## Note: This page was created with the CommandTemplate
##
## If you're modifying this page please take a look at the
## latest version of CommandTemplate to ensure that you're
## using the latest version of the CommandTemplate
##
## See HelpOnCommandTemplate for description of formatting

'''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||
|| -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

= See Also =
[[nu_correct]], [[mri_fill]]

= 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