Commit 0fa2b1b1 authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
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merged correct syntax

parent 4aa8a609
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......@@ -47,7 +47,7 @@ Versions of analysis code can be assigned a digital object identified (DOI) usin
#### Reproducible methods detail ![reproduce](../../img/icon-reproduce.png)
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) servers;
1. access data stored on the WIN [Open Data](data.md) 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)
Detailed guidance on how to use the Open Analysis wrapper will be produced during one of our [documentation hacks](../events/doc-hack-1.md)
#### 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) to list some of the pages and sections which may be beneficial for readers. See also our guide on [how to license](repo-license) your material.
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.
#### Creating a doi
We recommend using zenodo to create a doi for your material. See see the [creating a doi](analysis/doi) page for instructions.
We recommend using zenodo to create a doi for your material. See see the [creating a doi](analysis/doi.md) page for instructions.
## Working group members (alphabetically)
We are grateful to the following WIN members for their contributions to developing the Open Analysis tools
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......@@ -34,7 +34,7 @@ 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](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](doi.md) and any supporting papers.
### CONTRIBUTING.md
......@@ -48,4 +48,4 @@ 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](repo-license.md) for a more complete discussion of which license you should consider applying to your code.
......@@ -74,17 +74,17 @@ You can log into [WIN XNAT](https://xnat.win.ox.ac.uk) using your WIN IT account
The [XNAT](https://xnat.org) website has useful background information about the XNAT platform.
#### BIDS in XNAT
For the current overview of how BIDS works in XNAT, see the [BIDS](./data/bids) page.
For the current overview of how BIDS works in XNAT, see the [BIDS](./data/bids.md) page.
#### Python libraries
There are several python libraries that can be used to write scripts against the XNAT API. See [python libraries](data/python) for more info on pyxnat, xnatpy and dax.
There are several python libraries](data/python.md) that can be used to write scripts against the XNAT API. See [python libraries](data/python.md) for more info on pyxnat, xnatpy and dax.
#### Docker in XNAT
To see how Docker works in XNAT, see the [Docker](data/docker) page.
To see how Docker works in XNAT, see the [Docker](data/docker.md) page.
#### Case Studies
The [OPDC project](data/opdc) uploaded DICOM data from jalapeno using python and dcmtk.
The [OPDC project](data/opdc.md) uploaded DICOM data from jalapeno using python and dcmtk.
TODO: More case studies!
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......@@ -43,7 +43,7 @@ You will first need to enable a container for a project (provided you have suffi
### BIDS Containers (DICOM to NIFTI + BIDS, BIDS MRIQC)
For examples on how to use BIDS related containers see the [BIDS](bids) page.
For examples on how to use BIDS related containers see the [BIDS](bids.md) page.
### FSL Containers
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......@@ -60,7 +60,7 @@ If you are able to write something, you are welcome to add just a few words, sen
## 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, I 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, I need to know about it!), but please try to be respectful and courteous, as per the [community participation guidelines](community/CODE_OF_CONDUCT.md).
## Do I *really* have to use GitHub?
If this process really doesn't work for you, I'd still love to receive your feedback one way or another. By email is just fine 😊.
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