pipeline_mritotal.pl

stereotaxic registration pipeline with BEaST brain masking

pipeline_mritotal.pl <input.mnc> <output.xfm> <output.mnc> [options]

DESCRIPTION

pipeline_mritotal.pl performs stereotaxic registration of an MRI volume to a standard template space (typically ICBM 152), combined with brain extraction using the BEaST algorithm. The pipeline produces a linear transformation file mapping the input to Talairach space and a resampled volume in stereotaxic coordinates.

The script uses bestlinreg_s2 for robust linear registration and mincbeast for brain mask extraction. An initial transform can be provided to seed the registration, and intensity correction can be applied. The –fallback option enables a fallback registration strategy if the primary registration fails. Nonlinear masking (–nlmask) can improve brain extraction accuracy.

OPTIONS

--verbose

Print progress information during processing.

--clobber

Overwrite output files if they already exist.

--fallback

Enable a fallback registration strategy if the primary registration fails or produces poor results.

--correct

Apply intensity correction to the input volume before registration.

--model_dir <dir>

Path to the directory containing the reference model files.

--model_name <name>

Base name of the reference model to use for registration.

--initial <xfm>

An initial linear transform to seed the registration, useful when an approximate alignment is already known.

--nlmask

Use nonlinear registration to improve brain mask accuracy.

--beastlib <dir>

Path to the BEaST brain masking library directory.

EXAMPLES

Register a volume to stereotaxic space:

pipeline_mritotal.pl input.mnc output.xfm output_tal.mnc \
  --model_dir /opt/minc/share/icbm152_model_09c \
  --model_name icbm_avg_152

Register with intensity correction and BEaST library:

pipeline_mritotal.pl input.mnc output.xfm output_tal.mnc \
  --model_dir /opt/minc/share/icbm152_model_09c \
  --model_name icbm_avg_152 --correct \
  --beastlib /opt/minc/share/beast-library-1.1

Register with an initial transform and fallback:

pipeline_mritotal.pl input.mnc output.xfm output_tal.mnc \
  --model_dir /opt/minc/share/icbm152_model_09c \
  --model_name icbm_avg_152 --initial init.xfm --fallback

AUTHOR

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

COPYRIGHTS

Copyright © McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University.

SEE ALSO

bestlinreg_s2, mincbeast, mritotal