<input directory>

input directory

<output directory>

output directory

-no1d

disable 1d normalization

-nonmax_suppress (0/1)

turn non-maximum suppression on (1) or off (0) when using interior of surfaces

-conform

interpolate and embed volume to be 256^3

-gentle

perform kinder gentler normalization

-f <path to file>

use control points file (usually control.dat)

-fonly <fname>

use only control points file

-lonly <fname>

use only control points in label file

-label <fname>

use control points in label file

-w <mri_vol c> <mri_vol b>

write ctrl point(c) and bias field(b) volumes

-a <float a>

use control point with intensity a above target (default=25.0)

-b <float b>

use control point with intensity b below target (default=10.0)

-g <float g>

use max intensity/mm gradient g (default=1.000)

-n <int n>

use n 3d normalization iterations (default=2)

-u

print usage

-prune <boolean>

turn pruning of control points on/off (default=off). Useful if white is expanding into gm

-MASK maskfile

-atlas <path to gca> <path to gca transform> <min distance of control points from non-brain>

use atlas to exclude control points from being in non-brain regions

-noskull

-monkey

turns off 1d, sets num_3d_iter = 1

-nosnr

disable snr normalization

-sigma sigma

smooth bias field

-aseg aseg

-renorm volume

load volume and use all points in it that are exactly 110 as control points

-checknorm volume min max

load volume and remove all control points that aren't in [min max] in volume

-r controlpoints biasfield

for reading

-surface <surface> <xform>

normalize based on the skelaton oft he interior or the transformed surface

-v Gvx Gvy Gvz

for debugging

-d Gx Gy Gz

for debugging

wm

wm volume of the cortical reconstruction is used as the input for mri_fill