Chapter 9 Data Access
9.1 BIDs and Derivative Directories
Log onto Sylvester https://sylvester911.biabl.org/
Your ID will be: USERNAME-analy
To get your password use the password recovery feature.
Here’s the general structure of the datasets:
STUDY_DIR/ |-- code/ |-- scanlist.sh # my code for generating scan list |-- STUDY.csv # full list of IDs with available scans |-- derivatives/ # processed NIFTI images |-- pT1T2/ # these are the preprocessed images used in analyses i.e., freesurfer |-- sub-001/ |-- sub-001_T1w.nii.gz |-- sub-001_inplaneT2w.nii.gz |-- freesurfer/ |-- sub-001/ |-- sub-002/ |-- sourcedata/ # This is where we should put PDF printouts from the scanner |-- sub-001/ # BIDS organized raw NIFTI images |-- sub-002/ dataset_description.json # general dataset description that should contain full study name, funding, and people participants.json # demographics data dictionary participants.tsv # demographics file
9.2 Output Tables
Github repositories are private. You will have to provide your GitHub username and the study name to be added as a collaborator.
Downloading the current dataset is simple and through GitHub’s version control you can keep track of files if they are updated.
Click on “Clone or download” and then click on “Download Zip”.