Substitute relative paths with absolute links.

docs/gitlab/4-4-create-gitlab-pages-site.md

@@ -18,12 +18,12 @@ Use the magic of Jekyll to transform markdown pages into a website
 
 > **Note**
 >
-> This guide describes how to publish your project with **GitLab** Pages. If you are planning to publish a GitHub repo, see the [GitHub Pages Guide](../4-3-you-make-your-pages-site) instead!
+> This guide describes how to publish your project with **GitLab** Pages. If you are planning to publish a GitHub repo, see the [GitHub Pages Guide]({% link docs/gitlab/4-3-you-make-your-pages-site.md %}) instead!
 
 
 ## 1. Turn your repo into a GitLab Pages site!
 
-Now the magic! Turn the simple collection of files made in [the previous tutorial](../4-1-you-make-your-repo) into something which looks like a user friendly website!
+Now the magic! Turn the simple collection of files made in [the previous tutorial]({% link docs/gitlab/4-1-you-make-your-repo.md %}) into something which looks like a user friendly website!
 
 
 **Start from a WIN template**

docs/gitlab/gitlab-tutorials.md

@@ -21,30 +21,30 @@ Follow the below tutorials (left in the navigation panel) to set up and use GitL
 **NOTE: These tutorials contain gifs of the processes being demonstrated on GitHub rather than GitLab. These are being included as they are still a useful demonstration. Please stay tuned for a GitLab based update.**
 
 ### 1. Tools for git and GitLab
-- [1.1 Using the command line](../1-1-tools-command-line)
-- [1.2 Writing in markdown](../1-2-tools-markdown)
-- [1.3 Text editors](../1-3-tools-atom)
+- [1.1 Using the command line]({% link docs/gitlab/1-1-tools-command-line.md %})
+- [1.2 Writing in markdown]({% link docs/gitlab/1-2-tools-markdown.md %})
+- [1.3 Text editors]({% link docs/gitlab/1-3-tools-atom.md %})
 
 ### 2. Getting started
-- [2.1 Your GitLab account](../2-1-starting-gitlab-account)
-- [2.2 Global git configuration](../2-2-starting-configure-git)
-- [2.3 Your local repository](../2-3-starting-local-repo)
-- [2.4 Basic git commands](../2-4-starting-git-basics)
+- [2.1 Your GitLab account]({% link docs/gitlab/2-1-starting-gitlab-account.md %})
+- [2.2 Global git configuration]({% link docs/gitlab/2-2-starting-configure-git.md %})
+- [2.3 Your local repository]({% link docs/gitlab/2-3-starting-local-repo.md %})
+- [2.4 Basic git commands]({% link docs/gitlab/2-4-starting-git-basics.md %})
 
 ### 3. Collaborating on GitLab
-- [3.1 Collaborating on GitLab](../3-1-collaborating-stranger-or-collaborator)
-- [3.2 Collaborating with a stranger](../3-2-collaborating-fork-their-repo)
-- [3.3 Play with this page](../3-3-collaborating-play-with-this-page)
+- [3.1 Collaborating on GitLab]({% link docs/gitlab/3-1-collaborating-stranger-or-collaborator.md %})
+- [3.2 Collaborating with a stranger]({% link docs/gitlab/3-2-collaborating-fork-their-repo.md %})
+- [3.3 Play with this page]({% link docs/gitlab/3-3-collaborating-play-with-this-page.md %})
 
 ### 4. Making and publishing your repository
-- [4.1 Make a repository](../4-1-you-make-your-repo)
-- [4.2 Create a doi](../4-2-you-doi)
-- [4.3 Create a GitHub Pages site](../4-3-you-make-your-pages-site)
-- [4.4 Create a GitLab Pages site](../4-4-create-gitlab-pages-site)
+- [4.1 Make a repository]({% link docs/gitlab/4-1-you-make-your-repo.md %})
+- [4.2 Create a doi]({% link docs/gitlab/4-2-you-doi.md %})
+- [4.3 Create a GitHub Pages site]({% link docs/gitlab/4-3-you-make-your-pages-site.md %})
+- [4.4 Create a GitLab Pages site]({% link docs/gitlab/4-4-create-gitlab-pages-site.md %})
 
 ### 5. Managing your project on GitLab
-- [5.1 GitLab issues](../5-1-projectmanagement-issues)
-- [5.2 GitLab milestones](../5-2-projectmanagement-milestones)
+- [5.1 GitLab issues]({% link docs/gitlab/5-1-projectmanagement-issues.md %})
+- [5.2 GitLab milestones]({% link docs/gitlab/5-2-projectmanagement-milestones.md %})
 
 ## Who should I ask for further advice about using GitLab
 The Open WIN community are a great resource for support in using GitLab. [Join the community](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/contact/) and try asking your question on slack!

docs/gitlab/repo-doi.md

@@ -15,7 +15,7 @@ How to create a doi in zenodo for your GitLab project
 
 ---
 
-*Note this is a duplicate of [tutorial 4.2 Create a DOI](../4-2-you-doi)*
+*Note this is a duplicate of [tutorial 4.2 Create a DOI]({% link docs/gitlab/4-2-you-doi.md %})*
 
 Zenodo is free to use tool for creating a digital object identifier (doi) for your shared resources. A doi is essential for enabling other researchers to cite and reuse your material, and for you to receive proper attribution. Your doi entry will include your [ORCID ID](https://info.orcid.org/benefits-for-researchers/), so it can be tracked against all your other research outputs.
 

docs/gitlab/repo-include.md

@@ -33,14 +33,14 @@ Take a look at the Open WIN "[Data Sharing Decision Tree](https://git.fmrib.ox.a
 4. **What do we need?**: Describe what contributions you would like to receive. Link to your CONTRIBUTING.md file for more information.
 5. **Who are we?**: Identify who you are. Link to your lab pages.
 6. **Contact us**: Give clear instructions for how people can get in touch.
-7. **Acknowledgements and citation**: Give clear guidance on how people should cite your material. This should include the [doi for the repository](../repo-doi) and any supporting papers.
+7. **Acknowledgements and citation**: Give clear guidance on how people should cite your material. This should include the [doi for the repository]({% link docs/gitlab/repo-doi.md %}) and any supporting papers.
 
 
 ### CONTRIBUTING.md
 This file describes what contributions you would like to this material and how people should get in touch. Remember, an important benefit of sharing your resource is to invite collaborators. Make it easy for people to get involved.
 
 ### CITATION.cff
-This is a standardised file format which provides the exact metadata people will need to cite your repository (using the [doi you generate](../repo-doi)). It is easy to read by machines and humans, and is quickly becoming a sector standard - look out for a CITATION.cff in other software tools you use!
+This is a standardised file format which provides the exact metadata people will need to cite your repository (using the [doi you generate]({% link docs/gitlab/repo-doi.md %}). It is easy to read by machines and humans, and is quickly becoming a sector standard - look out for a CITATION.cff in other software tools you use!
 
 You can generate a CITATION.cff for your project using [this online tool from Citation File Format](https://citation-file-format.github.io/cff-initializer-javascript/#/).
 
@@ -51,4 +51,4 @@ This file lists the terms of reuse of your material. GitLab will suggest some st
 
 Any material you produce while employed by the University of Oxford should be [copyright to the University](https://innovation.ox.ac.uk/university-members/commercialising-technology/ip-patents-licenses/software-copyright/)
 
-See the [licensing guide](../repo-license) for a more complete discussion of which license you should consider applying to your code.
+See the [licensing guide]({% link docs/repo-license.md %}) for a more complete discussion of which license you should consider applying to your code.

docs/open-leadership.md

@@ -16,7 +16,7 @@ Find out about the principles guiding this project
 
 This project is being developed with the guiding principle of "Open Leadership". The Open Leadership framework was developed by Mozilla to support open source community projects. It describes a set of tools and practices which have been used in creating this repository along with exercises which have helped design effective paths to contribution. These principles were passed to the Open WIN Community Coordinator through participation in the [Open Life Science](https://openlifesci.org) program.
 
-![Mozilla Open Leadership structure](../../img/img-open-leadership.png)
+![Mozilla Open Leadership structure]({% link img/img-open-leadership.png %})
 
 # Mozilla Open Leadership Framework
 
@@ -53,11 +53,11 @@ We are working open as this is an effective way to develop a user focused and in
 
 The open canvas is designed to help define project goals, strategy and resource needs to create a minimum viable product (MVP). The images below describe the sections for the open canvas and the model we have drafted for the future [Open WIN Ambassadors](ambassadors.md) program.
 
-![Open canvas section descriptions](../../img/mozilla-framework/open-canvas-instruc.png)
+![Open canvas section descriptions](% link img/mozilla-framework/open-canvas-instruc.png %)
 
 <!-- <img src="/img/mozilla-framework/open-canvas-instructpng" alt="Open canvas section descriptions"  width="100%" height="50%"> -->
 
-![Open canvas for WIN Open Ambassadors Program](../../img/mozilla-framework/open-canvas-ambas.png)
+![Open canvas for WIN Open Ambassadors Program]({% link img/mozilla-framework/open-canvas-ambas.png %})
 
 <!-- <img src="/img/mozilla-framework/open-canvas-ambasspng" alt="Open canvas for WIN Open Ambassadors Program"  width="100%" height="50%"> -->
 
@@ -65,37 +65,37 @@ The open canvas is designed to help define project goals, strategy and resource
 
 A project README is your welcome mat. It should set the tone for the project, clearly describe the motivations and orient potential contributors.
 
-The README for the Open WIN Community is the [home page of this repository](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/blob/master/README.md?ref_type=heads)             (../index.md).
+The README for the Open WIN Community is the [home page of this repository](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/blob/master/README.md?ref_type=heads)             ({% link index.md %}).
 
 ### Project Roadmap
 
 The roadmap outlines the plan for work ahead and should be shared openly with potential contributors. It summarises your vision and timeline for tasks. It is shared so people can see your progress along with the path you intend to travel. Openness here fosters trust and demonstrates an intention to involve your community in your activities.
 
-Take a look at our [roadmap for the community](community/roadmap.md).
+Take a look at our [roadmap for the community]({% link docs/community/roadmap.md %}).
 
 ### Personas and pathways
 
 This exercise helps you think about the different people who will engage with the project, how they will find you, and how you will help to develop them into sustained contributors and future leaders of the project.
 
-Take a look at our [personas and pathways analysis for the community](community/personas-and-pathways.md).
+Take a look at our [personas and pathways analysis for the community]({% link docs/community/personas-and-pathways.md %}).
 
 ### Code of conduct
 
 This sets out how we will interact with each other when working on this project, and how we will report and take appropriate actions against violations of this code of conduct
 
-Take a look at our [participation guidelines](community/CODE_OF_CONDUCT.md) and how we will support enacting University wide policies on harassment
+Take a look at our [participation guidelines]({% link docs/community/CODE_OF_CONDUCT.md %}) and how we will support enacting University wide policies on harassment
 
 ### Contributor guidelines
 
 This describes how you can engage with the project, both as a one-time contributor or sustained participant.
 
-Take a look at our [contributing guidelines](CONTRIBUTING.md).
+Take a look at our [contributing guidelines]({% link docs/CONTRIBUTING.md %}).
 
 ### License and citing the repository
 
 We would love for others to use, share and reference this repository and the materials contained within. We have applied a CC-BY 4.0 licence  so you can share and adapt the materials here as long as attribution is given to this project.
 
-Take a look at our [license and citation guidelines](LICENSE.md).
+Take a look at our [license and citation guidelines]({% link docs/LICENSE.md %}).
 
 ### Publish your project openly
 

docs/protocols.md

@@ -14,7 +14,7 @@ How to share your magnetic resonance imaging protocols
 
 ---
 
-![open-protocols](../../img/img-open-mrprot-flow.png)
+![open-protocols]({% link img/img-open-mrprot-flow.png %})
 
 ## 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.
 
-[![For WIN members](../../img/btn-win.png)](../protocols/protocols_guide_internal-how-1)      [![For external researchers](../../img/btn-external.png)](../protocols/protocols_guide_external)
+[![For WIN members]({% link img/btn-win.png %})]({% link docs/protocols/protocols_guide_internal-how-1.md %})      [![For external researchers]({% link img/btn-external.png %})]({% link docs/protocols/protocols_guide_external.md %})
 
 
 <!-- ## Citation

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.
 
-![gif - external](../../../img/img-protocols/gif_external.gif)
+![gif - external]({% link img/img-protocols/gif_external.gif %})
 
 ### 1. Access the MR Protocols database
 Available here: [http://open.win.ox.ac.uk/protocols/](http://open.win.ox.ac.uk/protocols/)

docs/protocols/protocols_guide_internal-how-1.md

@@ -13,7 +13,7 @@ nav_order: 2
 
 ---
 
-<!-- ![open-protocols](../../../img/img-open-mrprot-flow.png) -->
+<!-- ![open-protocols]({% link img/img-open-mrprot-flow.png %}) -->
 
 
 ## 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.
 
-![gif-log in](../../../img/img-protocols/gif_login.gif)
+![gif-log in]({% link img/img-protocols/gif_login.gif %})
 
 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.
 
-![gif - add new protocol](../../../img/img-protocols/gif_add-protocol.gif)
+![gif - add new protocol]({% link img/img-protocols/gif_add-protocol.gif %})
 
 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).
 
-![gif - top details](../../../img/img-protocols/gif_top-details.gif)
+![gif - top details]({% link img/img-protocols/gif_top-details.gif %})
 
 ### 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.
 
-![gif - sequence details](../../../img/img-protocols/gif_sequence-details.gif)
+![gif - sequence details]({% link img/img-protocols/gif_sequence-details.gif %})
 
 ### 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.
 
-![gif - references](../../../img/img-protocols/gif_references.gif)
+![gif - references]({%link img/img-protocols/gif_references.gif %})

docs/protocols/protocols_guide_internal-how-2.md

@@ -13,7 +13,7 @@ nav_order: 3
 
 ---
 
-<!-- ![open-protocols](../../../img/img-open-mrprot-flow.png) -->
+ <!--![open-protocols]({% link img/img-open-mrprot-flow.png %}) -->
 
 
 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.

docs/protocols/protocols_guide_internal-how-3.md

@@ -13,12 +13,12 @@ nav_order: 4
 
 ---
 
-<!-- ![open-protocols](../../../img/img-open-mrprot-flow.png) -->
+<!--![open-protocols]({% link img/img-open-mrprot-flow.png %})-->
 
 
 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.
 
-![gif - update](../../../img/img-protocols/gif_update.gif)
+![gif - update]({% link img/img-protocols/gif_update.gif %})
 
 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`)

docs/protocols/protocols_guide_internal-how-4.md

@@ -13,7 +13,7 @@ nav_order: 5
 
 ---
 
-<!-- ![open-protocols](../../../img/img-open-mrprot-flow.png) -->
+<!--![open-protocols]({% link img/img-open-mrprot-flow.png %})-->
 
 
 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.

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
 
 ---
 
-<!-- ![open-protocols](../../../img/img-open-mrprot-flow.png) -->
+ <!--![open-protocols]({% link img/img-open-mrprot-flow.png %}) -->
 
 
 *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 ![version-control](../../../img/icon-version-control.png)
-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 ![version-control]({% link img/icon-version-control.png %})
+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 ![doi](../../../img/icon-doi.png)
+### Citable research output ![doi]({% link img/icon-doi.png %})
 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 ![reproduce](../../../img/icon-reproduce.png)
+### Reproducible methods detail ![reproduce]({% link img/icon-reproduce.png %})
 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.
 
 

docs/protocols/protocols_guide_internal.md

@@ -14,4 +14,4 @@ nav_exclude: true
 
 ---
 
-![open-protocols](../../../img/img-open-mrprot-flow.png)
+![open-protocols]({% link img/img-open-mrprot-flow.png %})

docs/tasks.md

@@ -14,16 +14,14 @@ How to share your experimental tasks
 
 ---
 
-![open-tasks](../../img/img-open-tasks-flow.png)
+![open-tasks]({% link img/img-open-tasks-flow.png %})
 
 ## Purpose
 The Open Tasks working group aims to encourage and incentivise researchers designing experimental tasks for functional neuroimaging to share these tasks openly with other researchers. They have established online repository for these paradigms to be shared, alongside documentation and analysis scripts for behavioural results. This working group also aims to train new members of the centre in open-source coding languages for paradigm development, and sharing reproducible environments.
 
 <br>
 
-<!-- [![For WIN members](../../img/btn-win.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/tasks/#for-win-members)      [![For external researchers](../../img/btn-external.png)](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/tools/tasks/#for-external-researchers) -->
-
-[![For WIN members](../../img/btn-win.png)](../tasks/tasks_guide_internal-how-1)      [![For external researchers](../../img/btn-external.png)](../tasks/tasks_guide_external)
+[![For WIN members]({% link img/btn-win.png %})]({% link docs/tasks/tasks_guide_internal-how-1.md %})      [![For external researchers]({% link img/btn-external.png %})]({% link docs/tasks/tasks_guide_external.md %})
 
 ## Contributors
 We are grateful to the following WIN members for their contributions to developing the Open Tasks

docs/tasks/tasks_guide_internal-how-1.md

@@ -13,7 +13,7 @@ nav_order: 2
 
 ---
 
-<!-- ![open-tasks](../../../img/img-open-tasks-flow.png) -->
+ <!--![open-tasks]({% link img/img-open-tasks-flow.png %})-->
 
 
 ## Contents
@@ -42,7 +42,7 @@ We think the [Pavlovia](https://pavlovia.org) system for task sharing is a great
 ## How do I add my task to the Open WIN Tasks repository(s)?
 Once you've been added as a member of the WIN Open Tasks reposistory and/or the OPEN_WIN Pavlovia repository (see above), you can add your repositories to these groups! In WIN GitLab, go to your repository, and then click on "Members", then "Invite Group", and choose "open-science" in your group to invite. In PsychoPy, go to [Pavlovia GitLab](https://gitlab.pavlovia.org/), and then click on "Settings", "Members", "Invite Group", and choose "OPEN_WIN" as the group. We recommend that you add the repository to the group with 'reporter' permissions. See below for an example of how to do this:
 
-![Pavlovia example](../../../img/pavlovia_OPENWIN_walkthrough.png)
+![Pavlovia example]({% link img/pavlovia_OPENWIN_walkthrough.png %})
 
 
 ## Who can I get further advice?

docs/tasks/tasks_guide_internal-why-use.md

@@ -15,14 +15,14 @@ Why you should consider using the WIN MR tasks repository.
 
 ---
 
-<!-- ![open-tasks](../../../img/img-open-tasks-flow.png) -->
+ ![open-tasks]({% link img/img-open-tasks-flow.png %}) 
 
 ## Benefits
-### Version control ![version-control](../../../img/icon-version-control.png)
-The [WIN Open Tasks repository](https://git.fmrib.ox.ac.uk/open-science) is maintained in the WIN GitLab server. WIN members are invited to deposit their task code and materials when they are using a stable version, by cloning from their own GitLab or GitHub repository.  This implies that WIN members will be using a git process when developing their task, and as such their development journey will be version controlled. Find out more about [using GitLab](../gitlab)
+### Version control ![version-control]({% link img/icon-version-control.png %})
+The [WIN Open Tasks repository](https://git.fmrib.ox.ac.uk/open-science) is maintained in the WIN GitLab server. WIN members are invited to deposit their task code and materials when they are using a stable version, by cloning from their own GitLab or GitHub repository.  This implies that WIN members will be using a git process when developing their task, and as such their development journey will be version controlled. Find out more about [using GitLab]({% link docs/gitlab.md %})
 
-### Citable research output ![doi](../../../img/icon-doi.png)
-Versions of task materials can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading individual task repositories from GitLab. Once a DOI has been created, your task material becomes a citable object which you can add to your list of research outputs. Find out how to [create a doi for your repository](../gitlab/4-2-you-doi).
+### Citable research output ![doi]({% link img/icon-doi.png %})
+Versions of task materials can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading individual task repositories from GitLab. Once a DOI has been created, your task material becomes a citable object which you can add to your list of research outputs. Find out how to [create a doi for your repository]({% link docs/gitlab/4-2-you-doi.md %}).
 
-### Reproducible methods detail ![reproduce](../../../img/icon-reproduce.png)
+### Reproducible methods detail ![reproduce]({% link img/icon-reproduce.png %})
 WIN members will be supported in developing the necessary and sufficient documentation and running environments to enable others to launch, maintain and adapting their tasks. This facilitates effective re-use and modification of tasks within a research group, and with external collaborators.

docs/tools.md

@@ -14,7 +14,7 @@ How to use WIN infrastructure to share each stage of your research output
 
 ---
 
-![tools](../../img/img-tools.png)
+![tools]({% link img/img-tools.png %})
 
 WIN have created a number of tools to help you share your research output effectively and openly. In some cases these have been built using infrastructure. In most cases, however, it has been necessary to design custom databases and software solutions to suite our specific needs.
 

docs/using-this-repo.md

@@ -46,18 +46,18 @@ An "issue" is a term used by GitLab for a place to track ideas, enhancements, ta
 Folks with a WIN IT account can leave feedback on this site by commenting on the [issues in our GitLab repository](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues).  You are welcome to comment on any issue that feels relevant. If you are new to the community you might like to first have a go with the issues labelled "good first issue".
 
 ## Creating a GitLab account to comment
-To comment on the issues you will need a WIN GitLab login. If you haven’t got a WIN GitLab account, take a look at [this guide](../gitlab/2-1-starting-gitlab-account) for how to create one.
+To comment on the issues you will need a WIN GitLab login. If you haven’t got a WIN GitLab account, take a look at [this guide]({% link docs/gitlab/2-1-starting-gitlab-account.md %}) for how to create one.
 
 ## Do I have to write something?
 No. If you don't feel like writing out something, you are very welcome to add a quick emoji to something someone else has written. Feedback on other people's feedback is also really helpful!
 
-![github-issue-emoji](../../img/img-github-issue-emoji.png)
+![github-issue-emoji]({% link img/img-github-issue-emoji.png %})
 
 If you are able to write something, you are welcome to add just a few words, sentences, or paragraphs if you'd like. Whatever works for you is great.
 
 ## Will my comments be public?
 Yes. We'd really like for all feedback to be public. This will ensure that everything is transparent and well recorded. The aim is to show that community members have had input on these pages, and we’ve listened to and incorporated your feedback.
 
-Please don’t be worried about being critical (if something’s not right, we need to know about it!), but please try to be respectful and courteous, as per the [community participation guidelines](../community/CODE_OF_CONDUCT).
+Please don’t be worried about being critical (if something’s not right, we need to know about it!), but please try to be respectful and courteous, as per the [community participation guidelines]({% link docs/community/CODE_OF_CONDUCT.md %}).