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Replace one rogue markdown [ref](url) to ref <url>_ RST #759

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May 16, 2024
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Replace one rogue markdown [ref](url) to ref <url>_ RST #759

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8 changes: 4 additions & 4 deletions docs/reproin.rst
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
================
Reproin
Reproin
================

This tutorial is based on `Dianne Patterson's University of Arizona tutorials <https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/heudiconv.html#lesson-3-reproin-py>`_
Expand All @@ -10,14 +10,14 @@ MR scanners.

If you can control how your image sequences are named at the scanner, you can use the *reproin* naming convention.
If you cannot control such naming, or already have collected data, you can provide your custom heuristic mapping into *reproin* and thus in effect use reproin heuristic.
That will be a topic for another tutorial but meanwhile you can checkout `reproin/issues/18 <https://github.com/ReproNim/reproin/issues/18#issuecomment-834598084>`_ for a brief HOWTO.
That will be a topic for another tutorial but meanwhile you can checkout `reproin/issues/18 <https://github.com/ReproNim/reproin/issues/18#issuecomment-834598084>`_ for a brief HOWTO.

Get Example Dataset
-------------------

This example uses a phantom dataset: `reproin_dicom.zip <https://datasets.datalad.org/?dir=/repronim/heudiconv-reproin-example>`_ generated by the University of Arizona on their Siemens Skyra 3T with Syngo MR VE11c software on 2018_02_08.

The ``REPROIN`` directory is a simple reproin-compliant DICOM (.dcm) dataset without sessions.
The ``REPROIN`` directory is a simple reproin-compliant DICOM (.dcm) dataset without sessions.
(Derived dwi images (ADC, FA etc.) that the scanner produced have been removed.::

[user@local ~/reproin_dicom/REPROIN]$ tree -I "*.dcm"
Expand Down Expand Up @@ -82,7 +82,7 @@ If not, ReproIn heuristic bases it on the value of the DICOM "Study Description"
Reproin Scanner File Names
****************************

* For both BIDS and *reproin*, names are composed of an ordered series of key-value pairs, called [*entities*](https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/entities.yaml).
* For both BIDS and *reproin*, names are composed of an ordered series of key-value pairs, called `*entities* <https://github.com/bids-standard/bids-specification/blob/master/src/schema/objects/entities.yaml>`_.
Each key and its value are joined with a dash ``-`` (e.g., ``acq-MPRAGE``, ``dir-AP``).
These key-value pairs are joined to other key-value pairs with underscores ``_``.
The exception is the modality label, which is discussed more below.
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