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Data Dictionary

All outputs are written to a BIDS outputs derivatives directory.

BIDS filename conventions

RBC output filenames follow the BIDS derivatives naming scheme. Each filename is built from key-value pairs called entities, separated by underscores:

Entity Meaning Example
sub- Subject identifier sub-01
ses- Session label (optional) ses-baseline
task- Task performed during fMRI task-rest
acq- Acquisition variant (optional) acq-VNavNorm
run- Run index when a scan is repeated run-1
space- Coordinate space the image is aligned to space-MNI152NLin6Asym
atlas- Brain parcellation used atlas-schaefer200
reg- Nuisance regression strategy applied reg-36parameter
from- / to- Source and target spaces of a transform from-T1w_to-MNI152NLin6Asym
desc- Free-text description of the file content desc-brain

Entities in square brackets (e.g., [_ses-{ses}]) are included only when the dataset contains that information.

Anatomical outputs

Produced by rbc anatomical. These are structural (T1-weighted) processing results.

File Suffix Description Created by Format
*_desc-brain_T1w.nii.gz T1w Skull-stripped, bias-corrected brain image ANTs brain extraction + N4 bias correction 3D NIfTI
*_desc-T1w_mask.nii.gz mask Binary mask delineating brain tissue ANTs brain extraction 3D NIfTI, binary mask
*_desc-csf_mask.nii.gz mask Cerebrospinal fluid discrete segmentation mask (thresholded at 0.95) FSL FAST tissue segmentation 3D NIfTI, binary mask
*_desc-gm_mask.nii.gz mask Gray matter discrete segmentation mask (thresholded at 0.95) FSL FAST tissue segmentation 3D NIfTI, binary mask
*_desc-wm_mask.nii.gz mask White matter discrete segmentation mask (thresholded at 0.95) FSL FAST tissue segmentation 3D NIfTI, binary mask
*_desc-wmBBR_mask.nii.gz mask White matter boundary used for boundary-based registration (BBR) of functional data to anatomy FSL WM boundary extraction 3D NIfTI, binary mask
*_from-T1w_to-MNI152NLin6Asym_mode-image_xfm.nii.gz xfm Nonlinear warp field mapping subject anatomy to MNI152NLin6Asym template space ANTs registration 3D NIfTI, displacement field
*_from-MNI152NLin6Asym_to-T1w_mode-image_xfm.nii.gz xfm Inverse warp field mapping MNI152NLin6Asym template space back to subject anatomy ANTs registration 3D NIfTI, displacement field

Functional outputs

Produced by rbc functional. These are functional MRI (BOLD) processing results. Requires anatomical outputs.

File Suffix Description Created by Format
*_sbref.nii.gz sbref Single-volume reference image used for motion estimation Extracted from BOLD timeseries 3D NIfTI
*_desc-preproc_bold.nii.gz bold Motion-corrected BOLD timeseries in native subject space (after despiking and slice-timing correction) FSL MCFLIRT 4D NIfTI
*_desc-motionParams_motion.1D motion Six rigid-body motion parameters (3 translations, 3 rotations) estimated during motion correction FSL MCFLIRT Text, 6-column 1D file
*_desc-relsDisplacement_motion.rms motion Frame-to-frame relative root-mean-square displacement over time FSL MCFLIRT Text, single-column RMS file
*_desc-maxDisplacement_motion.rms motion Absolute root-mean-square displacement of each volume relative to the reference FSL MCFLIRT Text, single-column RMS file
*_desc-brain_mask.nii.gz mask Binary brain mask in native BOLD space FSL BET 3D NIfTI, binary mask
*_from-bold_to-T1w_mode-image_desc-linear_xfm.mat xfm Affine transformation matrix aligning BOLD to the T1w anatomical image ANTs boundary-based registration 4x4 affine matrix
*_space-MNI152NLin6Asym_desc-preproc_bold.nii.gz bold BOLD timeseries resampled to MNI152NLin6Asym template space in a single interpolation step (before denoising) ANTs resampling 4D NIfTI
*_space-MNI152NLin6Asym_desc-bold_mask.nii.gz mask Brain mask warped to template space at the BOLD resolution ANTs resampling 3D NIfTI, binary mask
*_space-MNI152NLin6Asym_reg-{regressor}_desc-preproc_bold.nii.gz bold Denoised BOLD timeseries in template space after nuisance regression and bandpass filtering. {regressor} is 36parameter or aCompCor Nuisance regression 4D NIfTI
*_desc-{regressor}_regressors.1D regressors Nuisance regressor matrix used for denoising. {regressor} is 36parameter or aCompCor Computed from motion parameters and tissue masks Text, multi-column 1D file

Metrics outputs

Produced by rbc metrics. Voxel-wise and region-wise summary measures computed from the denoised BOLD data. All are in MNI152NLin6Asym template space and tagged with the regression strategy used.

File Suffix Description Created by Format
*_reg-{regressor}_alff.nii.gz alff Amplitude of Low-Frequency Fluctuations, the sum of spectral power in the 0.01-0.1 Hz band at each voxel Frequency-domain analysis 3D NIfTI
*_reg-{regressor}_desc-smooth_alff.nii.gz alff Spatially smoothed ALFF map Gaussian kernel smoothing 3D NIfTI
*_reg-{regressor}_desc-smoothZstd_alff.nii.gz alff Z-scored (standardized) smoothed ALFF, normalized within the brain mask Z-score normalization 3D NIfTI
*_reg-{regressor}_falff.nii.gz falff Fractional ALFF, the ratio of low-frequency power (0.01-0.1 Hz) to total power at each voxel Frequency-domain analysis 3D NIfTI
*_reg-{regressor}_desc-smooth_falff.nii.gz falff Spatially smoothed fALFF map Gaussian kernel smoothing 3D NIfTI
*_reg-{regressor}_desc-smoothZstd_falff.nii.gz falff Z-scored smoothed fALFF, normalized within the brain mask Z-score normalization 3D NIfTI
*_reg-{regressor}_reho.nii.gz reho Regional Homogeneity, Kendall's W measuring local synchronization in a 26-voxel neighborhood AFNI 3dReHo 3D NIfTI
*_reg-{regressor}_desc-smooth_reho.nii.gz reho Spatially smoothed ReHo map Gaussian kernel smoothing 3D NIfTI
*_reg-{regressor}_desc-smoothZstd_reho.nii.gz reho Z-scored smoothed ReHo, normalized within the brain mask Z-score normalization 3D NIfTI
*_atlas-{atlas}_reg-{regressor}_desc-mean_timeseries.tsv timeseries Mean BOLD signal averaged within each region of the specified atlas. Atlases: schaefer_200, schaefer_300, schaefer_400, schaefer_1000, aal Region-wise averaging TSV, regions x timepoints
*_atlas-{atlas}_reg-{regressor}_desc-pearson_correlations.tsv correlations Pairwise Pearson correlation matrix between all atlas region timeseries Pearson correlation TSV, regions x regions

All metrics files include space-MNI152NLin6Asym in the filename (omitted from the table for readability).

QC outputs

Produced by rbc qc. A single summary file per functional run containing quality control metrics in XCP-D format.

File Suffix Description Created by Format
*_space-MNI152NLin6Asym_reg-{regressor}_desc-xcp_quality.tsv quality Single-row TSV with 24 quality control metrics (see columns below) QC aggregation TSV, 1 row

QC columns

Column Type Description
sub string Subject identifier
ses string Session label
task string Task label
run integer Run number
desc string Pipeline variant description
regressors string Nuisance regression strategy name
space string Coordinate space (MNI152NLin6Asym)
meanFD float Mean framewise displacement in mm (Jenkinson method)
relMeansRMSMotion float Mean relative RMS of translation parameters
relMaxRMSMotion float Maximum relative RMS of translation parameters
nVolCensored integer Number of volumes exceeding the FD threshold (0.2 mm)
meanDVInit float Mean DVARS before denoising
meanDVFinal float Mean DVARS after denoising
nVolsRemoved integer Number of non-steady-state volumes removed
motionDVCorrInit float Correlation between motion and DVARS before denoising
motionDVCorrFinal float Correlation between motion and DVARS after denoising
coregDice float Dice coefficient for BOLD-to-T1w coregistration overlap
coregJaccard float Jaccard index for BOLD-to-T1w coregistration overlap
coregCrossCorr float Cross-correlation for BOLD-to-T1w coregistration
coregCoverage float Coverage metric for BOLD-to-T1w coregistration
normDice float Dice coefficient for T1w-to-MNI normalization overlap
normJaccard float Jaccard index for T1w-to-MNI normalization overlap
normCrossCorr float Cross-correlation for T1w-to-MNI normalization
normCoverage float Coverage metric for T1w-to-MNI normalization

Pass/fail criteria: A run passes RBC quality thresholds when both median(FD) <= 0.2 mm and normCrossCorr >= 0.8.

Longitudinal outputs

Produced by the rbc longitudinal subcommand group (template, anatomical, functional, metrics, qc, all). Anatomical outputs aligned to a subject-specific longitudinal template built from multiple sessions. Note: longitudinal metrics, QC, and the combined all stage are not yet implemented (tracker: #301).

File Suffix Description Created by Format
*_space-longitudinal_desc-brain_T1w.nii.gz T1w Skull-stripped brain image aligned to the subject's longitudinal template ANTs registration to longitudinal template 3D NIfTI
*_space-longitudinal_desc-T1w_mask.nii.gz mask Brain mask in longitudinal template space ANTs registration to longitudinal template 3D NIfTI, binary mask
*_space-longitudinal_desc-csf_mask.nii.gz mask CSF mask in longitudinal template space ANTs registration to longitudinal template 3D NIfTI, binary mask
*_space-longitudinal_desc-gm_mask.nii.gz mask Gray matter mask in longitudinal template space ANTs registration to longitudinal template 3D NIfTI, binary mask
*_space-longitudinal_desc-wm_mask.nii.gz mask White matter mask in longitudinal template space ANTs registration to longitudinal template 3D NIfTI, binary mask
*_from-T1w_to-longitudinal_mode-image_xfm.nii.gz xfm Warp field mapping subject anatomy to the longitudinal template ANTs registration 3D NIfTI, displacement field
*_from-longitudinal_to-T1w_mode-image_xfm.nii.gz xfm Inverse warp field mapping longitudinal template back to subject anatomy ANTs registration 3D NIfTI, displacement field