| Deletions are marked like this. | Additions are marked like this. |
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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|| || -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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| 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 |
Index TableOfContents
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
Methods Description
description description
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>