Commit 6323d74e authored by Cassandra Gould van Praag's avatar Cassandra Gould van Praag
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fix markdown

parent b13ca243
......@@ -2,8 +2,23 @@
title: 'Open Data Process Diagram - Appendices'
---
Appendix 1 - DICOM Headers to be scrubbed
=========================================
# Contents
- [Appendix 1 - DICOM Headers to be scrubbed](#dicom-scrub)
- [Appendix 2 - BIDS Compliance](#BIDS)
- [Appendix 3 - Scrubbing .json files](#json-scrub)
- [Appendix 4 - Quality Control](#qc)
- [Appendix 5 - Defacing](#deface)
- [Appendix 6 -- Upload to XNAT](#upload)
- [Appendix 7 -- Data freeze](#data-freeze)
- [Appendix 8 - Digital object identifiers (DOI)](#doi)
- [Appendix 9 - Data usage agreement (DUA)](#dua)
- [Appendix 10 -- Advice from Research Data Oxford](#rdo)
- [Relevant policy and guidance](#policy)
- [Acknowledgements](#acknowledgements)
<a name="dicom-scrub"></a>
# Appendix 1 - DICOM Headers to be scrubbed
List of DICOM identifying fields that need to be scrubbed included in
McGill Centre for Integrative Neuroscience Open Science Guidance Open
......@@ -15,68 +30,70 @@ acquisition site. Fields identified by McGill have been checked against
DICOM fields appearing in data acquired on WIN 3T (OHBA) for human
participant.
----------------------------------- ----------------------------------------------------------------------------------------------------------------------------------
**Field name** **In WIN dicom example (if field present)**
PatientAddress n/a
PatientAge 042Y
PatientBirthDate+D10 19751005
PatientBirthName n/a
PatientID W3T\_2016\_11\_090
PatientMotherBirthName n/a
PatientName W3T\_2016\_11\_090
PatientReligiousPreference n/a
PatientSex F
PatientTelephoneNumbers n/a
Patient Size 1.62
Patient Weight 64
OtherPatientIDs n/a
OtherPatientName n/a
OtherPatientNames n/a
AcquisitionDate 20180515
AcquisitionTime 90931.46
ContentDate 20180515
ContentTime 384 values: 091507.445000, 091507.448000, 091507.450000, 091507.452000\...
DeviceSerialNumber 66093
FrameOfReferenceUID 1.3.12.2.1107.5.2.43.66093.1.20180515090420048.0.0.0
InstanceCreationDate 20180515
InstanceCreationTime 384 values: 091507.445000, 091507.448000, 091507.450000, 091507.452000\...
InstitutionAddress Warneford Lane StreetNo,Oxford,District,GB,OX3 7JX
InstitutionalDepartmentName BE3597
Institution Name Warneford Hospital
IssuerOfPatientID n/a
MediaStorageSOPInstanceUID n/a
OperatorsName n/a
PerformedProcedureStepDescription n/a
PerformedProcedureStepID 0
PerformedProcedureStepStartDate 20180515
PerformedProcedureStepStartTime 85830.014
PerformingPhysicianName Blank
PhysiciansOfRecord n/a
ReferencedSOPInstanceUID n/a
ReferringPhysicianName Blank
RequestedProcedureDescription n/a
RequestingPhysician Blank
SeriesDate 20180515
SeriesInstanceUID 2 values: 1.3.12.2.1107.5.2.43.66093.2018051509150468746204326.0.0.0, 1.3.12.2.1107.5.2.43.66093.2018051509093178111004205.0.0.0
SeriesTime 2 values: 091507.443000, 091508.436000
SOPInstanceUID 384 values: 1.3.12.2.1107.5.2.43.66093.2018051509150469069804346, ...
StationName AWP66093
StudyDate 20180515
StudyDescription OHBA Projects\^2018\_108 RESTAND
StudyInstanceUID MR20180515085649
StudyTime 85829.922
----------------------------------- ----------------------------------------------------------------------------------------------------------------------------------
Appendix 2 - BIDS Compliance
============================
|**Field name**|**In WIN dicom example (if field present)**|
|--------------|-------------------------------------------|
PatientAddress | n/a|
PatientAge | 042Y|
PatientBirthDate+D10 | 19751005|
PatientBirthName | n/a|
PatientID | W3T\_2016\_11\_090|
PatientMotherBirthName | n/a|
PatientName | W3T\_2016\_11\_090|
PatientReligiousPreference | n/a|
PatientSex | F|
PatientTelephoneNumbers | n/a|
Patient Size | 1.62|
Patient Weight | 64|
OtherPatientIDs | n/a|
OtherPatientName | n/a|
OtherPatientNames | n/a|
AcquisitionDate | 20180515|
AcquisitionTime | 90931.46|
ContentDate | 20180515|
ContentTime | 384 values: 091507.445000,| 091507.448000, 091507.450000, 091507.452000\...
DeviceSerialNumber | 66093|
FrameOfReferenceUID | 1.3.12.2.1107.5.2.43.66093.1.20180515090420048.0.0.0|
InstanceCreationDate | 20180515|
InstanceCreationTime | 384 values: 091507.445000,| 091507.448000, 091507.450000, 091507.452000\...
InstitutionAddress | Warneford Lane| StreetNo,Oxford,District,GB,OX3 7JX
InstitutionalDepartmentName | BE3597|
Institution Name | Warneford Hospital|
IssuerOfPatientID | n/a|
MediaStorageSOPInstanceUID | n/a|
OperatorsName | n/a|
PerformedProcedureStepDescription | n/a|
PerformedProcedureStepID | 0|
PerformedProcedureStepStartDate | 20180515|
PerformedProcedureStepStartTime | 85830.014|
PerformingPhysicianName | Blank|
PhysiciansOfRecord | n/a|
ReferencedSOPInstanceUID | n/a|
ReferringPhysicianName | Blank|
RequestedProcedureDescription | n/a|
RequestingPhysician | Blank|
SeriesDate | 20180515|
SeriesInstanceUID | 2 values:| 1.3.12.2.1107.5.2.43.66093.2018051509150468746204326.0.0.0, 1.3.12.2.1107.5.2.43.66093.2018051509093178111004205.0.0.0
SeriesTime | 2 values: 091507.443000, 091508.436000|
SOPInstanceUID | 384 values:| 1.3.12.2.1107.5.2.43.66093.2018051509150469069804346, ...
StationName | AWP66093|
StudyDate | 20180515|
StudyDescription | OHBA Projects\^2018\_108 RESTAND|
StudyInstanceUID | MR20180515085649|
StudyTime | 85829.922|
<a name="BIDS"></a>
# Appendix 2 - BIDS Compliance
Data should be confirmed as BIDS compliant using the BIDS-validator
docker image available from
[[https://github.com/bids-standard/bids-validator\#docker-image]{.underline}](https://github.com/bids-standard/bids-validator#docker-image).
[https://github.com/bids-standard/bids-validator\#docker-image](https://github.com/bids-standard/bids-validator#docker-image).
This could be installed on XNAT.
Appendix 3 - Scrubbing .json files
==================================
<a name="json-scrub"></a>
# Appendix 3 - Scrubbing .json files
.json sidecar files are generated for each nifti image to conform with
BIDS specification. These files contain essential metadata which
......@@ -84,24 +101,27 @@ describes the acquisition of the data. They may also contain potentially
identifiable information relating to the participant which should not be
distributed openly.
Appendix 4 - Quality Control
============================
<a name="qc"></a>
# Appendix 4 - Quality Control
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.
Appendix 5 - Defacing
=====================
<a name="deface"></a>
# Appendix 5 - Defacing
Consider using fsl\_deface. Other defacing tools are available.
Consider running QC on defaced images using
[[https://github.com/raamana/visualqc/blob/master/docs/VisualQC\_TrainingManual\_v1p4.pdf]{.underline}](https://github.com/raamana/visualqc/blob/master/docs/VisualQC_TrainingManual_v1p4.pdf)
[https://github.com/raamana/visualqc/blob/master/docs/VisualQC\_TrainingManual\_v1p4.pdf](https://github.com/raamana/visualqc/blob/master/docs/VisualQC_TrainingManual_v1p4.pdf)
<a name="upload"></a>
# Appendix 6 - Upload to XNAT
Appendix 6 -- Upload to XNAT
============================
TBD (not exhaustive)
......@@ -115,8 +135,8 @@ TBD (not exhaustive)
completed (e.g. DICOMS scrubbed) before data are made publicly
available.
Appendix 7 -- Data freeze
=========================
<a name="data-freeze"></a>
# Appendix 7 - Data freeze
The data freeze process as applied for the Dementias Platform UK (DPUK)
is computationally expensive -- multiple freeze generates duplicates of
......@@ -126,12 +146,13 @@ Consider developing a cost model of the platform to indicate to
researchers the cost of snapshots carried by WIN. A cost model would
also be useful for project and infrastructure grant applications.
Appendix 8 - Digital object identifiers (DOI)
=============================================
<a name="doi"></a>
# Appendix 8 - Digital object identifiers (DOI)
A DOI is essential to ensure that the data shared can be effectively
attributed to the authors via [[FAIR
principles]{.underline}](https://www.go-fair.org/fair-principles/).
attributed to the authors via [FAIR
principles](https://www.go-fair.org/fair-principles/).
Oxford Research Online (ORA) is the University's preference for
generating a DOI.
......@@ -148,12 +169,13 @@ Routes considered to address URL persistence:
2. ORA amend DOI entries when they are informed of a change or if they
are running periodic checks.
Research Data (<https://researchdata.ox.ac.uk>) agree that ORA will be
[Research Data](https://researchdata.ox.ac.uk) agree that ORA will be
motivated to carry some of the burden, with their focus on effective
curation. Opened discussions with ORA on 10^th^ June 2021.
Appendix 9 - Data usage agreement (DUA)
=======================================
<a name="dua"></a>
# Appendix 9 - Data usage agreement (DUA)
Research Services (<research.services@admin.ox.ac.uk>.) can provide
template agreements for data sharing.
......@@ -165,7 +187,7 @@ be tailored to the specific needs of a particular project. Research
Services can advise on this, and also offer to check drafts as they are
prepared before producing a final signature-ready copy.
Example DUA from Donders Repository ([https://data.donders.ru.nl/](https://data.donders.ru.nl/?0))
Example DUA from [Donders Repository]([https://data.donders.ru.nl/](https://data.donders.ru.nl/?0)
--------------------------------------------------------------------------------------------------
I request access to the data collected in the digital repository of the
......@@ -226,8 +248,9 @@ that I access these data under the following terms:
6. Failure to abide by these guidelines will result in termination of
my privileges to access these data.
Appendix 10 -- Advice from Research Data Oxford
===============================================
<a name="rdo"></a>
# Appendix 10 -- Advice from Research Data Oxford
- Define what a breach looks like (how, why, impact) and demonstrate
that you have shown due diligence in preventing it.
......@@ -250,23 +273,11 @@ Research Data would be pleased to partner with us on this project. They
are interested in growing their experience of working directly with
specific examples.
Acknowledgements
================
Created using materials from: Das et al, 2019, \"MCIN Open Science
Guidance: Data Preparation Checklist\"
[[https://loris.ca/MCINOpenScienceGuidance\_DataPrepChecklist.pdf]{.underline}](https://loris.ca/MCINOpenScienceGuidance_DataPrepChecklist.pdf)
Inspired by Huijser, Dorien, Achterberg, Michelle, Wierenga, Lara, Van
\'t Veer, Anna, Klapwijk, Eduard, Van Erkel, Raymond, & Hettne,
Kristina. (2020, June 19). MRI data sharing guide. Zenodo.
http://doi.org/10.5281/zenodo.3822290
<a name="policy"></a>
# Relevant policy and guidance
Relevant policy and guidance
============================
University of Oxford Policy on the Management of Data Supporting
Research Outputs
## University of Oxford Policy on the Management of Data Supporting Research Outputs
<https://researchdata.ox.ac.uk/university-of-oxford-policy-on-the-management-of-data-supporting-research-outputs/>
......@@ -296,3 +307,15 @@ found and understood. Where data is deposited somewhere other than the
University's institutional data repository (the Oxford Research Archive
for Data, or ORA-Data), a data record should also be created in ORA-Data
which describes and points to the data.
<a name="acknowledgements"></a>
# Acknowledgements
Created using materials from: Das et al, 2019, \"MCIN Open Science
Guidance: Data Preparation Checklist\"
[https://loris.ca/MCINOpenScienceGuidance\_DataPrepChecklist.pdf](https://loris.ca/MCINOpenScienceGuidance_DataPrepChecklist.pdf)
Inspired by Huijser, Dorien, Achterberg, Michelle, Wierenga, Lara, Van
\'t Veer, Anna, Klapwijk, Eduard, Van Erkel, Raymond, & Hettne,
Kristina. (2020, June 19). MRI data sharing guide. Zenodo.
http://doi.org/10.5281/zenodo.3822290
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