# default recon-all config parameters

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: -ants-n4
    action: enable
    descr: Use ANTS N4BiasFieldCorrection 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: -ants-denoise
    action: enable
    descr: Use ANTS DenoiseImage before mri_segment

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

DoRemesh:
    value: True
    flags: -remesh
    action: enable
    descr: Use Martin's code to remesh ?h.orig to improve triangle quality after topo fix
    
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)