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

Links

FreeSurfer, FsFast

Methods Description

description
description

References

References/Lastname###

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 3 as of 2008-04-29 11:45:28 → ⇥
  Size: 2370
  Editor: localhost
  Comment: converted to 1.6 markup
-Deletions are marked like this.
+Additions are marked like this.
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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
-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||
|| -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||
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+Line 46:
-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
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+Line 59:
-["nu_correct"], ["mri_fill"]
+[[nu_correct]], [[mri_fill]]
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+Line 71:
-["References/Lastname###"]
+[[References/Lastname###]]