volume_pol

Polynomial intensity normalization between volumes.

volume_pol [options] <input> <template> [output_file]

DESCRIPTION

volume_pol performs polynomial intensity normalization of an input MINC volume to match the intensity distribution of a template volume. The tool fits a polynomial mapping function between the joint intensity histograms of the input and template, producing a normalized output volume or printing the polynomial coefficients.

OPTIONS

--verbose

Print progress information during processing.

--quiet

Suppress all non-essential output.

--clobber

Overwrite existing output files.

--source_mask mask

Apply a mask to the input (source) volume for histogram computation.

--target_mask mask

Apply a mask to the template (target) volume for histogram computation.

--order n

Set the polynomial order for the intensity mapping.

--hist histogram.dat

Write the histogram data to the specified file.

--joint joint_histogram

Write the joint histogram to the specified file.

--expfile file

Write the polynomial expression to the specified file.

--min min

Set the minimum intensity value for histogram computation.

--max max

Set the maximum intensity value for histogram computation.

--noclamp

Do not clamp output values to the input range.

--kl

Report the Kullback-Leibler divergence between the normalized and target histograms.

--ks

Report the Kolmogorov-Smirnov statistic between the normalized and target histograms.

EXAMPLES

Normalize input to match template intensity:

volume_pol input.mnc template.mnc normalized.mnc

Normalize with masks and polynomial order 4:

volume_pol --source_mask src_mask.mnc --target_mask tgt_mask.mnc \
    --order 4 input.mnc template.mnc normalized.mnc

Save the joint histogram:

volume_pol --joint joint_hist.dat input.mnc template.mnc normalized.mnc

AUTHOR

Vladimir S. Fonov - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright © 2011 by Vladimir S. Fonov

SEE ALSO

minc_nuyl, inormalize