_description: Default configuration for brainana preprocessing pipeline
general:
  verbose: 2
  anat_only: false
  gpu_device: auto
bids_filtering:
  subjects: null
  sessions: null
  tasks: null
  runs: null
template:
  output_space: NMT2Sym:res-05
anat:
  synthesis_level: subject
  conform:
    enabled: true
  skullstripping_segmentation:
    enabled: true
    method: fastSurferCNN
    fastSurferCNN:
      gpu_device: auto
      batch_size: 8
      plane_weight_coronal: 0.4
      plane_weight_axial: 0.4
      plane_weight_sagittal: 0.2
      fix_V1_WM: true
  bias_correction:
    enabled: true
    algorithm: N4BiasFieldCorrection
    shrink_factor: 2
    bspline_fitting: '[ 150 ]'
    rescale_mean_to_100: true
  surface_reconstruction:
    enabled: true
    use_t1wt2wcombined: false
func:
  coreg_runs_within_session: true
  conform:
    enabled: true
  slice_timing_correction:
    enabled: true
    repetition_time: null
    slice_timing: null
    tzero: null
    slice_time_ref: 0.5
    slice_encoding_direction: null
  motion_correction:
    enabled: true
    dof: 6
    cost: mutualinfo
    smooth: 1.0
    ref_vol: mid
    cost_tolerance: 0.01
    parameter_tolerance: 0.01
  despike:
    enabled: false
    c1: 5
    c2: 10
    localedit: true
    ignore_first_volumes: 0
  bias_correction:
    enabled: true
    algorithm: N4BiasFieldCorrection
    shrink_factor: 2
    bspline_fitting: '[ 100 ]'
    rescale_mean_to_100: true
  skullstripping:
    enabled: true
registration:
  anat2template_xfm_type: syn
  func2anat_xfm_type: syn
  func2template_xfm_type: syn
  interpolation: BSpline
  enable_fireants: true
  keep_func_resolution: true
