Standardization of Neuroimaging Data Management inside Synapsy

Annual Meeting 2021 in Les Diablerets, Switzerland
by Patric Hagmann and Sebastien Tourbier
14 October 2021

Keys of Synapsy Data Management Plan (DMP) for neuroimaging data

Community standard to organize and describe neuroimaging data along with metadata: Brain Imaging Data Structure (BIDS) - https://bids.neuroimaging.io/

Distributed data versioning and management system tailored to neuroimaging data: Datalad - https://www.datalad.org/

Distributed storage of neuroimaging data accross the different institution servers with access controlled by PIs.

Implementation overview

BRAIN IMAGING DATA STRUCTURE (BIDS)

Dataset can be validated with bids-validator:


	$ bids-validator "/media/localadmin/HagmannHDD/Seb/PsychoDev/NiftiBIDSCompliant" --ignoreSubjectConsistency
	bids-validator@1.7.2

	[...]

	    Summary:                   Available Tasks:        Available Modalities:
	    9212 Files, 47.25GB        rest                    MTR                  
	    346 - Subjects                                     T1w                  
	    6 - Sessions                                       T2map                
	                                                       dwi                  
	                                                       bold                  
	                                                       T1map                
	                                                       fieldmap

Datalad

Allow to manage and keep track of all changes:


$ git log


commit 336790df4aaa75eb49fc4a3a235d3058fdb3c4cd (ssh_horus/master, master, refs/basis/adjusted/master(unlocked))
Author: Sebastien Tourbier
Date:   Mon Jul 12 11:09:23 2021 +0200

    Update README and CHANGES

[...]

commit b8790bab140029c5f9acee6e7eab324c833b465e
Author: Sebastien Tourbier
Date:   Fri Jul 9 07:36:14 2021 +0200

    Initial upload with 346 subjects that pass bids-validator 1.7.2

Allow to publish and share easily datasets with institutional data storage server


$ datalad siblings


.: here(+) [git]
.: ssh_horus(+) [stockage-horus.chuv.ch:/********************/NiftiBIDSCompliant (git)]

DATASET CATALOG

All datasets can be easily referenced in the NCCR-SYNAPSY organization on GitHub

Progress

Expected achievements w/r DMP

By February 2022:
- DMP introduced for most of neuroimaging cohorts and fully implemented in a few.

This will:
- Complete imaging data manager training
- Ease the sharing of Synapsy neuroimaging cohorts on open data repositories to fully satisfy SNSF FAIR research data requirements,
- Facilitate future collaborations between groups,
- Enable the analysis of Synapsy neuroimaging cohort with a collection of automated processing pipelines (https://bids-apps.neuroimaging.io/).

Beyond February 2022

Perspectives

Complete the implementation of the DMP for all cohorts

To fully exploit the catalog with the development of a search engine

Requirements:

Data manager resources in the laoratories

Resources for coordination and IT support and implementation

Thanks to all the ones involved

and more... with special thanks to Sébastien!