# auto-generated config file
# recon-all version: 7.3.2 (freesurfer-linux-ubuntu20_x86_64-7.3.2-20220804-6354275)

GCA:
    value: RB_all_2020-01-02.gca
    flags: -gca
    descr: Gaussian Classifier Array atlas used for segmentation

GCASkull:
    value: RB_all_withskull_2020_01_02.gca
    flags: -gca-skull
    descr: Gaussian Classifier Array atlas used for skull stripping

DoAntsN3:
    value: False
    flags: -ants-n3
    action: enable
    descr: Use ANTS N3BiasFieldCorrection instead of MNI N3

DoAntsN4:
    value: True
    flags: -no-ants-n4
    action: disable
    descr: Do not use ANTS N4BiasFieldCorrection instead of MNI N3

DoAntsDenoising:
    value: True
    flags: -no-ants-denoise
    action: disable
    descr: Do not use ANTS DenoiseImage before mri_segment

DoRemesh:
    value: True
    flags: -no-remesh
    action: disable
    descr: Do not use Martin's code to remesh ?h.orig to improve triangle quality after topo fix

DoDecimation:
    value: False
    flags: -decimate
    action: enable
    descr: Allow decimation of surface ?h.orig.nofix, good for high res

DecimationFaceArea:
    value: 0.5
    flags: -decimation-area
    descr: Desired area (mm2) of a face after decimation

RipWMSA:
    value: False
    flags: -rip-wmsa
    action: enable
    descr: Allow ripping/freezing of WMSA (77, 78, 79) voxels when placing white surface

RipLesion:
    value: False
    flags: -rip-lesion
    action: enable
    descr: Allow ripping/freezing of Lesion-labeled (25, 57) voxels when placing white surface

CBVfindFirstPeakD1:
    value: False
    flags: -first-peak-d1
    action: enable
    descr: Refinement of target surf location in MRIScomputeBorderValues with first derivative (d1)

DefectsCortex:
    value: True
    flags: -no-defects-cortex
    action: disable
    descr: Limits defects to cortex when running defects2seg, ie, remove from medial wall (visualization only)

UseSamseg:
    value: False
    flags: -samseg
    action: enable
    descr: Run samseg and samseg2recon (t1 and cross only)

UseSynthSeg:
    value: False
    flags: -synthseg
    action: enable
    descr: Run synthseg instead of ca_reg and ca_label (won't create m3z)

TopoFitLevel:
    value: 0
    flags: -topofit
    descr: TopoFit Level

SynthStrip:
    value: False
    flags: -synthstrip
    action: enable
    descr: Run synthstrip instead of mri_watershed
