Index TableOfContents
Name
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.
Synopsis
mri_normalize [input directory] [output directory]
Arguments
Positional Arguments
argA |
brief description |
detailed description (eg, help file information) |
argB |
brief description |
detailed description (eg, help file information) |
Required Flagged Arguments
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
description
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>