From 0f735d360e5f72812ebee260242ee7563ba4aaa0 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 15 May 2024 21:23:56 -0400 Subject: [PATCH] Replace one rogue markdown [ref](url) to `ref `_ RST --- docs/reproin.rst | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/docs/reproin.rst b/docs/reproin.rst index 871d8e4f..912288b4 100644 --- a/docs/reproin.rst +++ b/docs/reproin.rst @@ -1,5 +1,5 @@ ================ -Reproin +Reproin ================ This tutorial is based on `Dianne Patterson's University of Arizona tutorials `_ @@ -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 `_ for a brief HOWTO. +That will be a topic for another tutorial but meanwhile you can checkout `reproin/issues/18 `_ for a brief HOWTO. Get Example Dataset ------------------- This example uses a phantom dataset: `reproin_dicom.zip `_ 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" @@ -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* `_. 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.