Configuration Generator

general

(logging level: 0=ERROR, 1=INFO, 2=DEBUG)
(process anatomical data only; skip functional)
(GPU device for skull stripping, segmentation, registration: "auto", -1 for CPU, or index 0..N)

bids_filtering

(comma-separated list; leave empty for all)
(comma-separated list; leave empty for all)
(comma-separated list; leave empty for all)
(comma-separated list; leave empty for all)

template

(output space: T1w or TEMPLATE_NAME[:DESCRIPTION])

anat

(T1w/T2w synthesis when multiple images exist: "subject" = cross-session, "session" = within-session)
(HIGHLY RECOMMENDED: conform input to template space via FLIRT rigid registration)
(HIGHLY RECOMMENDED: brain extraction and segmentation)
advanced settings

fastSurferCNN

(inference batch size, ≥1)
(coronal plane weight, 0–1)
(axial plane weight, 0–1)
(sagittal plane weight, 0–1)
(fix thin V1 white matter by registering template V1 WM to subject space)
(apply N4 bias field correction)
advanced settings
(algorithm; currently only N4BiasFieldCorrection)
(shrink factor for speed, >0)
(N4 B-spline mesh resolution, integer)
(rescale mean intensity to 100)
(run surface reconstruction)
advanced settings
(use T1w and T2w combined (enhanced T1w) image if available)

func

(coregister all runs within each session before other steps)
(HIGHLY RECOMMENDED: conform functional image to target space via FLIRT rigid registration)
(apply slice timing correction)
advanced settings
(repetition time in seconds; leave empty to use metadata)
(slice acquisition times in seconds; leave empty to use metadata)
(reference time in seconds; leave empty to compute from metadata)
(reference slice position, 0–1; 0.5 = middle slice)
(slice encoding axis; leave empty to use metadata)
(apply motion correction / realignment)
advanced settings
(degrees of freedom: 6, 9, or 12)
(registration cost function)
(smoothing factor)
(reference volume: index, "Tmean", or "mid")
(cost convergence tolerance)
(parameter convergence tolerance)
(remove temporal outliers / despiking)
advanced settings
(first cutoff, >0, must be < c2)
(second cutoff, >0, must be > c1)
(use local editing)
(number of initial volumes to exclude, ≥0)
(fMRIPrep-style nuisance regressors; regressors only, the BOLD image is never modified. Motion-derived columns require motion_correction)
advanced settings
(framewise displacement above this flags a motion outlier; macaque-scaled)
(standardized DVARS above this flags a motion outlier)
(bias correction on mean functional image, for registration only)
advanced settings
(algorithm; currently only N4BiasFieldCorrection)
(shrink factor for speed, >0)
(N4 B-spline mesh resolution, integer)
(rescale mean intensity to 100)
(HIGHLY RECOMMENDED: brain extraction on functional data)

registration

(transform for anatomical to template)
(transform for functional to anatomical)
(transform for functional to template)
(resampling interpolation method)
(attempt FireANTs for syn registration; fallback to ANTs if unavailable)
(preserve native functional resolution when resampling)