inormalize
intensity normalize a MINC volume following a registered model volume
inormalize [options] <infile> [<outfile>]
DESCRIPTION
inormalize normalizes the intensity of a MINC volume, optionally relative to a model volume. It supports several normalization methods including ratio of means, ratio of medians, mean of ratios, mean of log-ratios, and median of ratios. The normalization can be performed along specific axes (z/y/x-normalize) to correct for slice-to-slice intensity variation. A mask can be used to restrict the normalization to a specific region.
OPTIONS
-clobber- Overwrite an existing output file.
-noclobber- Do not overwrite an existing output file (default).
-verbose- Print progress information.
-quiet- Do not print progress information.
-print- Print the normalization parameters without writing an output file.
-compress- Compress the output file.
-nocompress- Do not compress the output file.
-nocache- Do not use volume caching.
-const <val>- Normalize to a constant value.
-const2 <val1> <val2>- Normalize using two constant values.
-range <pct>- Set the percentage of voxels to use for range estimation.
-model <model.mnc>- Specify a model volume for relative normalization.
-znormalize- Normalize along the z-axis (transverse slices).
-ynormalize- Normalize along the y-axis (coronal slices).
-xnormalize- Normalize along the x-axis (sagittal slices).
-minvoxels <n>- Set the minimum number of voxels required per slice (default: 1000).
-constrained- Use constrained normalization.
-rms- Use root mean square normalization method.
-vr- Use variance ratio normalization method.
-ratioOfMeans- Use ratio of means normalization method.
-ratioOfMedians- Use ratio of medians normalization method.
-meanOfRatios- Use mean of ratios normalization method.
-meanOfLogRatios- Use mean of log-ratios normalization method.
-medianOfRatios- Use median of ratios normalization method (default).
-mask- Specify a mask volume for restricting normalization.
-useVoxelCoord- Use voxel coordinates for mask evaluation (default).
-useWorldCoord- Use world coordinates for mask evaluation.
-threshold <min> <max>- Set intensity thresholds for voxel selection.
-nonormalize- Do not apply normalization; report parameters only.
EXAMPLES
inormalize input.mnc output_normalized.mnc
inormalize -model model.mnc -znormalize input.mnc normalized.mnc
inormalize -ratioOfMeans -mask brain_mask.mnc -model model.mnc input.mnc normalized.mnc
AUTHOR
Andrew Janke - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © 2000 by Andrew Janke