DOC: convert README to markdown #23
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# A studyforrest.org dataset extension
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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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## Eye movement events for the Forrest Gump movie
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Two groups of participants (each n=15) watched this movie. One in a lab setup,
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another one in a MRI scanner. The original data are described in Hanke et al.
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(2016, http://www.nature.com/articles/sdata201692). This dataset contains
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eye movements results of fixations, saccades, post-saccadic oscillations,
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and pursuit events. Details of the detection procedure are available in:
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Asim H. Dar, Adina S. Wagner & Michael Hanke (2019).
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[REMoDNaV: Robust Eye Movement Detection for Natural Viewing](https://github.com/psychoinformatics-de/paper-remodnav/blob/master/main.tex)
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For more information about the project visit: http://studyforrest.org
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## Dataset content
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For each participant and recording run in the original dataset, two files are
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provided in this dataset:
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- `sub-??_task-movie_run-?_events.tsv`
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- `sub-??_task-movie_run-?_events.png`
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The TSV files are BIDS-compliant event (text) files that contain one detected
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eye movement event per line. For each event the following properties are given
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(in columns):
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- `onset`: start time of an even, relative to the start of the recording (in
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seconds)
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- `duration`: duration of an event (in seconds)
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- `label`: event type label, known labels are:
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- `FIXA`: fixation
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- `PURS`: pursuit
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- `SACC/ISAC`: saccade
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- `LPSO/ILPS`: low-velocity post-saccadic oscillation
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- `HPSO/IHPS`: high-velocity post-saccadic oscillation
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- `start_x`, `start_y`: the gaze coordinate at the start of an event (in pixels)
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- `end_x`, `end_y`: the gaze coordinate at the end of an event (in pixels)
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- `amp`: movement amplitude of an event (in degrees)
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- `peak_vel`: peak velocity of an event (in degrees/second)
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- `med_vel`: median velocity of an event (in degrees/second)
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- `avg_vel`: mean peak velocity of an event (in degrees/second)
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The PNG files contain a visualization of the detected events together with the
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gaze coordinate time series, for visual quality control. The algorithm
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parameters are also rendered into the picture.
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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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|
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### Retrieve dataset content
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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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```
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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*.
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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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```
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datalad get -n <path/to/subdataset>
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|
```
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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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|
### Stay 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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|
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### Find out what has been done
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|
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DataLad datasets contain their history in the `git log`. By running `git log`
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(or a tool that displays Git history) in the dataset or on specific files, you
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|
can find out what has been done to the dataset or to individual files by whom,
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and when.
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|
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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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139
README.rst
139
README.rst
|
|
@ -1,139 +0,0 @@
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A studyforrest.org dataset extension
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************************************
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|license| |access|
|
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Eye movement events for the Forrest Gump movie
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||||||
==============================================
|
|
||||||
|
|
||||||
Two groups of participants (each n=15) watched this movie. One in a lab setup,
|
|
||||||
another one in a MRI scanner. The original data are described in Hanke et al.
|
|
||||||
(2016, http://www.nature.com/articles/sdata201692). This dataset contains
|
|
||||||
eye movements results of fixations, saccades, post-saccadic oscillations,
|
|
||||||
and pursuit events. Details of the detection procedure are available in:
|
|
||||||
|
|
||||||
Asim H. Dar, Adina S. Wagner & Michael Hanke (2019). `REMoDNaV: Robust
|
|
||||||
Eye Movement Detection for Natural Viewing
|
|
||||||
<https://github.com/psychoinformatics-de/paper-remodnav/blob/master/main.tex>`__
|
|
||||||
|
|
||||||
For more information about the project visit: http://studyforrest.org
|
|
||||||
|
|
||||||
|
|
||||||
Dataset content
|
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||||||
---------------
|
|
||||||
|
|
||||||
For each participant and recording run in the original dataset, two files are
|
|
||||||
provided in this dataset:
|
|
||||||
|
|
||||||
- ``sub-??_task-movie_run-?_events.tsv``
|
|
||||||
- ``sub-??_task-movie_run-?_events.png``
|
|
||||||
|
|
||||||
The TSV files are BIDS-compliant event (text) files that contain one detected
|
|
||||||
eye movement event per line. For each event the following properties are given
|
|
||||||
(in columns):
|
|
||||||
|
|
||||||
- ``onset``: start time of an even, relative to the start of the recording (in
|
|
||||||
seconds)
|
|
||||||
- ``duration``: duration of an event (in seconds)
|
|
||||||
- ``label``: event type label, known labels are:
|
|
||||||
- ``FIXA``: fixation
|
|
||||||
- ``PURS``: pursuit
|
|
||||||
- ``SACC`/`ISAC``: saccade
|
|
||||||
- ``LPSO`/`ILPS``: low-velocity post-saccadic oscillation
|
|
||||||
- ``HPSO`/`IHPS``: high-velocity post-saccadic oscillation
|
|
||||||
- ``start_x``, ``start_y``: the gaze coordinate at the start of an event (in pixels)
|
|
||||||
- ``end_x``, ``end_y``: the gaze coordinate at the end of an event (in pixels)
|
|
||||||
- ``amp``: movement amplitude of an event (in degrees)
|
|
||||||
- ``peak_vel``: peak velocity of an event (in degrees/second)
|
|
||||||
- ``med_vel``: median velocity of an event (in degrees/second)
|
|
||||||
- ``avg_vel``: mean peak velocity of an event (in degrees/second)
|
|
||||||
|
|
||||||
The PNG files contain a visualization of the detected events together with
|
|
||||||
with the gaze coordinate time series, for visual quality control. The
|
|
||||||
algorithm parameters are also rendered into the picture.
|
|
||||||
|
|
||||||
|
|
||||||
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
|
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^^^^^^^^^^^^^^^
|
|
||||||
|
|
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A DataLad dataset can be ``cloned`` by running::
|
|
||||||
|
|
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datalad clone https://github.com/psychoinformatics-de/studyforrest-data-eyemovementlabels.git
|
|
||||||
|
|
||||||
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.
|
|
||||||
|
|
||||||
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-PPDL-blue.svg
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:target: http://opendatacommons.org/licenses/pddl/summary
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:alt: PDDL-licensed
|
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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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