Index

Name

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

Synopsis

mri_normalize <input directory> <output directory>

Arguments

Positional Arguments

<input directory>

input directory

<output directory>

output directory

Required Flagged Arguments

none

Optional Flagged Arguments

-no1d

disable 1d normalization

-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)

-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)

-v

verbose

-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

Outputs

wm

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

Description

mri_normalize converts orig or nu volume from cortical reconstruction as input into a new volume where white matter image values all range around 110

Examples

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

Bugs

None

See Also

nu_correct, mri_fill

Links

FreeSurfer, FsFast

Methods Description

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References

References/Lastname###

Reporting Bugs

Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

BruceFischl