data_dictionary.md

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.

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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
*_space-MNI152NLin6Asym_desc-brain_T1w.nii.gz	T1w	Skull-stripped brain image warped to MNI152NLin6Asym template space	ANTs resampling	3D NIfTI

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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 (FSL format)	ANTs boundary-based registration	4x4 affine matrix
*_from-bold_to-T1w_mode-image_desc-linearITK_xfm.txt	xfm	Same BOLD-to-T1w affine in ITK format, used by ANTs for composing longitudinal transforms	Converted from FSL via rbc.core.fsl2itk	ITK affine text
*_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-regressed_bold.nii.gz	bold	Nuisance-regressed BOLD in template space (no bandpass filtering). {regressor} is 36parameter or aCompCor	AFNI 3dTproject	4D NIfTI
*_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	AFNI 3dTproject -bandpass	4D NIfTI
*_desc-{regressor}_regressors.1D	regressors	Raw (unfiltered) nuisance regressor matrix. {regressor} is 36parameter or aCompCor. Carried forward for longitudinal regression reuse	Computed from motion parameters and tissue masks	Text, multi-column 1D file
*_desc-{regressor}Filtered_regressors.1D	regressors	Bandpass-filtered nuisance regressor matrix matching what 3dTproject -bandpass applied. For provenance only	FFT-based bandpass filter	Text, multi-column 1D file

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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).

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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.

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Longitudinal outputs

Produced by the rbc longitudinal subcommand group (template, anatomical, functional, metrics, qc, all). These workflows consume cross-sectional derivatives and align them to a subject-specific longitudinal template built from multiple sessions. rbc long is a shorthand alias.

Template

Produced by rbc longitudinal template. One template per subject, one transform per session.

File	Suffix	Description	Created by	Format
*_ses-longitudinal_T1w.nii.gz	T1w	Unbiased within-subject T1w template built from all sessions	FreeSurfer mri_robust_template	3D NIfTI
*_ses-longitudinal_from-{ses}_to-longitudinal_mode-image_xfm.txt	xfm	Affine transform mapping a single session's T1w to the longitudinal template. One file per session, identified by the from- entity	FreeSurfer LTA, converted to ITK via rbc.core.fsl2itk	ITK affine text

Anatomical

Produced by rbc longitudinal anatomical.

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
*_from-longitudinal_to-MNI152NLin6Asym_mode-image_xfm.nii.gz	xfm	Warp field mapping longitudinal template space to MNI152NLin6Asym	ANTs registration	3D NIfTI, displacement field
*_from-MNI152NLin6Asym_to-longitudinal_mode-image_xfm.nii.gz	xfm	Inverse warp field mapping MNI152NLin6Asym back to longitudinal template space	ANTs registration	3D NIfTI, displacement field

Functional

Produced by rbc longitudinal functional.

File	Suffix	Description	Created by	Format
*_space-longitudinal_sbref.nii.gz	sbref	Motion reference volume warped to longitudinal template space	ANTs warping (composed BOLD-to-longitudinal)	3D NIfTI
*_space-longitudinal_desc-preproc_bold.nii.gz	bold	Preprocessed BOLD warped to longitudinal template space	ANTs warping (composed BOLD-to-longitudinal)	4D NIfTI
*_space-longitudinal_desc-brain_mask.nii.gz	mask	BOLD brain mask in longitudinal template space	ANTs warping (nearest-neighbor)	3D NIfTI, binary mask
*_from-bold_to-longitudinal_mode-image_xfm.nii.gz	xfm	Composite BOLD-to-longitudinal-template warp field	ANTs compose transforms	3D NIfTI, displacement field
*_space-longitudinal_reg-{regressor}_desc-regressed_bold.nii.gz	bold	Nuisance-regressed BOLD (no bandpass) in longitudinal space, per regressor strategy	AFNI 3dTproject	4D NIfTI
*_space-longitudinal_reg-{regressor}_desc-preproc_bold.nii.gz	bold	Nuisance-regressed + bandpass-filtered BOLD in longitudinal space, per regressor strategy	AFNI 3dTproject -bandpass	4D NIfTI

Metrics

Produced by rbc longitudinal metrics. Identical to the cross-sectional metrics structure, but computed in space-longitudinal from the longitudinal-space denoised BOLD.

File	Suffix	Description	Created by	Format
*_space-longitudinal_reg-{regressor}_alff.nii.gz	alff	Amplitude of Low-Frequency Fluctuations (0.01-0.1 Hz)	Frequency-domain analysis	3D NIfTI
*_space-longitudinal_reg-{regressor}_desc-smooth_alff.nii.gz	alff	Spatially smoothed ALFF map	Gaussian kernel smoothing	3D NIfTI
*_space-longitudinal_reg-{regressor}_desc-smoothZstd_alff.nii.gz	alff	Z-scored smoothed ALFF, normalized within the brain mask	Z-score normalization	3D NIfTI
*_space-longitudinal_reg-{regressor}_falff.nii.gz	falff	Fractional ALFF (ratio of low-frequency to total power)	Frequency-domain analysis	3D NIfTI
*_space-longitudinal_reg-{regressor}_desc-smooth_falff.nii.gz	falff	Spatially smoothed fALFF map	Gaussian kernel smoothing	3D NIfTI
*_space-longitudinal_reg-{regressor}_desc-smoothZstd_falff.nii.gz	falff	Z-scored smoothed fALFF	Z-score normalization	3D NIfTI
*_space-longitudinal_reg-{regressor}_reho.nii.gz	reho	Regional Homogeneity (Kendall's W, 26-voxel neighborhood)	AFNI 3dReHo	3D NIfTI
*_space-longitudinal_reg-{regressor}_desc-smooth_reho.nii.gz	reho	Spatially smoothed ReHo map	Gaussian kernel smoothing	3D NIfTI
*_space-longitudinal_reg-{regressor}_desc-smoothZstd_reho.nii.gz	reho	Z-scored smoothed ReHo	Z-score normalization	3D NIfTI
*_space-longitudinal_atlas-{atlas}_reg-{regressor}_desc-mean_timeseries.tsv	timeseries	Mean BOLD signal per atlas region	Region-wise averaging	TSV, regions x timepoints
*_space-longitudinal_atlas-{atlas}_reg-{regressor}_desc-pearson_correlations.tsv	correlations	Pairwise Pearson correlation matrix between atlas regions	Pearson correlation	TSV, regions x regions

QC

Produced by rbc longitudinal qc. Evaluates registration quality by measuring overlap between the anatomical brain mask and the BOLD brain mask in longitudinal template space.

File	Suffix	Description	Created by	Format
*_space-longitudinal_desc-registration_quality.tsv	quality	Single-row TSV with mask overlap metrics (see columns below)	Registration QC	TSV, 1 row

Longitudinal QC columns

Column	Type	Description
sub	string	Subject identifier
ses	string	Session label
task	string	Task label
run	integer	Run number
dice	float	Dice coefficient between anat and BOLD masks in longitudinal space
jaccard	float	Jaccard index between anat and BOLD masks in longitudinal space
coverage	float	Coverage of the smaller mask by the overlap region
cross_corr	float	Pearson correlation between flattened binary masks
passed	boolean	Whether the run passes the Dice threshold (>= 0.85)