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-studyforrest.org Dataset
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-************************
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-
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-|license| |access| |doi|
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-Retinotopic Mapping
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-===================
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-
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-All participants in the phase2 extension of the studyforrest dataset underwent
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-retinotopic mapping with standard flickering checkerboard stimulus (ring and
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-wedges). More information on the procedure and the results can be found in:
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-
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- Ayan Sengupta, Falko R. Kaule, J. Swaroop Guntupalli, Michael B. Hoffmann,
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- Christian Häusler, Jörg Stadler, Michael Hanke. `An extension of the
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- studyforrest dataset for vision research
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- <http://biorxiv.org/content/early/2016/03/31/046573>`_. (submitted for
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- publication)
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-
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-For further information about the project visit: http://studyforrest.org
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-
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-Content
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--------
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-
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-``code/``:
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- source code for retinotopic mapping analysis.
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-
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- - The main script is *process_retmap* and a Python based GUI *easyret_gui* to
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- call it from an easy to use front end. The *process_retmap* script calls the
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- Python scripts *RetMap_phaseshift* for post processing phase shift (if
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- required) and *combine_volumes* for combining the clw/ccw maps and ecc/con
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- maps together.
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-
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-``src/``:
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- links to repositories containing all inputs for the analysis
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-
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-``sub-??/``:
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- analysis results per participant
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-
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- ``surface_maps/``:
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- contains eccentricity and polar angle maps of left and right hemispheres
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- of a particular participant's cortical surface in *MGH* format
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-
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- ``post_processing/``:
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- contains the post-processed/combined compressed *NIfTI* files in a
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- participant's bold3Tp2 image template space
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- (see ``src/templatetransforms``), before it is aligned to the
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- *T1 structural* and represented on cortical surfaces.
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-
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-``qa/``:
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- contains the *pyretmap_subjQuali.ods* file which details the quality of the
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- participant-wise retinotopic maps produced by the *processing pipeline*.
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-
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-
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-How to obtain the data files
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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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-
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-.. |doi|
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- image:: https://img.shields.io/badge/doi-missing-lightgrey.svg
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- :target: http://dx.doi.org/
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- :alt: DOI
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Laura Waite