adni_preprocess.pl

preprocess ADNI images for distortion correction analysis

adni_preprocess.pl [options] <input.mnc> <output.mnc>

DESCRIPTION

adni_preprocess.pl performs preprocessing of ADNI (Alzheimer’s Disease Neuroimaging Initiative) phantom MRI scans to prepare them for geometric distortion correction analysis. The pipeline includes the following steps:

1. Image denoising to reduce noise in the phantom scan.
2. Non-parametric non-uniformity intensity correction (N3) to correct for MRI field inhomogeneity.
3. Centre-of-mass calculation to align the phantom to a standard position.
4. Intensity normalisation.

The resulting preprocessed volume is suitable for input to downstream distortion analysis tools such as phantomfit.pl.

OPTIONS

--verbose

Print progress information during processing.

--clobber

Overwrite existing output files.

EXAMPLES

Preprocess an ADNI phantom scan:

adni_preprocess.pl input_phantom.mnc preprocessed.mnc

Preprocess with verbose output, overwriting any existing result:

adni_preprocess.pl --verbose --clobber raw_phantom.mnc clean_phantom.mnc

AUTHOR

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

COPYRIGHTS

Copyright (C) Vladimir S. Fonov and McGill University. Licensed under the terms of the GNU General Public License version 3 or later.

SEE ALSO

phantomfit.pl(1), lego_core_extract.pl(1), nu_correct(1)