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===== 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.


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==== Instructions ====

Data Inventory Entries should include:

   -  Heading = Dataset Name
  -   1-line Description
  -   MCIN Contact Person
  -   Reference Website
  -   Version Number of release
  -   Release Date
  -   N_groups (eg. patients, healthy controls, genotype, ???)
  -   N_subjects (total in each group)
  -   N_timepoints (average, variance)
  -   Modalities present
  -   Brief summary of planned projects/analyses
  -   Derived processed data
  -   Requires access permission? (Data Access Agreement, MCIN approver)
  -   License or link to license
  -   Path (Including server)
  -   Unix group https://contacts.acelab.ca/groups.php
  -   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
  * DICOM or nii/mnc (+ version of conversion tool if nii/mnc)
  * Magnet strength + manufacturer
  * Sequences available (eg: T1w, T2w, T1c, FLAIR, PDw)
  * Diffusion (# directions measured) DTI BIDS: https://docs.google.com/document/d/1cQYBvToU7tUEtWMLMwXUCB_T8gebCotE1OczUpMYW60/edit
  * Image size/voxel spacing
  * Pre-processing applied?
19. Functional Imaging
  * DICOM or nii/mnc (+ version of conversion tool if nii/mnc)
  * Resting state (avg/variance in #/size of volumes, length, TR/TE time) + corresponding physiological data
  * fMRI (avg/variance in #/size of volumes, length, TR time) Details of task, Stimulus available?, to classify the task use a cognitive ontology (e.g., https://www.ncbi.nlm.nih.gov/pubmed/21643732)
  * EEG/MEG (# channels, time length (avg/variance), sampling rate) see EEG BIDS spec: https://docs.google.com/document/d/1ArMZ9Y_quTKXC-jNXZksnedK2VHHoKP3HCeO5HPcgLE/edit; iEEG BIDS: https://docs.google.com/document/d/1qMUkoaXzRMlJuOcfTYNr3fTsrl4SewWjffjMD5Ew6GY/edit
  * PET see PET BIDS: https://docs.google.com/document/d/1mqMLnxVdLwZjDd4ZiWFqjEAmOmfcModA_R535v3eQs0/edit
  * ASL see ASL BIDS: https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c/edit#heading=h.prrzvwchfio6
20. Imaging Quality Control:
  * Sequences where QC available
  * Rater name
  * Distribution of PASS/FAIL/other images
21. Physiological Data
  * see NeuroData without borders spec: https://www.nwb.org/2017/11/11/nwb-2-0-beta-released/
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


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===== Datasets =====


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==== 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...

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==== 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 
  * Old version on LORIS (imaging downloads not available, awaiting upgrade): https://abide.loris.ca

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==== 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 

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==== ADNI ====

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

  * Agreement to sign:     http://adni.loni.usc.edu/wp-content/uploads/how_to_apply/ADNI_Data_Use_Agreement.pdf
  * Path :                 ace-storage-2:/data1/Raw_Study_Data/ADNI
  * Unix read-only group : adni
  * Approval :             PJ Toussaint, Alan Evans

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==== 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 

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==== 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 :             

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==== 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 

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==== 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]]

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==== 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

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==== nki-rs ====

  * Originally downloaded by Jose Maria Chema Mateos.
  * T1 and DTI data for a subset of subjects is being used (200 subjects aged 7-84 without a history of psychiatric or neurological disease).
  * The MRI protocol can be found here: http://fcon_1000.projects.nitrc.org/indi/enhanced/mri_protocol.html
  * We do not have any assessment data, but a dictionary of the available items is here: http://fcon_1000.projects.nitrc.org/indi/enhanced/assessments.html

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

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

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==== PAC 2018 ====

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

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

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==== RECEPTOR_MAP ====

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

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==== Cam-CAN ====

  *  Specifics on the data available in the Cam-CAN dataset are available here: https://camcan-archive.mrc-cbu.cam.ac.uk/dataaccess/


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