pipeline_classify.pl
brain tissue classification using classify_clean
pipeline_classify.pl <t1> [t2] [pd] <output> --model_dir <dir> --model_name <name> [options]
DESCRIPTION
pipeline_classify.pl performs brain tissue classification on MRI volumes using the classify_clean tool. It classifies voxels into white matter (WM), grey matter (GM), and cerebrospinal fluid (CSF) tissue classes based on T1-weighted input, with optional T2-weighted and proton-density (PD) volumes for improved accuracy.
The script requires a model directory and model name that specify the atlas priors used during classification. An optional brain mask can restrict classification to the brain region, and an optional linear transform can place the input into stereotaxic space prior to classification. Markov Random Field (MRF) regularization can be enabled for spatially smoother results.
OPTIONS
--verbose- Print progress information during processing.
--clobber- Overwrite the output file if it already exists.
--mask <file>- Brain mask in stereotaxic space to restrict classification to brain tissue.
--xfm <xfm>- Linear transformation file mapping the input volume to stereotaxic space.
--mrf- Enable Markov Random Field regularization for spatially smoother classification results.
--model_dir <dir>- Path to the directory containing the atlas model files used for classification priors.
--model_name <name>- Base name of the atlas model files within the model directory.
EXAMPLES
Classify brain tissue using T1 only:
pipeline_classify.pl t1_tal.mnc classified.mnc \
--model_dir /opt/minc/share/icbm152_model_09c \
--model_name icbm_avg_152
Classify with T1, T2, and PD inputs and a brain mask:
pipeline_classify.pl t1_tal.mnc t2_tal.mnc pd_tal.mnc classified.mnc \
--model_dir /opt/minc/share/icbm152_model_09c \
--model_name icbm_avg_152 --mask brain_mask.mnc
Classify with MRF regularization:
pipeline_classify.pl t1_tal.mnc classified.mnc \
--model_dir /opt/minc/share/icbm152_model_09c \
--model_name icbm_avg_152 --mrf --clobber
AUTHOR
Vladimir S. Fonov - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.