//     Automatic Segmentation Parameter File

// Atlases
Common Coordinate Image: /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/templateSkull.nrrd
Common Coordinate Image Type: T1
Tissue Segmentation Atlas Directory: /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/ABC_skull/
Tissue Segmentation Atlas Type: T1

// Loop
Loop: 1
Atlas Loop: /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/ABC_stripped/
Loop - Number of iterations: 1
ROI Atlas File: /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template.nrrd

ROI Second Atlas File: 

// Subcortical Structures
Subcortical Structure Segmentation: 0
Amygdala Left: 
Amygdala Right: 
Caudate Left: 
Caudate Right: 
Hippocampus Left: 
Hippocampus Right: 
Pallidus Left: 
Pallidus Right: 
Putamen Left: 
Putamen Right: 
Lateral Ventricle Left: 
Lateral Ventricle Right: 

// Generic ROI Maps
Generic ROI Segmentation: 1
ROI File 1: /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/SubCortical.gipl.gz
ROI File 2: 
ROI File 3: 
ROI File 4: 
ROI File 5: 

// Parcellation Maps
Parcellation Map Segmentation: 1
Tissue Map: Hard
Parcellation File 1: /scratch/kykwan_fluxm/leshi/MRI/MonkeyAtlas_used_forT1/rhesusMonkeyT1_RAI/template_parc.gipl.gz
Parcellation File 2: 
Parcellation File 3: 

// Tissue Segmentation
EM Software: ABC
Filter Iterations: 10
Filter TimeStep: 0.01
Filter Method: Curvature flow
Max Bias Degree: 4
Initial Distribution Estimator: robust
Prior 1: 1.3
Prior 2: 1
Prior 3: 0.7
Prior 4: 1
Prior 5: 1
Prior 6: 1
Prior 7: 1
Prior 8: 1
Prior 9: 1
Fluid Atlas Warp: 1
Fluid Atlas Affine: 0
Fluid Atlas FATW: 0
ANTS Warp for ABC: 0
Fluid Atlas Warp Iterations: 50
Fluid Atlas Warp Max Step: 0.1
ANTS with brainmask: 1
Use Initital Affine Transform: 1
Atlas Linear Mapping: affine
Image Linear Mapping: id

// Grid Template
Rigid Registration: 1
Is ROIAtlasGridTemplate: 1
GridTemplate SizeX: 0
GridTemplate SizeY: 0
GridTemplate SizeZ: 0
GridTemplate SpacingX: 0
GridTemplate SpacingY: 0
GridTemplate SpacingZ: 0
Registration Initialization: useCenterOfHeadAlign
Use T1 initial transform: 0

// Atlas Warping
Warping Method: BRAINSDemonWarp
// - Fluid Warping parameters
Alpha: 0.01
Beta: 0.01
Gamma: 0.001
Max Perturbation: 0.5
NumBasis: 0.01
Scale 4 - Number Of Iterations: 50
Scale 2 - Number Of Iterations: 25
Scale 1 - Number Of Iterations: 100
// - BRAINSDemonWarp parameters
Registration Filter Type: LogDemons
Deformation Field Smoothing Sigma: 2
Pyramid Levels: 5
Moving Shrink Factors: 16,16,16
Fixed Shrink Factors: 16,16,16
Iteration Count Pyramid Levels: 300,50,30,20,15
// - ANTS parameters
ANTS Iterations: 
ANTS CC weight: 0
ANTS CC region radius: 0
ANTS MI weight: 0
ANTS MI bins: 0
ANTS MSQ weight: 0
ANTS CC weight for 2nd modality: 1
ANTS CC region radius for 2nd modality: 2
ANTS MI weight for 2nd modality: 0
ANTS MI bins for 2nd modality: 32
ANTS MSQ weight for 2nd modality: 0
ANTS Registration Type: GreedyDiffeomorphism
ANTS Registration Step: 
ANTS Gaussian Smoothing: 0
ANTS Gaussian Sigma: 0
ANTS Number of Threads: 1

// Skull Stripping
Delete Vessels: 0

// Intensity Rescaling
Intensity Rescaling: Histogram quantile

// Regional histogram
Quantiles: 1,5,33,50,66,95,99
Point Spacing: 10

// N4 ITK Bias Field Correction
N4 ITK Bias Field Correction: 1
N4 Number of iterations: 50,40,30
N4 Spline distance: 0
N4 Shrink factor: 4
N4 Convergence threshold: 0.0001
N4 BSpline grid resolutions: 1,1,1
N4 BSpline alpha: 0
N4 BSpline beta: 0.5
N4 Histogram sharpening: 0
N4 BSpline order: 3

Bias Correction stripped image: 0
The Version of Slicer Used: 4.3

// Reorientation
Reorientation: 0
Input Orientation: 
Output Orientation: 

// Multi-Atlas Segmentation
Label Fusion Algorithm: Weighted Majority Voting
Intensity Energy Weight: 0.5
Harmonic Energy Weight: 0.5
Shape Energy Weight: 0.5
Multi-atlas directory: