From e406f55618a23ac6bc3004173a525d65021526e6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?S=C3=A9amus=20O=27Sullivan?=
<seamus.osullivan@psych.ox.ac.uk>
Date: Thu, 12 Dec 2024 00:43:50 +0000
Subject: [PATCH] Fix broken links for protocols pages.
---
docs/protocols.md | 4 ++--
docs/protocols/protocols_guide_external.md | 2 +-
docs/protocols/protocols_guide_internal-how-1.md | 12 ++++++------
docs/protocols/protocols_guide_internal-how-2.md | 2 +-
docs/protocols/protocols_guide_internal-how-3.md | 4 ++--
docs/protocols/protocols_guide_internal-how-4.md | 2 +-
docs/protocols/protocols_guide_internal-why-use.md | 10 +++++-----
docs/protocols/protocols_guide_internal.md | 2 +-
8 files changed, 19 insertions(+), 19 deletions(-)
diff --git a/docs/protocols.md b/docs/protocols.md
index af4e0ab5..08fcb062 100644
--- a/docs/protocols.md
+++ b/docs/protocols.md
@@ -14,7 +14,7 @@ How to share your magnetic resonance imaging protocols
---
-
+
## Purpose
@@ -32,7 +32,7 @@ Available here: [http://open.win.ox.ac.uk/protocols/](http://open.win.ox.ac.uk/p
Training guides are available for WIN members and external users. Access the guides below or via the left navigation menu.
-[](../protocols/protocols_guide_internal-how-1) [](../protocols/protocols_guide_external)
+[]({% link docs/protocols/protocols_guide_internal-how-1.md %}) []({% link docs/protocols/protocols_guide_external.md %})
<!-- ## Citation
diff --git a/docs/protocols/protocols_guide_external.md b/docs/protocols/protocols_guide_external.md
index 1a3f7d0e..c65aae10 100644
--- a/docs/protocols/protocols_guide_external.md
+++ b/docs/protocols/protocols_guide_external.md
@@ -22,7 +22,7 @@ A guide for external researchers on how to use the Open WIN MR protocols databas
## For external researchers
External researchers are able to search the database for MR protocols which research teams have chosen to make openly available. These may be deposited to support publications as supplementary methods material, or they may form the main body of research in sequence development.
-
+
### 1. Access the MR Protocols database
Available here: [http://open.win.ox.ac.uk/protocols/](http://open.win.ox.ac.uk/protocols/)
diff --git a/docs/protocols/protocols_guide_internal-how-1.md b/docs/protocols/protocols_guide_internal-how-1.md
index 2e1ebee2..ebc699af 100644
--- a/docs/protocols/protocols_guide_internal-how-1.md
+++ b/docs/protocols/protocols_guide_internal-how-1.md
@@ -13,7 +13,7 @@ nav_order: 2
---
-<!--  -->
+<!--  -->
## Contents
@@ -50,7 +50,7 @@ You might want to add a statement such as "available for re-use, but I'm unable
Only WIN members (as determined by SSO authentication) are able to deposit protocols in the database.
-
+
To log in:
1. Go to [https://open.win.ox.ac.uk/protocols/](https://open.win.ox.ac.uk/protocols/)
@@ -63,7 +63,7 @@ To log in:
Protocols are saved to individual user profiles.
-
+
1. Once you are logged in, you will see the `Add Protocol` icon.
2. Click on `Add Protocol`, and you will be taken to the `Add new protocol` page.
@@ -81,7 +81,7 @@ You can enter details about your protocol which are relevant to the study as a w
NOTE: If you are publishing customised pulse sequences, please be sure to indicate your willingness and requirements for sharing them (see [3.4.1 Custom Sequences](#3-4-1-custom-sequences) below).
-
+
### 3.1 Project, hardware and species
Some fields of this section are autmatically retrieved from your pdf and other ones have to be added by selecting the appropriate items from the dropdown menus like:
@@ -141,7 +141,7 @@ You can add details specific to individual sequences. These details may make the
Each of the sections below should be completed for each sequence.
-
+
### 5.1 Sequence name
This is identified from the pdf. You can update it or add any additional context where necessary.
@@ -181,4 +181,4 @@ Add any references which are relevant to this protocol for example the accompany
We recommend that you consider using the [CRediT](https://casrai.org/credit/) system for identifying individual author contributions. You may wish to order authors alphabetically.
-
+
diff --git a/docs/protocols/protocols_guide_internal-how-2.md b/docs/protocols/protocols_guide_internal-how-2.md
index 7ec823d6..6c93f2e9 100644
--- a/docs/protocols/protocols_guide_internal-how-2.md
+++ b/docs/protocols/protocols_guide_internal-how-2.md
@@ -13,7 +13,7 @@ nav_order: 3
---
-<!--  -->
+ <!-- -->
We suggest using the free tool Zenodo for creating a Digital Object Identifier (DOI) for your protocol. This will allow others to cite your protocol independently from other work in the study and add contributors who may not be named elsewhere.
diff --git a/docs/protocols/protocols_guide_internal-how-3.md b/docs/protocols/protocols_guide_internal-how-3.md
index edc0f37c..f4f8d609 100644
--- a/docs/protocols/protocols_guide_internal-how-3.md
+++ b/docs/protocols/protocols_guide_internal-how-3.md
@@ -13,12 +13,12 @@ nav_order: 4
---
-<!--  -->
+<!---->
If you are using the protocols database to track changes made to your protocol while piloting, you can amend the entry and create a new version that can be reviewed at any point.
-
+
1. Go to `my protocols` and find the entry you would like to update.
2. Select if you are adding a new protocol pdf file (`Update with new protocol file`) or making changes to other parts of the entry (`Update keeping existing protocol file`)
diff --git a/docs/protocols/protocols_guide_internal-how-4.md b/docs/protocols/protocols_guide_internal-how-4.md
index 3cb704ac..79ca39ff 100644
--- a/docs/protocols/protocols_guide_internal-how-4.md
+++ b/docs/protocols/protocols_guide_internal-how-4.md
@@ -13,7 +13,7 @@ nav_order: 5
---
-<!--  -->
+<!---->
You can track how many times your protocol has been viewed and downloaded from the `Engagement Statistics` panel. Views and downloads are separated into internal to Oxford (users have logged in with an SSO) or external. When reporting on the impact of your entry, remember to also include the Zenodo views and downloads statistics, if you have used Zenodo to create a DOI.
diff --git a/docs/protocols/protocols_guide_internal-why-use.md b/docs/protocols/protocols_guide_internal-why-use.md
index 0ac6ef92..4b7708dc 100644
--- a/docs/protocols/protocols_guide_internal-why-use.md
+++ b/docs/protocols/protocols_guide_internal-why-use.md
@@ -15,20 +15,20 @@ Why you should consider using the WIN MR protocols database to record and share
---
-<!--  -->
+ <!-- -->
*The MR protocol database has been developed to share MR protocols internally across WIN as well as externally. The database provides access to standard protocols and to the latest experimental protocols uploaded by WIN members. The database facilitates sharing your MR sequence within and between research groups and helps you to keep track of updates using version control. Each deposited protocol contains all information necessary to reproduce that sequence on an appropriately licensed scanner, allowing yourself and others to have a permanent and full record of your data acquisition methodology.*
## Benefits
-### Version control 
-The MR Protocols database is version controlled, so WIN members are invited to upload their protocols during piloting to keep track of optimisation and final versions. Comments and notes can be added to each entry so you can keep well structured documentation about why certain decisions were made. You can also link database entries with acquired data held on the [Open Data](../../data) server
+### Version control 
+The MR Protocols database is version controlled, so WIN members are invited to upload their protocols during piloting to keep track of optimisation and final versions. Comments and notes can be added to each entry so you can keep well structured documentation about why certain decisions were made. You can also link database entries with acquired data held on the [Open Data]({% link docs/data.md %}) server.
-### Citable research output 
+### Citable research output 
Versions (with minor and major edits) can be assigned a digital object identifier (DOI) using the [Oxford Research Archive (ORA) Data repository](https://deposit.ora.ox.ac.uk) using the stable link provided by the MR Protocols database. Once a DOI has been created, your MR protocol becomes a citable object which you can add to your list of research outputs.
-### Reproducible methods detail 
+### Reproducible methods detail 
Depositing your MR protocol in the database is as simple as uploading the sequence pdf available from the scanner console, or alternatively you can upload the .exar file used by our [Siemens scanners](https://www.win.ox.ac.uk/about/facilities). Sequences' details are captured from either document and parsed into a unified machine readable and searchable format. You can upload a single sequence or all sequences used in a single imaging session (a protocol) together.
diff --git a/docs/protocols/protocols_guide_internal.md b/docs/protocols/protocols_guide_internal.md
index e8ca57cc..ac79f8a2 100644
--- a/docs/protocols/protocols_guide_internal.md
+++ b/docs/protocols/protocols_guide_internal.md
@@ -14,4 +14,4 @@ nav_exclude: true
---
-
+
--
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