# auto-generated config file
# recon-all version: 8.2.0 (freesurfer-linux-ubuntu22_x86_64-8.2.0-20260314-d932c45)

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

SkipNuIntensityCor:
    value: False
    flags: -skip-nu-intensity-cor
    action: enable
    descr: Turns off -nuintensitycor and forces nu.mgz to be a link to orig.mgz

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

CblumFromSynthSeg:
    value: False
    flags: -cblum-from-synthseg
    action: enable
    descr: Run mri_synthseg and insert the cerebellum wm and gm into the aseg

SynthSegForSurf:
    value: False
    flags: -synthseg-for-surf
    action: enable
    descr: Use synthseg instead of aseg.presurf.mgz for surface operations

DoSynthSR:
    value: False
    flags: -synthsr
    action: enable
    descr: Run mri_synthsr on input (rawavg) to convert to T1w contrast

UseSynthMorph:
    value: True
    flags: -synthmorph
    action: enable
    descr: Run fs-synthmorph-reg instead of mri_ca_register

TopoFitLevel:
    value: 0
    flags: -topofit
    descr: TopoFit Level (1 or 2)

JosaReg:
    value: 0
    flags: -josareg
    action: enable
    descr: Use JOSA surface-based registration

UseGPU:
    value: 0
    flags: -gpu
    action: enable
    descr: Use GPU for those GPU-enabled programs

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

LongTransferBaseBFS:
    value: True
    flags: -transfer-base-bfs
    action: enable
    descr: Transfer brain.finalsurfs (BFS) edits to long from the base rather than from the cross

UseStopMaskSCM:
    value: False
    flags: -stopmask-scm
    action: enable
    descr: Use stop mask when creating white.preaparc and white surfaces

FixEntoWM:
    value: True
    flags: -fix-ento-wm
    action: enable
    descr: Fix the WM in the area around entorhinal cortex and gyrus ambiens

NoFixEntoWM:
    value: False
    flags: -no-fix-ento-wm
    action: enable
    descr: Do not fix the WM in the area around entorhinal cortex and gyrus ambiens

FixGA:
    value: True
    flags: -fix-ga
    action: enable
    descr: Fix the cortex label around gyrus ambiens

NoFixGA:
    value: False
    flags: -no-fix-ga
    action: enable
    descr: Turn off fix to the cortex label around gyrus ambiens

FixACJ:
    value: True
    flags: -fix-acj
    action: enable
    descr: Fix the WM in the area between amygdala and cortex

NoFixACJ:
    value: False
    flags: -no-fix-acj
    action: enable
    descr: Turn off the fix the WM in the area between amygdala and cortex (if it is on)

FixMCADura:
    value: True
    flags: -fix-mca-dura
    action: enable
    descr: Segment the MCA/dura area between front and temp and remove from brain mask

NoFixMCADura:
    value: False
    flags: -no-fix-mca-dura
    action: enable
    descr: Do not segment the MCA/dura area between front and temp and remove from brain mask

FixVSinus:
    value: True
    flags: -fix-vsinus
    action: enable
    descr: Segment the venous sinuses and remove from brain mask

NoFixVSinus:
    value: False
    flags: -no-fix-vsinus
    action: enable
    descr: Do not segment the venous sinuses and remove from brain mask

SkipDone:
    value: False
    flags: -skip-done
    action: enable
    descr: When recon-all.done exists and recon-all.error does not exist, do not process

UseGifti:
    value: False
    flags: -gii
    action: enable
    descr: Use GIFTI (.gii) output. Experimental.
