pipeline_em_classify.pl
EM-based brain tissue classification
pipeline_em_classify.pl <t1_sel> <t2_sel> <pd_sel> <source_list> <t1_tal>
DESCRIPTION
pipeline_em_classify.pl performs brain tissue classification using an Expectation-Maximization (EM) algorithm. Unlike the standard classification pipeline which uses classify_clean, this script uses em_classify to iteratively estimate tissue class parameters and assign voxels to white matter, grey matter, and cerebrospinal fluid.
The script takes T1, T2, and PD selection flags, a source list file describing the input volumes, and a T1 volume in Talairach space. The EM approach can be more robust in cases where the standard classifier produces suboptimal results, particularly with non-standard intensity distributions.
OPTIONS
-verbose- Print progress information during processing.
-clobber- Overwrite output files if they already exist.
EXAMPLES
Run EM classification with all three modalities:
pipeline_em_classify.pl 1 1 1 sources.txt t1_tal.mnc
Run EM classification with T1 only:
pipeline_em_classify.pl 1 0 0 sources.txt t1_tal.mnc
AUTHOR
Vladimir S. Fonov - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.