| |access|
|
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Pre-aligned MRI data
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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:
|
|
||||||
|
|
||||||
* BOLD fMRI timeseries aligned to subject-specific template images
|
|
||||||
and using transformations available from
|
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https://github.com/psychoinformatics-de/studyforrest-data-templatetransforms
|
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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 corresponds to one template image
|
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||||||
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.
|
|
||||||
|
|
||||||
Lastly, the ``code/`` directory contains the source code for computing all
|
|
||||||
files contained, as well as a number of validation analyses.
|
|
||||||
|
|
||||||
|
|
||||||
How to obtain the dataset
|
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||||||
-------------------------
|
|
||||||
|
|
||||||
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>`_.
|
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||||||
|
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||||||
Get the dataset
|
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||||||
^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
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.
|
|
||||||
|
|
||||||
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
|
|
||||||
``remotes/origin/master``). Running::
|
|
||||||
|
|
||||||
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 ``git 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
|
|
||||||
^^^^^^^^^^^^^^^^
|
|
||||||
|
|
||||||
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.
|
|
||||||
|
|
||||||
.. |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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