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data_inventory

Data Inventory

This page describes the datasets on MCIN resources and requirements for access to these datasets. Some are available for all to use with no restrictions, but most need the user to be approved and added to a list of users.


Instructions

Data Inventory Entries should include:

  1. Heading = Dataset Name
  2. 1-line Description
  3. MCIN Contact Person
  4. Reference Website
  5. Version Number of release
  6. Release Date
  7. N_groups (eg. patients, healthy controls, genotype, ???)
  8. N_subjects (total in each group)
  9. N_timepoints (average, variance)
  10. Modalities present
  11. Brief summary of planned projects/analyses
  12. Derived processed data
  13. Requires access permission? (Data Access Agreement, MCIN approver)
  14. License or link to license
  15. Path (Including server)
  16. Permissions - Raw data should be read only in order prevent data loss or alteration, Raw data directories need to allow r - - Ordered List Itemead and execute in order to allow users and programs to traverse the directory structure.

For different data types, please list the following as completely as possible:

18. Structural MRI

19. Functional Imaging

20. Imaging Quality Control:

  • Sequences where QC available
  • Rater name
  • Distribution of PASS/FAIL/other images

21. Physiological Data

22. Clinical Metadata:

  • Name of disorder/condition/pathology studied
  • Main quantitative clinical metrics?
  • Diagnostic label categories and distribution of subjects
  • Age (avg/variance)
  • Gender balance
  • Number of data collection sites
  • Other behavioural information available

23. Genetics:

  • SNPs, WGS, RNA-seq etc.
  • Format: bam, vcf etc.

24. N_subjects for each modality for each visit


Datasets


ABCD (new)

https://data-archive.nimh.nih.gov/abcd The ABCD Data Repository is a part of the National Institute of Mental Health Data Archive (NDA), a collection of repositories that also includes the RDoC Database (RDoCdb), the National Database for Clinical Trials related to Mental Illness (NDCT), the NIH Pediatric MRI Repository (PedsMRI), and the National Database for Autism Research (NDAR).

  • Path : ace-lab-1.acelab.ca:/home/users/shared/abac
  • Unix read-write group : abac
  • Approval: pending…

ABIDE

ABIDE is the Autism Brain Imaging Data Exchange from http://fcon_1000.projects.nitrc.org/indi/abide/abide_I.html

  • License: Creative Commons, Attribution-NonCommercial-Share Alike License
  • Path : ace-storage-2:/data1/Raw_Study_Data/abide
  • Unix group(s) : abide
  • No approval needed, just put in a GLPI ticket to be added to the group

ABIDE II

ABIDE II is the Autism Brain Imaging Data Exchange from http://fcon_1000.projects.nitrc.org/indi/abide/abide_II.html

  • License: Creative Commons, Attribution-NonCommercial-Share Alike License
  • Path : ace-storage-2:/data1/Raw_Study_Data/ABIDE_II
  • Unix group(s) : abide
  • No approval needed, just put in a GLPI ticket to be added to the group

ADNI

ADNI is the Alzheimer’s Disease Neuroimaging Initiative from http://adni.loni.usc.edu


COBRE

COBRE is the Center for Biomedical Research Excellence from http://cobre.mrn.org

  • License : Creative Commons, Attribution-NonCommercial-Share Alike License
  • Path : ace-storage-2:/data1/Raw_Study_Data/cobre
  • Unix read-only group : cobre
  • Approvals : No approval needed, permissions are 755

CONNECTOME

CONNECTOME comes from the Connectome Coordination Facility at https://www.humanconnectome.org

  • License :
  • Path : ace-storage-2:/data1/Raw_Study_Data/connectome
  • Unix read-only group : connectome
  • Approvals :

CoRR

Consortium for Reliability and Reproducibility (CoRR) at http://fcon_1000.projects.nitrc.org/indi/CoRR/html/

CoRR includes 33 datasets, of which 32 are currently available for download, consisting of:

  1629 Subjects
  3357 Anatomical Scans
  5093 Resting Functional Scans
  1302 Diffusion Scans
  300 CBF and ASL Scans
  • License : May vary by datasets and providers
  • Path : ace-storage-2:/data1/Raw_Study_Data/corr
  • Unix read-only group : corr
  • Approvals : Reza Adalat

ICBM

ICBM 152 Linear Linear ICBM Average Brain (ICBM152) Stereotaxic Registration Model

* https://www.mcgill.ca/bic/software/tools-data-analysis/anatomical-mri/atlases/icbm152lin


MCIC

The MCIC Collection: A Shared Repository of Multi-Modal, Multi-Site Brain Image Data from a Clinical Investigation of Schizophrenia

  • Path : ace-storage-2:/data1/Raw_Study_Data/mcic

nki-rs

* Only using neuroimaging data so does not require a data usage agreement per:

http://fcon_1000.projects.nitrc.org/indi/enhanced/access.html


PAC 2018

http://www.photon-ai.com/pac

  • Path : ace-lab-1.acelab.ca:/home/users/
  • Unix read-write group : pac

RECEPTOR_MAP

  • License :
  • Path : ace-storage-2:/data1/Raw_Study_Data/ICMB
  • Unix read-only group : receptor_map
  • Approvals : Reza Adalat

Cam-CAN


data_inventory.txt · Last modified: 2019/03/05 19:56 by sdyke