Introduction to BIDS

The Brain Imaging Data Structure (BIDS) provides a simple and intuitive way to organize and describe your neuroimaging and behavioral data. It has been widely adopted as a standard that many processing pipelines understand. 
BIDS Specification
The main specification lives here https://bids-specification.readthedocs.io/en/stable/​
Organization Principles
BIDS principles can be summarized as:
NIFTI files are the chosen imaging format
Key data is accompanied by json file providing parameters and descriptions
Folder structure and files are named in a consistant manner as prescribed by the specification
Directory Structure
Overall directories hierarchy is as follows ([] indicates optional fields):
sub-<participant_label>[/ses-<session_label>]/<data_type>/ 
[code/] 
[derivatives/] 
[stimuli/]
[sourcedata/]
Single Session Example
 sub-control01 
anat
sub-control01_T1w.nii.gz sub-control01_T1w.json 
sub-control01_T2w.nii.gz sub-control01_T2w.json
func
sub-control01_task-nback_bold.nii.gz 
sub-control01_task-nback_bold.json 
sub-control01_task-nback_events.tsv 
sub-control01_task-nback_physio.tsv.gz 
sub-control01_task-nback_physio.json 
sub-control01_task-nback_sbref.nii.gz
dwi
sub-control01_dwi.nii.gz 
sub-control01_dwi.bval 
sub-control01_dwi.bvec
fmap
sub-control01_phasediff.nii.gz 
sub-control01_phasediff.json 
sub-control01_magnitude1.nii.gz
sub-control01_scans.tsv
Additional files and folders containing raw data may be added as needed for special cases. They should be named using all lowercase with a name that reflects the nature of the scan (e.g., “calibration”). Naming of files within the directory should follow the same scheme as above (e.g., “sub-control01_calibration_Xcalibration.nii.gz”)
BIDS Entity Table
The name of the file depends on modality, acquisition parameters and other considerations. The BIDS Entity Table table compiles the entities (key-value pairs) described throughout the specification, and establishes a common order within a filename. For example, if a file has an acquisition and reconstruction label, the acquisition entity must precede the reconstruction entity. 
Format considerations
Filenames are case sensitive
Recommended: Zero-padding for subjects i.e sub_01
NOT Recommended: Zero-padding for runs and echo (and they MUST be integers)
Units: SI
Time: YYYY-MM-DDThh:mm:ss
Last modified 11mo ago