Raw MR BIDS🔗

Each participant/session folder within rawdata/ contains raw imaging data organized into modality-specific subfolders (e.g., anat/, func/, dwi/), with filenames encoding acquisition details (task, direction, run, etc.). See File-Based Data for a general introduction to BIDS.

Folder	Modality	Key Files
anat/	sMRI	T1w, T2w
	qMRI	QALAS (inv-0 → inv-4) files
	MRS	Localizers (aqc-mrsLocAx, aqc-mrsLocCor)
func/	fMRI	Resting-state BOLD runs
fmap/	fMRI	EPI fieldmap pairs acquired in AP/PA directions for each func/ BOLD run
	qMRI	B1+ fieldmaps
dwi/	dMRI	DWI; gradient magnitude/direction (.bval/.bvec); single-band reference images (*_sbref.nii.gz)
mrs/	MRS	Metabolite spectra and water reference scans ({svs|ref}.nii.gz), each acquired via short echo time and HERCULES edited spectra (acq-{shortTE|hercules})

Raw BIDS Folder Structure🔗

 How To Read File Trees →
# All NIfTI files include sidecar JSON metadata ({FILENAME}.json)
hbcd/
└── rawdata/
    └── sub-[ID]/
        └── ses-[V0X]/
            ├── anat/
            │   ├── *_{T1w|T2w}.nii.gz                      # Structural MRI
            │   ├── *_inv-{0-4}_QALAS.nii.gz                # Quantitative MRI (QALAS)
            │   └── *_acq-mrsLoc{Ax|Cor}_run-{X}_T2w.nii.gz # MRS localizers
            │
            ├── func/
            │   └── *_task-rest_dir-PA_run-{X}_bold.nii.gz  # Resting-state fMRI
            │
            ├── fmap/
            │   ├── *_dir-{AP|PA}_run-{X}_epi.nii.gz        # fMRI fieldmaps
            │   ├── *_acq-{anat|famp}_run-{X}_TB1TFL.nii.gz # qMRI Siemens B1+ fieldmaps
            │   └── *_acq-{tr1|tr2}_run-{X}_TB1AFI.nii.gz   # qMRI GE/Philips B1+ fieldmaps
            │
            ├── dwi/
            │   ├── *_dir-{AP|PA}_run-{X}_dwi.nii.gz        # Diffusion MRI
            │   ├── *_dir-{AP|PA}_run-{X}_dwi.bval
            │   ├── *_dir-{AP|PA}_run-{X}_dwi.bvec
            │   └── *_dir-{AP|PA}_run-{X}_sbref.nii.gz
            │
            └── mrs/
                ├── *_acq-{shortTE|hercules}_run-{X}_svs.nii.gz # Spectroscopy (SVS)
                └── *_acq-{shortTE|hercules}_run-{X}_ref.nii.gz # Reference scans

BIDS Conversion Procedures🔗

For MRI, DICOM images are converted using an HBCD-customized version of dcm2niix. For MRS, vendor-specific formats (Siemens .dat, Philips data/list, GE P-file) are converted using spec2nii v0.7.0.

Additional post-processing is performed for MRI to ensure consistency across vendors. This includes converting QALAS to five 3D NIfTI files (labeled by inversion time) and hardcoding missing or inconsistent metadata fields for various modalities as follows:

Field	DWI (Philips)	EPI (Philips)	BOLD (Philips)	T1w (Philips & GE)	QALAS (Philips, Siemens, GE)
PhaseEncodingDirection
TotalReadoutTime
SliceTiming
{Small|Large}Delta
RepetitionTime
T2Prep
InversionTime