mri_normalize - converts orig or nu volume into normalized white matter volume


mri_normalize <input directory> <output directory>


Positional Arguments

<input directory>

input directory

<output directory>

output directory

Required Flagged Arguments


Optional Flagged Arguments


disable 1d normalization

-nonmax_suppress (0/1)

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


interpolate and embed volume to be 256^3


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)


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



turns off 1d, sets num_3d_iter = 1


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


Normalize the white matter, optionally based on control points. The input volume is converted into a new volume where white matter image values all range around 110.


Example 1

mri_normalize SUBJECT/mri/nu SUBJECT/mri/wm

Uses the nu volume (nonuniformity corrected volume), and creates the wm volume, with white matter voxels around 110 image value

Example 2

mri_normalize -noskull -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz

Uses the norm volume, and creates the brain volume, making use of the aseg and masking with brainmask.



See Also

nu_correct, mri_fill


FreeSurfer, FsFast


"Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction", Dale, A.M., Fischl, B., Sereno, M.I. (1999) NeuroImage 9(2):179-194

Reporting Bugs

Report bugs to <>



mri_normalize (last edited 2018-01-03 17:31:02 by MorganFogarty)