NAME

mri_nu_correct.mni

SYNOPSIS

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DESCRIPTION

Wrapper for nu_correct, a program from the Montreal Neurological Insitute (MNI) used for correcting intensity non-uniformity (ie, bias fields). You must have the MNI software installed on your system to run this. See www.bic.mni.mcgill.ca/software/N3 for more info.

POSITIONAL ARGUMENTS

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REQUIRED-FLAGGED ARGUMENTS

ArgumentExplanation
--i involinput volume. Input can be any format accepted by mri_convert.
--o outvoloutput volume. Output can be any format accepted by mri_convert. If the output format is COR, then the directory must exist.
--n nitersNumber of iterations to run nu_correct. Default is 4. This is the number of times that nu_correct is repeated (ie, using the output from the previous run as the input for the next). This is different than the -iterations option to nu_correct.
--proto-iters NpPasses Np as argument of the -iterations flag of nu_correct. This is different than the --n flag above. Default is not to pass nu_correct the -iterations flag.
--stop threshPasses thresh as argument of the -stop flag of nu_correct. According to the nu_correct documentation, this threshold is the \"CV of change in field estimate below which iteration stops (suggest 0.01 to 0.0001)\". Default is not to pass nu_correct the -stop flag.
--uchar tal.xfmUse mri_make_uchar instead of conforming
--no-ucharDo not use mri_make_uchar (default)
--cmFor use with data that is higher than 1mm resolution.

OPTIONAL-FLAGGED ARGUMENTS

ArgumentExplanation
--helpprint help and exit
--debugturn on debugging
--versionprint version and exit

REPORTING

Report bugs to <freesurfer@nmr.mgh.harvard.edu>