@@ -45,10 +45,8 @@ Below we have collected some example responses in the formats required by [Wellc
**The details in the plans below were correct at the time of writing, however some aspects of how WIN manages your data may have changed. Please refer to the following WIN policies to ensure you have the most up to dat information about our data handling:**
- WIN data retention policy - <mark>coming soon</mark>
- WIN handling of personal Information - <mark>coming soon</mark>
- WIN data storage and back up infrastructure - <mark>coming soon</mark>
- WIN data retention policy, data security and handling of personal Information refer to our data provacy page [Processing personal data appropriately](https://www.win.ox.ac.uk/research/it/policies-and-governance/data-privacy)
-[WIN data storage and back up infrastructure](https://www.win.ox.ac.uk/research/it/i-want-to/store-access-and-protect-my-data/data-stores)
<!-- <details>
...
...
@@ -65,12 +63,12 @@ Prepared by Michiel Cottaar with feedback from Cassandra Gould van Praag and <ma
<details>
<summary><b>Expand for application sections</b></summary><br>
I will make any research outputs for access and reuse following FAIR principles and the open science guidelines and tools from WIN (https://www.win.ox.ac.uk/open-win). This is in line with my previous software releases such as file-tree(https://pypi.org/project/file-tree/), pipe-tree(https://open.win.ox.ac.uk/pages/ndcn0236/pipe-tree/), and MCMRSimulator.jl(https://open.win.ox.ac.uk/pages/ndcn0236/mcmrsimulator.jl/dev/).
I will make any research outputs for access and reuse following FAIR principles and the open science guidelines and tools from WIN (https://www.win.ox.ac.uk/open-win). This is in line with my previous software releases such as [file-tree](https://pypi.org/project/file-tree/), [pipe-tree](https://open.win.ox.ac.uk/pages/ndcn0236/pipe-tree/), and [MCMRSimulator.jl](https://open.win.ox.ac.uk/pages/ndcn0236/mcmrsimulator.jl/dev/).
<br><br>
<details>
<summary><b>DIPPI Sequence</b></summary><br>
Sequence development requires access to Siemens' proprietary sequence development environment, which is governed by Oxford's Master Research Agreement with Siemens Healthineers. According to this agreement, any sequence transfer requires contracts between those sites, the University of Oxford, and Siemens. The WIN physics group has extensive experience negotiating such contracts in a timely manner and in sharing their MRI sequence innovations around the world. I will exploit this expertise (collaborators Prof. Miller and Dr. Wu) to share the DIPPI sequence with all parties who can meet the contractual requirements of the Master Research Agreement.<br><br>
MRI protocols, which describe suggested acquisition schemes for DIPPI, will be made available under a CC-BY 4.0 license through the WIN MR Protocol database(https://open.win.ox.ac.uk/protocols).
MRI protocols, which describe suggested acquisition schemes for DIPPI, will be made available under a CC-BY 4.0 license through the [WIN MR Protocol database](https://open.win.ox.ac.uk/protocols).
<br><br>
</details>
<details>
...
...
@@ -82,7 +80,7 @@ Prepared by Michiel Cottaar with feedback from Cassandra Gould van Praag and <ma
<details>
<summary><b>Software</b></summary><br>
Software tools will be developed to fit the DIPPI model to estimate myelin thickness from DIPPI data. These tools will be included in a pipeline that can be used to fully process from raw DIPPI data to myelin maps. Once these tools are robust, they will be released as a python package on the WIN's own Gitlab page (https://git.fmrib.ox.ac.uk/) under a permissive open source license (MIT or Apache 2.0) and registered with both pypi and anaconda for easy installation. To improve discoverability, these tools would also be listed as affiliated with the FMRIB's Software Library (FSL; https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/OtherSoftware), which is used by over a thousand labs around the world. This software will be given its own DOI using Zenodo. <br><br>
The MR simulator (MCMRSimulator.jl) will be developed in public following modern software engineering practices including regular releases, a change log, automated testing, and documentation for both users and developers (https://open.win.ox.ac.uk/pages/ndcn0236/mcmrsimulator.jl/dev/). Version 0.3 is already released under the Apache 2 permissive license. This will facilitate early discovery of any bugs not caught by the automated tests as well as maximising the chance of it being used by someone to discover new MRI probes of microstructure.
The MR simulator (MCMRSimulator.jl) will be developed in public following modern software engineering practices including regular releases, a change log, automated testing, and documentation for both users and developers ([MCMRsimulator](https://open.win.ox.ac.uk/pages/ndcn0236/mcmrsimulator.jl/dev/)). Version 0.3 is already released under the Apache 2 permissive license. This will facilitate early discovery of any bugs not caught by the automated tests as well as maximising the chance of it being used by someone to discover new MRI probes of microstructure.
