data_inventory
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data_inventory [2018/02/20 19:29] csteel |
data_inventory [2019/04/25 19:03] (current) crogers [ABIDE] |
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| ===== Data Inventory ===== | ===== Data Inventory ===== | ||
| - | This page documents the requirements for access to a dataset stored on MCIN resources. Some are available for all to use with no restrictions, but most need the user to sign an agreement and/or be added to a list with the data originitator. | + | 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: | ||
| + | |||
| + | - 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 | ||
| + | |||
| + | |||
| + | ---- | ||
| + | |||
| + | ===== 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 ==== | ||
| Line 10: | Line 87: | ||
| * 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://abide.loris.ca | ||
| ---- | ---- | ||
| Line 84: | Line 162: | ||
| ---- | ---- | ||
| - | ==== RECEPTOR_MAP ==== | + | ==== nki-rs ==== |
| - | * License : | + | * Originally downloaded by Jose Maria Chema Mateos. |
| - | * Path : ace-storage-2:/data1/Raw_Study_Data/ICMB | + | * 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). |
| - | * Unix read-only group : receptor_map | + | * The MRI protocol can be found here: http://fcon_1000.projects.nitrc.org/indi/enhanced/mri_protocol.html |
| - | * Approvals : Reza Adalat | + | * 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: |
| - | ==== Instructions ==== | + | |
| - | Data Inventory Entries could include: | + | [[http://fcon_1000.projects.nitrc.org/indi/enhanced/access.html]] |
| - | + | ||
| - | * Heading | + | |
| - | * Description | + | |
| - | * Website | + | |
| - | * 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 read and execute in order to allow users and programs to traverse the directory structure. | + | |
| - | + | ||
| - | See the example below | + | |
| ---- | ---- | ||
| + | ==== PAC 2018 ==== | ||
| + | http://www.photon-ai.com/pac | ||
| - | ==== Raw Study Data Example ==== | + | * Path : ace-lab-1.acelab.ca:/home/users/ |
| + | * Unix read-write group : pac | ||
| - | 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 | + | ---- |
| + | ==== RECEPTOR_MAP ==== | ||
| - | * Path : ace-storage-2:/data1/Raw_Study_Data/Example | + | * License : |
| - | * Unix group : example_group | + | * Path : ace-storage-2:/data1/Raw_Study_Data/ICMB |
| - | * permissions : 0550 (owner: read and execute, group: read and execute, other: no access | + | * 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://camcan-archive.mrc-cbu.cam.ac.uk/dataaccess/ | ||
| + | ---- | ||
data_inventory.1519154950.txt.gz · Last modified: 2018/02/20 19:29 by csteel
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