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Index
Contents
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
Links
Methods Description
description description
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>