pipeline_nlr.pl

nonlinear registration pipeline

pipeline_nlr.pl <t1_tal> <mask> <out_grid> <out_xfm> <out_t1> [options]

DESCRIPTION

pipeline_nlr.pl performs hierarchical nonlinear registration of a T1-weighted volume in Talairach space to a standard template model. The pipeline uses nlfit_s or minctracc to compute a nonlinear deformation field that warps the subject anatomy to match the template as closely as possible.

The output consists of a deformation grid file, a combined nonlinear transformation file, and the nonlinearly resampled T1 volume. The –level option controls the resolution of the finest registration step, with lower values producing finer deformation fields at the cost of longer computation time.

A brain mask is required to restrict the registration to the brain region, preventing extracranial structures from influencing the result.

OPTIONS

--verbose

Print progress information during processing.

--clobber

Overwrite output files if they already exist.

--model_dir <dir>

Path to the directory containing the reference model files.

--model_name <name>

Base name of the reference model to use for nonlinear registration.

--level <n>

Finest resolution level for the hierarchical nonlinear registration. Lower values produce finer deformation fields. Default is 2.

EXAMPLES

Run nonlinear registration with default settings:

pipeline_nlr.pl t1_tal.mnc brain_mask.mnc nl_grid.mnc nl.xfm nl_t1.mnc \
  --model_dir /opt/minc/share/icbm152_model_09c \
  --model_name icbm_avg_152

Run with finer registration level:

pipeline_nlr.pl t1_tal.mnc brain_mask.mnc nl_grid.mnc nl.xfm nl_t1.mnc \
  --model_dir /opt/minc/share/icbm152_model_09c \
  --model_name icbm_avg_152 --level 1

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

nlfit_s, minctracc