This repo provides a brief overview of public datasets currently held on the HPC shared imaging drive. Derived data is made available where stated. Unless explicitly stated otherwise, freesurfer was run locally using v6.0.
- Code
- Authorship, usage and acknowledgements
- File and folder structure
- Individual datasets
- Human Connectome Project Datasets
- OpenNeuro datasets
- NIMH Data Archive datasets
Some generic code is included in this repository that mainly pertains to processing freesurfer on the cluster and or R functions around parsing output and reorganising data.
If you are using the existing variables available from the shared datasets, you do not need to include anyone as co-authors. However, if you are using variables generated by others (for example imaging metrics processed using specific pipelines, polygenic scores, bespoke phenotypic variables), please contact the person who has generated the variables before using them. Please check with them re. authorship in accordance with the University's authorship guidelines (see: http://www.medschl.cam.ac.uk/wp-content/uploads/2014/02/CoS14_68-Authorship_Code_of_Practice-FINAL.pdf?04c0fc). If you are unsure if variables were generated by a specific user or were UKB default please contact Richard or Jakob to check. All freesurfer reconstructions were run by Richard Bethlehem using funding from the BRC (see acknowledgement below)
If you are creating a new variable and would like to make it available for others to use please include the following:
- A readme file with the description of the variables, your name and contact information, and details of use
- A file, or a link to a webpage (github, OSF etc) with detailed methods you used for generating the variables including the code.
Finally, when making use of this resource please acknowledge the following funding sources that continue to make storage and processing of this dataset possible in your publications:
"This research was co-funded by the NIHR Cambridge Biomedical Research Centre to Richard A.I. Bethlehem and Edward Bullmore. The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care."
# /rds/project/rds-vm5VDLj6Ch8//
# .
# └── ABIDE
# ├── BIDS
# │ └── derivatives
# │ │ └── freesurfer
# │ │ └── <sub>
# │ │ └── <ses>
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# │ └── <sub>
# │ │ └── <ses>
# │ │ └── anat
# │ │ └── func
# └── participants.tsv
# └── Readme.md
# └── ADHD200
# ├── BIDS
# │ └── derivatives
# │ │ └── freesurfer
# │ │ └── <sub>
# │ │ └── <ses>
# │ │ └── <sub>
# │ └── <sub>
# │ │ └── <ses>
# │ │ └── anat
# │ │ └── func
# └── participants.tsv
# └── Readme.md
#____________________________
http://fcon_1000.projects.nitrc.org/indi/abide/
Autism Brain Imaging Database Exchange, 50/50 autism and neurotypical, mainly young adults, mainly males
- n: 2000
- age: 6+
- modalities: T1, Rest
- derived: freesurfer
Access protocol:: Fully open raw data, fully open processed data (contact rb643 for info)
http://fcon_1000.projects.nitrc.org/indi/adhd200/
ADHD200, 50/50 adhd and neurotypical, mainly young adults, mainly males
- n: 800
- age: 6+
- modalities: T1, Rest
- derived: freesurfer
Access protocol:: Fully open raw data, fully open processed data DUA required for phenotypes (contact rb643 for info)
http://adni.loni.usc.edu/
Approximately 8500 scans across multiple sites, multiple time-points mainly
Alzheimer, healthy controls, and MCI. Currently only holding ADNI1 ADNI2 and ADNI-GO
- n: 8500
- age: 45+
- modalities: T1,
- derived: freesurfer
Access protocol:: DUA required obtainable via LONI
https://dataverse.harvard.edu/dataverse/GSP
Brain genomics superstruct project
- n: 1570
- age: 12-45 years
- modalities: T1, Rest
- derived: freesurfer, euler
Access protocol:: DUA required for demographics, available via Harvard Dataverse
https://osf.io/axz5r/
Longitudinal preschool dataset (up to 8 time-points)
- n: 85
- age: 2-8 years
- modalities: T1, DTI, Rest
- derived: freesurfer, euler
Access protocol:: Fully open
- n: 700+
- age: 18-88 (equally sized 10yr bins)
- modalities: T1, T2, MT, Rest, Movie, Task, DTI
- derived: freesurfer, Rest (ICA-AROMA)
Access protocol:: Access through Cam-CAN portal, more derived data directly available there.
http://fcon_1000.projects.nitrc.org/indi/retro/dlbs.html
Dallas Lifespan Brain Study
- n: 315
- age: 18-88
- modalities: T1
- derived: freesurfer
Access protocol:: fully open
https://data.healthybrainnetwork.org/main.php
https://github.com/rb643/HBN
- n: 1592
- age: 6+ years
- modalities: T1, DTI, Rest, Movie
- derived: freesurfer, euler, rest (speedypp), Movie1 (speedypp), Movie2 (speedypp)
Access protocol:: Fully open raw data, DUA required for phenotypes (contact rb643 for info) Notes:: Data was processed by rb643 [@] medschl.cam.ac.uk and thus this folder includes a code repository and qc measures alongside raw data. No additional freesurfer was run, instead HBN provides QC-d freesurfer data.
http://fcon_1000.projects.nitrc.org/indi/enhanced/
- n: 941
- age: 18+
- modalities: T1, DTI, Rest (2-3 acquisitions), Task, Physio
- derived: freesurfer, euler
Access protocol:: Fully open raw data, DUA required for phenotypes (contact rb643 for info)
Longitudinal adolescent dataset (up to 3 time-points)
- n: 316
- age: 16-24 years
- modalities: T1, T2, MT, DTI, Rest
- derived: freesurfer, euler, Rest (ME-ICA), DTI (Schaeffer connectomes)
Access protocol:: Accessible to NSPN collaborators
https://www.oasis-brains.org/
Approximately 3000+ scans across multiple sites, multiple time-points mainly
Alzheimer, healthy controls, and MCI. Currently only holding OASIS 3
- n: 3033
- age: 45+
- modalities: T1,
- derived: freesurfer
Access protocol:: DUA required obtainable via OASIS website
https://offordcentre.com/studies/pond-network-imaging-sub-study/
Neurodevelopmental dataset mostly including ADHD, Autism and neurotypical individuals
- n: 700
- age: 10+
- modalities: T1,
- derived: freesurfer
Access protocol:: DUA required obtainable via POND network collaborators
http://fcon_1000.projects.nitrc.org/indi/retro/sald.html
Southwest University Adult Lifespan Dataset
- n: 494
- age: 18+
- modalities: T1, rest
- derived: freesurfer
Access protocol:: fully open
http://fcon_1000.projects.nitrc.org/indi/retro/wayne_11.html
Wayne State longitudinal dataset
- n: 200
- age: 18+
- modalities: T1, rest
- derived: freesurfer
Access protocol:: fully open
Access protocol:: All HCP datasets can be accessed with one DUA through NIMH Data Repository
- n: 1113
- modalities: T1, T2, Rest, DTI, Movie
- derived: freesurfer, euler
- n: 689
- age: 21+
- modalities: T1, T2, Rest, DTI, Movie
- derived: freesurfer, euler
- n: 655
- age: 6-21
- modalities: T1, T2, Rest, DTI, Movie
- derived: freesurfer, euler
Access protocol:: All OpenNeuro datasets are openly available
https://openneuro.org/datasets/ds002895 & https://www.biorxiv.org/content/10.1101/2020.06.16.155317v1
- n: 928
- age: 20-26
- modalities: T1 (3x), DWI, Rest
- derived: freesurfer
Notes
https://openneuro.org/datasets/ds002785 & https://www.biorxiv.org/content/10.1101/2020.06.16.155317v1
- n: 216
- age: 20-26
- modalities: T1, DWI, Rest (6x), Physio
- derived: freesurfer
Notes
https://openneuro.org/datasets/ds002790 & https://www.biorxiv.org/content/10.1101/2020.06.16.155317v1
- n: 226
- age: 20-26
- modalities: T1, DWI, Rest 4x), Task (WM), Physio
- derived: freesurfer
Notes
https://openneuro.org/datasets/ds001894/versions/1.3.1
Longitudinal Brain Correlates of Multisensory Lexical Processing in Children
- n: 188
- age: 8-14
- modalities: T1, T2, DWI, Task
- derived: euler, mriqc
Notes
https://openneuro.org/datasets/ds000228
MRI data of 3-12 year old children and adults during viewing of a short animated film
- n: 155
- age: 3-12
- modalities: T1, Movie
- derived: freesurfer, euler, mriqc
Notes
Access protocol:: All NDAR datasets require a single MTA with the NIMH Data Repository Note:: where shared these dataset have been converted to a largely BIDS compatible file/folder structure requiring significant effort from Jakob Seidlitz and Richard Bethlehem
https://nda.nih.gov/edit_collection.html?id=2274 Schizphrenia and bipolar consortium dataset
- n: 700+
- age: 8+
- modalities: T1,
- derived: freesurfer
https://nda.nih.gov/edit_collection.html?id=19 Longitudinal data autism high risk, up to 3 time-points
- n: 300+
- age: 0-2
- modalities: T1,
- derived: freesurfer (infant fs)
https://nda.nih.gov/edit_collection.html?id=2021 Sex balanced cohort of autism
- n: 300+
- age: 18+
- modalities: T1,
- derived: freesurfer
Longitudinal data, up to 3 time-points
- n: 514
- age: 2-8
- modalities: T1, T2
- derived: freesurfer, euler
https://nda.nih.gov/edit_collection.html?id=9 Longitudinal data autism high risk, up to 3 time-points
- n: 200+
- age: 0-2
- modalities: T1,
- derived: freesurfer (infant fs)