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[[TableOfContents]] <<TableOfContents>>
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mri_normalize - Procedure that takes the orig or nu volume from the cortical reconstruction as input and creates a new volume where white matter image values all range around 110. mri_normalize - converts orig or nu volume into normalized white matter volume
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mri_normalize [input directory] [output directory] mri_normalize <input directory> <output directory>
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|| argA || brief description || detailed description (eg, help file information) ||
|| argB || brief description || detailed description (eg, help file information) ||		 || <input directory> || input directory ||
|| <output directory> || output directory ||
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none
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        -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		 || -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 ||
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description 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.
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{{{
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}}}
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== 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.
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["nu_correct"], ["mri_fill"] [[nu_correct]], [[mri_fill]]
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["References/Lastname###"] "Cortical Surface-Based Analysis I: Segmentation and Surface Reconstruction", Dale, A.M., Fischl, B., Sereno, M.I. (1999) NeuroImage 9(2):179-194

Index

Contents

  1. Name
  2. Synopsis
  3. Arguments
    1. Positional Arguments
    2. Required Flagged Arguments
    3. Optional Flagged Arguments
  4. Outputs
  5. Description
  6. Examples
    1. Example 1
    2. Example 2
  7. Bugs
  8. See Also
  9. Links
  10. Methods Description
  11. References
  12. Reporting Bugs
  13. Author/s

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

-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

Outputs

wm

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

Description

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.

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

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.

Bugs

None

See Also

nu_correct, mri_fill

Links

FreeSurfer, FsFast

Methods Description

description
description

References

"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 <analysis-bugs@nmr.mgh.harvard.edu>

Author/s

BruceFischl

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