pipeline_relx_cls.pl
T2 relaxometry-based tissue classification
pipeline_relx_cls.pl <t1> <t2> <pd> <t2_relx> <output_cls> [options]
DESCRIPTION
pipeline_relx_cls.pl performs tissue classification that incorporates T2 relaxometry information in addition to the standard T1, T2, and PD contrast volumes. By using the T2 relaxation map as an additional feature, the classifier can better distinguish between tissue types that may have similar intensities on conventional contrasts but different relaxation properties.
The script takes T1-weighted, T2-weighted, and proton-density volumes along with a pre-computed T2 relaxation map, and produces a discrete tissue classification. Atlas priors for GM, WM, and CSF can be specified, and the age parameter allows age-appropriate classification thresholds.
OPTIONS
--verbose- Print progress information during processing.
--clobber- Overwrite the output file if it already exists.
--mask <file>- Brain mask to restrict classification to the brain region.
--atlas <file>- Atlas prior probability map for tissue classification.
--atlas_gm <file>- Atlas prior probability map specifically for grey matter.
--atlas_wm <file>- Atlas prior probability map specifically for white matter.
--atlas_csf <file>- Atlas prior probability map specifically for cerebrospinal fluid.
--xfm <file>- Linear transformation mapping the input volumes to the atlas space.
--age <n>- Subject age in years, used to adjust classification parameters for age-appropriate tissue boundaries. Default is 20.
--blur <n>- Blurring kernel size in millimetres applied to the atlas priors. Default is 4.
EXAMPLES
Classify using T2 relaxometry with default settings:
pipeline_relx_cls.pl t1_tal.mnc t2_tal.mnc pd_tal.mnc \
t2_relx.mnc relx_cls.mnc
Classify with custom atlas priors and age:
pipeline_relx_cls.pl t1_tal.mnc t2_tal.mnc pd_tal.mnc \
t2_relx.mnc relx_cls.mnc \
--atlas_gm gm_prior.mnc --atlas_wm wm_prior.mnc \
--atlas_csf csf_prior.mnc --age 65
Classify with a brain mask and transform:
pipeline_relx_cls.pl t1_tal.mnc t2_tal.mnc pd_tal.mnc \
t2_relx.mnc relx_cls.mnc --mask brain_mask.mnc --xfm tal.xfm
AUTHOR
Vladimir S. Fonov - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.
COPYRIGHTS
Copyright © McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.