ventricles_segmentation_pipeline.pl

ventricle segmentation pipeline using patch-based methods

ventricles_segmentation_pipeline.pl <input_t1.mnc> <output_prefix> --model-dir <dir> [options]

DESCRIPTION

ventricles_segmentation_pipeline.pl runs a patch-based segmentation pipeline specifically designed for segmenting the lateral ventricles from T1-weighted MRI volumes. The pipeline registers the input volume to an atlas library and uses non-local patch-based label fusion to produce a binary ventricle mask.

The model directory containing the atlas library must be specified. Preprocessing steps such as non-uniformity correction (N3) and NUYL intensity normalization can be enabled. A nonlinear brain mask constraint and manual initial transformations can be supplied for difficult cases.

OPTIONS

--verbose: Print progress information during processing.
--qc: Generate quality control images.
--clobber: Overwrite existing output files.
--model-dir <dir>: Path to the model directory containing the ventricle atlas library. This option is required.
--nuc: Apply N3 non-uniformity correction during preprocessing.
--cleanup: Remove temporary files after processing.
--nuyl: Apply NUYL intensity normalization during preprocessing.
--whole-head: Use the whole head (not just the brain) for registration and segmentation.
--subject <id>: Specify a subject identifier string for output naming.
--nlmask <mask.mnc>: Provide a nonlinear brain mask to constrain the segmentation region.
--manual-xfm <xfm>: Provide a manually created initial transformation for registration.
--search <n>: Search radius in voxels for the patch-based label fusion. Default: 1.
--reference <file>: Specify a reference volume for comparison or validation.
--nonbrainconstraint: Apply a constraint that prevents labels from being assigned outside the brain region.

EXAMPLES

Segment ventricles with the required model directory:

ventricles_segmentation_pipeline.pl subject_t1.mnc output_prefix \
    --model-dir /path/to/ventricle_model --verbose

Segment with preprocessing and quality control output:

ventricles_segmentation_pipeline.pl subject_t1.mnc output_prefix \
    --model-dir /path/to/ventricle_model --nuc --nuyl --qc --cleanup

Segment with a manual initial transform and non-brain constraint:

ventricles_segmentation_pipeline.pl subject_t1.mnc output_prefix \
    --model-dir /path/to/ventricle_model \
    --manual-xfm initial.xfm --nonbrainconstraint --clobber

AUTHOR

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

COPYRIGHTS