diff --git a/docs/community.md b/docs/community.md
index 4394a258574130d9289d809e8aeaa643db66a13b..58c8757ec717ef5f93f86dd02e97ac91f66a3fb9 100644
--- a/docs/community.md
+++ b/docs/community.md
@@ -29,8 +29,8 @@ If you are interested in learning more about open research, incorporating open r
👋 Subscribe to the [Open WIN mailing list](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/contact/#open-win-mailing-list-) to find out about events and resources as they are shared.
-👋 Say "hello" on our [Slack workspace](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/contact/#open-win-slack-) to follow and contribute to discussions about the [Open WIN Tools](tools.md), [events](events.md) or plans for the community.
+👋 Say "hello" on our [Slack workspace](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/contact/#open-win-slack-) to follow and contribute to discussions about the [Open WIN Tools](tools), [events](events) or plans for the community.
-👋 [Comment on this GitHub repository](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/contact/#comment-on-the-github-repository-), add an issue or submit a pull request to suggest changes to this documentation.
+👋 [Comment on this GitLab repository](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community), add an issue or submit a merge request to suggest changes to this documentation.
👋 [Email the Open WIN Community Coordinator](https://open.win.ox.ac.uk/pages/open-science/community/Open-WIN-Community/docs/contact/#email-the-open-win-community-coordinator-directly-) to introduce yourself, or ask a question about any aspect of this repository or the work of the Open WIN Community or Working Groups.
diff --git a/docs/community/community-goals.md b/docs/community/community-goals.md
index 074acfa30296c4df837063fd9b06ebfbc3462859..0e369b867dfc7359d751308cfab1ba23c0394360 100644
--- a/docs/community/community-goals.md
+++ b/docs/community/community-goals.md
@@ -26,7 +26,7 @@ As these stages near completion, we are entering the second phase of work to bui
The WIN Open Neuroimaging Community will address the above problems by working together to:
1. Develop tools, policies and governance recommendations to promote open research practices;
2. Identify our own barriers to working open and devising strategies to remove these barriers for ourselves and others;
-3. Create documentation and training materials to help others use the [Open WIN Tools](../tools.md);
+3. Create documentation and training materials to help others use the [Open WIN Tools](../../tools);
4. Build a community of researchers with the expertise and confidence to promote open research practices and the Open WIN Tools in our own labs and to wider audiences.
@@ -36,4 +36,4 @@ We intend to implement these solutions through regular co-working "hacks". These
## Ambassador program
Alongside the hacks, we will develop the WIN Open Ambassadors program for launch in 2021, where motivated individuals will be supported in sharing knowledge and sign posting their peers around open research practices and how they are implemented at WIN. The Ambassadors will be significant contributors to the community, and recognised for the value of their contribution. They will be invited to shape the governance of the community, and be consulted on policies, incentives, guiding principles and reward systems which will be devised to promote uptake of open research practices at WIN.
-Take a look at our drafted outline for the [Ambassadors program](../ambassadors.md). We would love to hear your thoughts on how it should be put together!
+Take a look at our drafted outline for the [Ambassadors program](../../ambassadors). We would love to hear your thoughts on how it should be put together!
diff --git a/docs/community/community-who.md b/docs/community/community-who.md
index 7882ffef100db4089f86f95a30f82d18ee36f4fa..633f2e30ce66a2aff1b18429c9c633ec5e497032 100644
--- a/docs/community/community-who.md
+++ b/docs/community/community-who.md
@@ -51,7 +51,7 @@ WIN GitLab: [@cassag](https://git.fmrib.ox.ac.uk/cassag)
This community feeds directly into the [WIN Open Neuroimaging Project](https://www.win.ox.ac.uk/open-neuroimaging/open-neuroimaging-project) and its working groups:
-* [Open Acquisition](../tools/acquisition.md) (lead: [Stuart Clare](https://www.win.ox.ac.uk/people/stuart-clare))
-* [Open Tasks](../tools/tasks.md) (lead: [Laurence Hunt](https://www.win.ox.ac.uk/people/laurnece-hunt))
-* [Open Analysis](../tools/analysis.md) (lead: [Mark Jenkinson](https://www.win.ox.ac.uk/people/mark-jenkinson))
-* [Open Data](../tools/data.md) (lead: [Clare Mackay](https://www.win.ox.ac.uk/people/clare-mackay))
+* [Open Acquisition](../../tools/acquisition) (lead: [Stuart Clare](https://www.win.ox.ac.uk/people/stuart-clare))
+* [Open Tasks](../../tools/tasks) (lead: [Laurence Hunt](https://www.win.ox.ac.uk/people/laurnece-hunt))
+* [Open Analysis](../../tools/analysis) (lead: [Mark Jenkinson](https://www.win.ox.ac.uk/people/mark-jenkinson))
+* [Open Data](../../tools/data) (lead: [Clare Mackay](https://www.win.ox.ac.uk/people/clare-mackay))
diff --git a/docs/community/mountain-of-engagement.md b/docs/community/mountain-of-engagement.md
index 25385add96be49b8bba37597247e84c4427d7c2b..209207c1d31a1a4d90f5de52440b6fe84a43175e 100644
--- a/docs/community/mountain-of-engagement.md
+++ b/docs/community/mountain-of-engagement.md
@@ -21,4 +21,4 @@ We want this community to grow in reach and ambition. We also want individual me
To achieve individual and community growth, we are following the "Mountain of Engagement" model. This is a tool for conceptualising how people will interact with your community, and building an understanding of how different people might grow from their first interaction to taking on some form of responsibility. Not all community members will progress to leadership, but it is useful to think about what actions or events may lead people to progress.
-We have used the Mountain of Engagement model to consider how our imaginary [personas](personas-and-pathways.md) might interact with the Open WIN community. This exercise has provided useful insight into how we can support progression for a variety of people.
+We have used the Mountain of Engagement model to consider how our imaginary [personas](../personas-and-pathways) might interact with the Open WIN community. This exercise has provided useful insight into how we can support progression for a variety of people.
diff --git a/docs/community/personas-and-pathways.md b/docs/community/personas-and-pathways.md
index 3e67ff192cdccac8b033be8a94e5071c6cae32cf..dd8cfa5e233878727546ea348041301e62cb203f 100644
--- a/docs/community/personas-and-pathways.md
+++ b/docs/community/personas-and-pathways.md
@@ -16,7 +16,7 @@ Who will our Community Members be, how will they find us and how will we support
This exercise helped us to think about who might be interested in joining our community, how we can connect with them, and the journey they might go on. It is designed to help us reach different audiences and be welcoming to diverse contributors.
-**Follow the sections linked in the side bar to walk through the exercise and understand how we arrived at our [persona descriptions and described their pathways](personas-and-pathways-descriptions.md) to engagement with this community.**
+**Follow the sections linked in the side bar to walk through the exercise and understand how we arrived at our [persona descriptions and described their pathways](../personas-and-pathways-descriptions) to engagement with this community.**
Our intention is to update this document as we gain a clearer idea of who we are engaging with or missing from the community. Please contact us if any of the ideas presented here do not resonate with you, or if they hit the right note! 🎶
diff --git a/docs/contact.md b/docs/contact.md
index 7abede3ae779e496d670f7ae04e69be0e2a35c69..fd48e93bdb462fbebea179a64ee462c253af2594 100644
--- a/docs/contact.md
+++ b/docs/contact.md
@@ -16,7 +16,7 @@ Connect with us via any of the means below as per your preference and interests
## Open WIN Slack 
-Anyone affiliated with a WIN member Department is invited to [join our Slack workspace](https://join.slack.com/t/openwin/signup). We have channels dedicated to each of the [sharing tools](tools.md), the [Open WIN community](community.md), and relevant external and internal [events](events.md).
+Anyone affiliated with a WIN member Department is invited to [join our Slack workspace](https://join.slack.com/t/openwin/signup). We have channels dedicated to each of the [sharing tools](../tools), the [Open WIN community](../community), and relevant external and internal [events](../events).
**Slack is where the conversation will be most active and we will share resources with each other. If you're new to the Community, this should be your first contact point!**
@@ -41,6 +41,7 @@ Anyone interested in the Open WIN Community or these resources can join the [WIN
You are very welcome to [email Cassandra Gould van Praag](mailto:cassandra.gouldvanpraag@psych.ox.ac.uk) directly to discuss any issue relating to open research at WIN, the community, or this repository.
-## Comment on the GitHub repository 
+## Comment on the GitLab repository
+<!--  -->
-If you want to report a problem or suggest an enhancement for this repository, we'd love for you to [open an issue](https://github.com/cassgvp/WIN-Open-Neuroimaging-Community/issues) on out GitHub page.
+If you want to report a problem or suggest an enhancement for this repository, we'd love for you to [open an issue](https://git.fmrib.ox.ac.uk/open-science/community/Open-WIN-Community/-/issues) on out GitLab page (requires a [WIN GitLab account](../gitlab/2-1-starting-gitlab-account).
diff --git a/docs/gitlab.md b/docs/gitlab.md
index 34e52ea7b3a2c55341d05e56cdd1acf099ff053f..67765c250a2be9cc0b92b0be76fb040bad4e8fab 100644
--- a/docs/gitlab.md
+++ b/docs/gitlab.md
@@ -24,7 +24,7 @@ WIN provide a git service using the open source [GitLab software](https://about.
GitLab is best used for the management of text-based documents with some pictures (not nifti brain images!). This mainly covers code and documentation. It is also useful for project management by logging issues and milestones, and tracking collaboration.
## GitLab Demystified!
-This 30 min presentation introduces GitLab and version control. It explains key terminology, demonstrates basic interaction with a repository, and showcases the potential of GitLab Pages. After watching this presentation, GitLab might feel a *bit* less intimidating!
+This 30 min presentation introduces GitLab and version control. It explains key terminology, demonstrates basic interaction with a repository, and showcases the potential of GitLab Pages. After watching this presentation, GitLab might feel a *bit* less intimidating!
<div style="padding:56.25% 0 0 0;position:relative;"><iframe src="https://player.vimeo.com/video/668637653?h=a710d4e187&badge=0&autopause=0&player_id=0&app_id=58479" frameborder="0" allow="autoplay; fullscreen; picture-in-picture" allowfullscreen style="position:absolute;top:0;left:0;width:100%;height:100%;" title="Introduction to version control with GitLab. Dr Cassandra Gould van Praag, WIN Reboot Camp, January 2022"></iframe></div><script src="https://player.vimeo.com/api/player.js"></script>
@@ -33,9 +33,7 @@ This 30 min presentation introduces GitLab and version control. It explains key
GitLab manages your version control. This means that each change you make to the remote repository is tracked and can be reversed. This is helpful for undoing changes (you can revert to earlier points in time) and tracking who has made changes on a collaborative project.
#### Citable research output 
-Your gitlab repository can be assigned a digital object identifier (doi). This means everything containing within your repository can be cited as a research output, be it code or documentation. Find out how to [create a doi for your repository](gitlab/4-2-you-doi.md).
-
-test link: [create a doi for your repository](gitlab/4-2-you-doi)
+Your gitlab repository can be assigned a digital object identifier (doi). This means everything containing within your repository can be cited as a research output, be it code or documentation. Find out how to [create a doi for your repository](../gitlab/repo-doi).
#### Managed and attributable collaboration
Git and GitLab are an excellent resource for inviting others to contribute to your material. Potential collaborators can be internal to WIN or external. Changes can be incorporated automatically if the collaborator is trusted and known to you (invited directly), or suggested via a "merge request" if the collaborator is not part of your invited group. This process also makes it very easy to follow who has made what contribution, so they can be appropriately attributed for their efforts.
diff --git a/docs/gitlab/repo-include.md b/docs/gitlab/repo-include.md
index e26287a56382030dc0e97be7dbc4999f5ef6fbed..bdaefc60be89da7f375ca4ca8b7c10e8b99f9b49 100644
--- a/docs/gitlab/repo-include.md
+++ b/docs/gitlab/repo-include.md
@@ -33,7 +33,7 @@ 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](gitlab/4-2-you-doi.md) 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](../repo-doi) and any supporting papers.
### CONTRIBUTING.md
@@ -47,4 +47,4 @@ 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.md) for a more complete discussion of which license you should consider applying to your code.
+See the [licensing guide](../repo-license) for a more complete discussion of which license you should consider applying to your code.
diff --git a/docs/tools/acquisition.md b/docs/tools/acquisition.md
index 0e61beaf4ee72be4c4fa093d21f9adb12f62a155..56fbcea872b7786525d8555e47bf0ceb832e4e13 100644
--- a/docs/tools/acquisition.md
+++ b/docs/tools/acquisition.md
@@ -35,7 +35,7 @@ Coming soon
## For WIN members
### Benefits
#### Version control 
-The acquisition database is version controlled, so WIN members are invited to upload their protocols during pilotting to keep track of optimisation and final versions. Comments and notes can be added to each entry to 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.md) server
+The acquisition database is version controlled, so WIN members are invited to upload their protocols during pilotting to keep track of optimisation and final versions. Comments and notes can be added to each entry to 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
#### Citable research output 
Versions (with minor and major edits) can be assigned a digital object identified (DOI) using the [Oxford Research Archive (ORA) Data repository](https://deposit.ora.ox.ac.uk) using the stable link provided by the acquisition database. Once a DOI has been created, your acquisition protocol becomes a citable object which you can add to your list of research outputs.
@@ -50,12 +50,12 @@ Both internal and external users can search the database using keyword terms bas
## How to use
### Access
-Access the [Open Acquisition Database](https://open.win.ox.ac.uk/protocols/) (requires a connection to the [FMRIB VPN](https://sharepoint.nexus.ox.ac.uk/sites/NDCN/FMRIB/IT/User%20Guides/VPN.aspx))
+Access the [Open Acquisition Database](https://open.win.ox.ac.uk/protocols/)
Coming soon
{: .label .label-yellow }
-Detailed guidance on how to use the Open Acquisition database will be produced during one of our [documentation hacks](../events/doc-hack-1.md)
+Detailed guidance on how to use the Open Acquisition database will be produced during one of our [documentation hacks](../../events/doc-hack-1)
## Working group members (alphabetically)
We are grateful to the following WIN members for their contributions to developing the Open Acquisition database
diff --git a/docs/tools/analysis.md b/docs/tools/analysis.md
index 4c120a29083656a35474d3ccba3b32e1dcaae8b1..56a806e8126ed9519e235d8bafbe65d09f6466a8 100644
--- a/docs/tools/analysis.md
+++ b/docs/tools/analysis.md
@@ -40,14 +40,14 @@ Coming soon
## For WIN members
### Benefits
#### Version control 
-WIN members will be encouraged to develop their analysis pipelines into standalone scripts and store these on the [WIN GitLab instance](https://git.fmrib.ox.ac.uk). We will support our members in using git to version control their code, and employ best practice in ensuring their pipelines are robust and accurate. Find out more about [using GitLab](gitlab.md)
+WIN members will be encouraged to develop their analysis pipelines into standalone scripts and store these on the [WIN GitLab instance](https://git.fmrib.ox.ac.uk). We will support our members in using git to version control their code, and employ best practice in ensuring their pipelines are robust and accurate. Find out more about [using GitLab](../../gitlab)
#### Citable research output 
-Versions of analysis code can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading them from GitLab. Once a DOI has been created, your analysis code 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.md).
+Versions of analysis code can be assigned a digital object identified (DOI) using [Zenodo](https://zenodo.org) by uploading them from GitLab. Once a DOI has been created, your analysis code 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).
#### Reproducible methods detail 
Alongside your analysis code, WIN members will be supported in implementing a "[wrapper](https://techterms.com/definition/wrapper)" script which can:
-1. access data stored on the WIN [Open Data](data.md) servers;
+1. access data stored on the WIN [Open Data](../data) servers;
2. access your GitLab code repository;
3. pull a stable version of the FSL analysis package in a [Singularity container](https://en.wikipedia.org/wiki/Singularity_(software));
4. Run the accessed data using the supplied code and the given version of FSL via the container on a high performance cluster.
@@ -62,13 +62,13 @@ External users will be able to access the shared code and singularity containers
Coming soon
{: .label .label-yellow }
-Detailed guidance on how to use the Open Analysis wrapper will be produced during one of our [documentation hacks](../events/doc-hack-1.md)
+Detailed guidance on how to use the Open Analysis wrapper will be produced during one of our [documentation hacks](../../events/doc-hack-1)
#### Repository template
-You are free to include whatever material you wish in your repository. We have created this [guide on what to include](analysis/repo-include.md) to list some of the pages and sections which may be beneficial for readers. See also our guide on [how to license](repo-license.md) your material.
+You are free to include whatever material you wish in your repository. We have created this [guide on what to include](../../gitlab/repo-include) to list some of the pages and sections which may be beneficial for readers. See also our guide on [how to license](../../gitlab/repo-license) your material.
#### Creating a doi
-We recommend using zenodo to create a doi for your material. See see the [creating a doi](gitlab/4-2-you-doi.md) page for instructions.
+We recommend using zenodo to create a doi for your material. See see the [creating a doi](../../gitlab/repo-doi) page for instructions.
## Working group members (alphabetically)
We are grateful to the following WIN members for their contributions to developing the Open Analysis tools