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

Links

FreeSurfer, FsFast

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

-  ⇤ ← Revision 1 as of 2004-10-07 10:49:11 → 
  Size: 2404
  Editor: DavidSalat
  Comment: Added mri_normalize
+   ← Revision 9 as of 2018-01-03 17:31:02 → ⇥
  Size: 3737
  Editor: MorganFogarty
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 10:
-[[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
-Line 27:
+Line 28:
-        -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 ||
-Line 44:
+Line 62:
-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.
-Line 48:
+Line 66:
+{{{
-Line 49:
+Line 68:
+}}}
-Line 52:
+Line 72:
+== 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.
-Line 57:
+Line 83:
-["nu_correct"], ["mri_fill"]
+[[nu_correct]], [[mri_fill]]
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+Line 88:
-= Methods Description =
{{{
description
description
}}}
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+Line 89:
-["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