icc_mask.pl

create an intra-cranial cavity mask for brain volume estimation

icc_mask.pl <input.mnc> <output_mask.mnc> --model <model> --icc-model <icc_mask>

DESCRIPTION

icc_mask.pl generates an intracranial cavity (ICC) mask for a given input MINC volume. The ICC mask encompasses the entire volume within the skull, including the brain, ventricles, and CSF spaces. This is useful for estimating total intracranial volume (ICV), which serves as an important normalisation factor in volumetric brain studies.

The tool works by performing nonlinear registration between the input volume and a reference model, then propagating a pre-defined ICC mask from the model space back to the native space of the input. The --model option specifies the reference anatomical model and the --icc-model option specifies the corresponding ICC mask in model space.

OPTIONS

--verbose: Print progress information during processing.
--clobber: Overwrite existing output files.
--model <model.mnc>: Path to the reference anatomical model volume.
--icc-model <icc_mask.mnc>: Path to the ICC mask in the reference model space.

EXAMPLES

Generate an ICC mask using a standard model:

icc_mask.pl subject_t1.mnc subject_icc.mnc \
    --model /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c.mnc \
    --icc-model /opt/minc/share/icbm152_model_09c/mni_icbm152_t1_tal_nlin_sym_09c_mask.mnc

Generate an ICC mask with verbose output:

icc_mask.pl --verbose --clobber subject.mnc icc_mask.mnc \
    --model model.mnc --icc-model model_icc.mnc

AUTHOR

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

COPYRIGHTS