beast_normalize

preprocess and normalize a MINC volume for BEaST brain extraction

beast_normalize <input.mnc> <output.mnc> <output_mask.mnc> [model_dir]

DESCRIPTION

beast_normalize is a Bash script that preprocesses and normalizes a MINC volume for use with mincbeast brain extraction. The script performs intensity normalization, linear registration to MNI stereotaxic space, and brain mask extraction to prepare input data in the format expected by the BEaST library.

The preprocessing pipeline includes:

1. Intensity non-uniformity correction using nu_correct
2. Linear registration to the MNI152 template using bestlinreg
3. Intensity normalization to match the BEaST library intensity range
4. Resampling to stereotaxic space
5. Generation of a brain mask in the native space of the input volume

The optional model_dir argument specifies the directory containing the MNI model files used for registration. If not provided, the default model directory from the minc-toolkit installation is used.

OPTIONS

beast_normalize does not accept option flags. All arguments are positional.

<input.mnc>

Input MINC volume (typically a T1-weighted MRI).

<output.mnc>

Output normalized MINC volume in stereotaxic space.

<output_mask.mnc>

Output brain mask in stereotaxic space.

[model_dir]

Optional path to the directory containing MNI model files for registration. Defaults to the standard minc-toolkit model directory.

EXAMPLES

Normalize a T1 volume using default model directory:

beast_normalize t1_native.mnc t1_stx.mnc brain_mask.mnc

Normalize using a custom model directory:

beast_normalize t1_native.mnc t1_stx.mnc brain_mask.mnc /opt/models/icbm152

AUTHOR

Simon Fristed Eskildsen, Pierrick Coupe - McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

COPYRIGHTS

Copyright © 2011 by Simon Fristed Eskildsen and Pierrick Coupe

SEE ALSO

mincbeast