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Fixed two dead URLs
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marcelzwiers committed May 13, 2021
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2 changes: 1 addition & 1 deletion docs/finalizing.rst
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Expand Up @@ -5,7 +5,7 @@ After a successful run of bidscoiner, the work to convert your data in a fully c

Adding more meta-data
---------------------
To make your dataset reproducable and shareable, you should add study-level meta-data in the modality agnostic BIDS files (BIDScoin saves stub versions of them). For instance, you should update the content of the ``dataset_description.json`` and ``README`` files in your bids folder and you may need to provide e.g. additional ``*_sessions.tsv`` or ``participants.json`` files (see the `BIDS specification <http://bids.neuroimaging.io/bids_spec.pdf>`__ for more information). Moreover, if you have behavioural log-files you will find that BIDScoin does not (yet) support converting these into BIDS compliant ``*_events.tsv/json`` files (advanced users are encouraged to use the bidscoiner `plug-in <advanced.html#plugins>`__ option and write their own log-file parser).
To make your dataset reproducable and shareable, you should add study-level meta-data in the modality agnostic BIDS files (BIDScoin saves stub versions of them). For instance, you should update the content of the ``dataset_description.json`` and ``README`` files in your bids folder and you may need to provide e.g. additional ``*_sessions.tsv`` or ``participants.json`` files (see the `BIDS specification <https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html>`__ for more information). Moreover, if you have behavioural log-files you will find that BIDScoin does not (yet) support converting these into BIDS compliant ``*_events.tsv/json`` files (advanced users are encouraged to use the bidscoiner `plug-in <advanced.html#plugins>`__ option and write their own log-file parser).

Data sharing utilities
----------------------
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2 changes: 1 addition & 1 deletion docs/tutorial.rst
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Expand Up @@ -4,7 +4,7 @@ Demo and tutorial
BIDS introduction and BIDScoin demo
-----------------------------------

A good starting point to learn more about BIDS and BIDScoin is to watch `this presentation <https://youtu.be/aRDK4Gj5qzE>`__ from the OpenMR Benelux 2020 meeting (`slides <https://osf.io/pm36z/>`__). The first 14 minutes `Robert Oostenveld <https://openmrbenelux.github.io/page-speakers/#robert>`__ provides a general overview of the BIDS standard, after which `Marcel Zwiers <https://www.linkedin.com/in/mzwiers>`__ presents the design of BIDScoin and demonstrates hands-on how you can use it to convert a dataset to BIDS.
A good starting point to learn more about BIDS and BIDScoin is to watch `this presentation <https://youtu.be/aRDK4Gj5qzE>`__ from the OpenMR Benelux 2020 meeting (`slides <https://osf.io/pm36z/>`__). The first 14 minutes Robert Oostenveld provides a general overview of the BIDS standard, after which Marcel Zwiers presents the design of BIDScoin and demonstrates hands-on how you can use it to convert a dataset to BIDS.

BIDScoin tutorial
-----------------
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2 changes: 1 addition & 1 deletion docs/workflow.rst
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Expand Up @@ -130,7 +130,7 @@ If the preview of the BIDS filename and meta-data both look good, you can store

.. figure:: ./_static/bidseditor_edit.png

The edit window for customizing a bidsmap run item, showing the ``acq`` value being set to ``phantom``
The edit window for customizing a bidsmap run item, featuring the ``TaskName`` value being set to something more informative

Finally, if all BIDS output names in the main window are fine, you can click on the ``Save`` button and proceed with running the bidscoiner tool. Note that the bidsmapper and bidseditor don't do anything except reading from and writing to a bidsmap yaml-file.

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