Commit b70190ca authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
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style cross links to block quote

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......@@ -12,7 +12,7 @@ This is the GitLab repository for the development and early consultation on the
Working out how to appropriately share data requires the navigation through various lines of guidance and legislation, notably GDPR. This is a complex process which is discipline and institutionally specific.
Individual researchers and Principle Investigators would benefit from a single resource which can be worked through to inform their decisions when preparing to share data.
Individual researchers and Principal Investigators would benefit from a single resource which can be worked through to inform their decisions when preparing to share data.
## The solution
We are developing a flow chart which researchers can walk through to address the question "Can I share my data on the [WIN XNAT Open Data server](https://cassgvp.github.io/WIN-Open-Neuroimaging-Community/docs/tools/data.html)?".
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......@@ -27,8 +27,10 @@
<a name="dicom-scrub"></a>
## Appendix 1 - DICOM Headers to be scrubbed
Relevant processes:
- [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
> Relevant processes:
> - [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
List of DICOM identifying fields that need to be scrubbed included in [McGill Centre for Integrative Neuroscience Open Science Guidance Open Science Data Preparation Checklist](http://loris.ca/MCINOpenScienceGuidance_DataPrepChecklist.pdf).
......@@ -92,9 +94,9 @@ StudyTime | 85829.922|
<a name="BIDS"></a>
## Appendix 2 - BIDS Compliance
Relevant processes:
- [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
- [Process 4 - Metadata](./decision-tree.md#process-4-metadata)
> Relevant processes:
> - [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
> - [Process 4 - Metadata](./decision-tree.md#process-4-metadata)
Data should be confirmed as BIDS compliant using the BIDS-validator docker image available from
[https://github.com/bids-standard/bids-validator\#docker-image](https://github.com/bids-standard/bids-validator#docker-image).
......@@ -103,24 +105,24 @@ This could be installed on XNAT. *to-do: check if BIDS validator already install
<a name="json-scrub"></a>
## Appendix 3 - Scrubbing .json files
Relevant processes:
- [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
> Relevant processes:
> - [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
.json sidecar files are generated for each nifti image to conform with BIDS specification. These files contain essential metadata which describes the acquisition of the data. They may also contain potentially identifiable information relating to the participant which should not be distributed openly.
<a name="qc"></a>
## Appendix 4 - Quality Control
Relevant processes:
- [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
> Relevant processes:
> - [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
Quality control (QC) assessments should be completed as a matter of course for research data, and as a courtesy for those wishing to reuse your data. QC can be performed on BIDS formatted data using mriqc. Mriqc is available as a container on XNAT. *to-do: check if mriqc container already installed*
<a name="deface"></a>
## Appendix 5 - Defacing
Relevant processes:
- [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
> Relevant processes:
> - [Process 3 - Deidentification](./decision-tree.md#process-3-deidentification)
Consider using fsl\_deface. Other defacing tools are available.
......@@ -130,8 +132,8 @@ Consider running QC on defaced images using
<a name="upload"></a>
## Appendix 6 - Upload to XNAT
Relevant processes:
- [Process 5 - Sharing and attribution](./decision-tree.md#process-5-sharing-and-attribution)
> Relevant processes:
> - [Process 5 - Sharing and attribution](./decision-tree.md#process-5-sharing-and-attribution)
TBD (not exhaustive)
......@@ -144,8 +146,8 @@ TBD (not exhaustive)
<a name="data-freeze"></a>
## Appendix 7 - Data freeze
Relevant processes:
- [Process 5 - Sharing and attribution](./decision-tree.md#process-5-sharing-and-attribution)
> Relevant processes:
> - [Process 5 - Sharing and attribution](./decision-tree.md#process-5-sharing-and-attribution)
The data freeze process as applied for the Dementias Platform UK (DPUK) is computationally expensive -- multiple freeze generates duplicates of data. Alternative methods could be investigated (e.g. ZFS snapshots).
......@@ -154,8 +156,8 @@ Consider developing a cost model of the platform to indicate to researchers the
<a name="doi"></a>
## Appendix 8 - Digital object identifiers (DOI)
Relevant processes:
- [Process 5 - Sharing and attribution](./decision-tree.md#process-5-sharing-and-attribution)
> Relevant processes:
> - [Process 5 - Sharing and attribution](./decision-tree.md#process-5-sharing-and-attribution)
A DOI is essential to ensure that the data shared can be effectively attributed to the authors via [FAIR
principles](https://www.go-fair.org/fair-principles/). Oxford Research Online (ORA) is the University's preference for
......@@ -174,8 +176,8 @@ Routes considered to address URL persistence:
<a name="dua"></a>
## Appendix 9 - Data usage agreement (DUA)
Relevant processes:
- [Process 5 - Sharing and attribution](./decision-tree.md#process-5-sharing-and-attribution)
> Relevant processes:
> - [Process 5 - Sharing and attribution](./decision-tree.md#process-5-sharing-and-attribution)
Research Services (<research.services@admin.ox.ac.uk>.) can provide template agreements for data sharing.
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......@@ -29,12 +29,12 @@ principles](https://www.go-fair.org/fair-principles/)
## Process 3 - Deidentification
*to-do: explanatory text here*
See also:
- [Appendix 1 - DICOM headers to be scrubbed](./decision-tree-appendicies.md#appendix-1-dicom-headers-to-be-scrubbed)
- [Appendix 2 - BIDS compliance](./decision-tree-appendicies.md#appendix-2-bids-compliance)
- [Appendix 3 - Scrubbing .json files](./decision-tree-appendicies.md#appendix-3-scrubbing-json-files)
- [Appendix 4 - Quality control](./decision-tree-appendicies.md#appendix-4-quality-control)
- [Appendix 5 - Defacing](./decision-tree-appendicies.md#appendix-5-defacing)
> See also:
> - [Appendix 1 - DICOM headers to be scrubbed](./decision-tree-appendicies.md#appendix-1-dicom-headers-to-be-scrubbed)
> - [Appendix 2 - BIDS compliance](./decision-tree-appendicies.md#appendix-2-bids-compliance)
> - [Appendix 3 - Scrubbing .json files](./decision-tree-appendicies.md#appendix-3-scrubbing-json-files)
> - [Appendix 4 - Quality control](./decision-tree-appendicies.md#appendix-4-quality-control)
> - [Appendix 5 - Defacing](./decision-tree-appendicies.md#appendix-5-defacing)
![](../img/p3.png)
......@@ -43,8 +43,8 @@ See also:
## Process 4 - Metadata
*to-do: explanatory text here*
See also:
- [Appendix 2 - BIDS compliance](./decision-tree-appendicies.md#appendix-2-bids-compliance)
> See also:
> - [Appendix 2 - BIDS compliance](./decision-tree-appendicies.md#appendix-2-bids-compliance)
![](../img/p4.png)
......@@ -52,11 +52,11 @@ See also:
## Process 5 - Sharing and attribution
*to-do: explanatory text here*
See also:
- [Appendix 6 - Upload to XNAT](./decision-tree-appendicies.md#appendix-6-upload-to-xnat)
- [Appendix 7 - Data freeze](./decision-tree-appendicies.md#appendix-7-data-freeze)
- [Appendix 8 - Digital object identifiers (DOI)](./decision-tree-appendicies.md#appendix-8-digital-object-identifiers-doi)
- [Appendix 9 - Data usage agreement (DUA)](./decision-tree-appendicies.md#appendix-9-data-usage-agreement-dua)
> See also:
> - [Appendix 6 - Upload to XNAT](./decision-tree-appendicies.md#appendix-6-upload-to-xnat)
> - [Appendix 7 - Data freeze](./decision-tree-appendicies.md#appendix-7-data-freeze)
> - [Appendix 8 - Digital object identifiers (DOI)](./decision-tree-appendicies.md#appendix-8-digital-object-identifiers-doi)
> - [Appendix 9 - Data usage agreement (DUA)](./decision-tree-appendicies.md#appendix-9-data-usage-agreement-dua)
![](../img/p5.png)
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