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data_inventory [2017/11/08 18:54] – [Instructions] ppatterson | data_inventory [2024/03/26 13:52] (current) – external edit 127.0.0.1 | ||
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===== Data Inventory ===== | ===== Data Inventory ===== | ||
- | This page documents | + | This page describes |
+ | |||
---- | ---- | ||
+ | ==== Instructions ==== | ||
+ | |||
+ | Data Inventory Entries should include: | ||
+ | |||
+ | | ||
+ | - | ||
+ | - MCIN Contact Person | ||
+ | - | ||
+ | - | ||
+ | - | ||
+ | - | ||
+ | - | ||
+ | - | ||
+ | - | ||
+ | - Brief summary of planned projects/ | ||
+ | - | ||
+ | - | ||
+ | - | ||
+ | - Path (Including server) | ||
+ | - Unix group https:// | ||
+ | - | ||
+ | |||
+ | 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:// | ||
+ | * Image size/voxel spacing | ||
+ | * Pre-processing applied? | ||
+ | 19. Functional Imaging | ||
+ | * DICOM or nii/mnc (+ version of conversion tool if nii/mnc) | ||
+ | * Resting state (avg/ | ||
+ | * fMRI (avg/ | ||
+ | * EEG/MEG (# channels, time length (avg/ | ||
+ | * PET see PET BIDS: https:// | ||
+ | * ASL see ASL BIDS: https:// | ||
+ | 20. Imaging Quality Control: | ||
+ | * Sequences where QC available | ||
+ | * Rater name | ||
+ | * Distribution of PASS/ | ||
+ | 21. Physiological Data | ||
+ | * see NeuroData without borders spec: https:// | ||
+ | 22. Clinical Metadata: | ||
+ | * Name of disorder/ | ||
+ | * Main quantitative clinical metrics? | ||
+ | * Diagnostic label categories and distribution of subjects | ||
+ | * Age (avg/ | ||
+ | * 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:// | ||
+ | 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:/ | ||
+ | *Unix read-write group : abac | ||
+ | *Approval: pending... | ||
+ | |||
+ | ---- | ||
+ | |||
==== ABIDE ==== | ==== ABIDE ==== | ||
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* Unix group(s) : abide | * Unix group(s) : abide | ||
* No approval needed, just put in a GLPI ticket to be added to the group | * 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:// | ||
---- | ---- | ||
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---- | ---- | ||
- | |||
==== CONNECTOME ==== | ==== CONNECTOME ==== | ||
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---- | ---- | ||
+ | ==== CoRR ==== | ||
+ | |||
+ | Consortium for Reliability and Reproducibility (CoRR) at http:// | ||
+ | |||
+ | 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 : | ||
+ | * Unix read-only group : corr | ||
+ | * Approvals : Reza Adalat | ||
+ | |||
---- | ---- | ||
- | ==== Instructions | + | ==== ICBM ==== |
- | All Data Inventory Entries should contain: | + | ICBM 152 Linear |
+ | Linear ICBM Average Brain (ICBM152) Stereotaxic Registration Model | ||
+ | |||
+ | * [[https:// | ||
+ | |||
+ | ---- | ||
+ | ==== MCIC ==== | ||
- | * Heading | + | The MCIC Collection: A Shared Repository of Multi-Modal, Multi-Site Brain Image Data from a Clinical Investigation of Schizophrenia |
- | * Description | + | |
- | * Path (Including server) | + | |
- | * Unix group https:// | + | |
- | * Permissions | + | |
- | See the example below | + | * Path : ace-storage-2:/ |
---- | ---- | ||
+ | ==== 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:// | ||
+ | * We do not have any assessment data, but a dictionary of the available items is here: http:// | ||
- | ==== Raw Study Data Example ==== | + | * Only using neuroimaging data so does not require a data usage agreement per: |
- | Raw Study Data Example is an example of a data inventory entry. The description tells us a bit about the data, perhaps it's source and so on so that someone reading it gets the general idea of the kind of data it contains | + | [[http:// |
- | | + | ---- |
- | * Unix group : example_group | + | ==== PAC 2018 ==== |
- | * permissions : 0550 (owner: | + | |
+ | http:// | ||
+ | |||
+ | | ||
+ | * Unix read-write | ||
---- | ---- | ||
+ | ==== RECEPTOR_MAP ==== | ||
+ | * License : | ||
+ | * Path : | ||
+ | * Unix read-only group : receptor_map | ||
+ | * Approvals : Reza Adalat | ||
+ | ---- | ||
+ | ==== Cam-CAN ==== | ||
+ | * Specifics on the data available in the Cam-CAN dataset are available here: https:// | ||
+ | |||
+ | |||
+ | ---- |