pipeline_longitudinal.pl

longitudinal brain analysis pipeline

pipeline_longitudinal.pl <candID> <visit1> [visit2] [visit3] [options]

DESCRIPTION

pipeline_longitudinal.pl runs the BIC longitudinal brain analysis pipeline, which processes multiple time-point MRI scans from the same subject to track brain changes over time. The pipeline registers all visits to a common subject-specific template, performs tissue classification and segmentation at each time point, and computes longitudinal measures such as atrophy rates.

The script takes a candidate identifier followed by one or more visit identifiers. Subject ages and gender can be provided for demographic-aware processing. The pipeline uses both linear and optionally nonlinear registration, and can incorporate PCA-based normalization for improved longitudinal consistency.

OPTIONS

--verbose

Print progress information during processing.

--clobber

Overwrite output files if they already exist.

--prefix <dir>

Base directory prefix for input and output files.

--model_dir <dir>

Path to the directory containing the reference model files.

--model <name>

Base name of the reference model to use for registration.

--ages <age1,age2,...>

Comma-separated list of ages corresponding to each visit, used for age-appropriate processing.

--gender <M|F>

Subject gender, used for gender-specific model selection when available.

--nonlinear

Enable nonlinear registration for more precise inter-visit alignment.

--pca

Enable PCA-based intensity normalization across time points for improved longitudinal consistency.

EXAMPLES

Process two visits for a subject:

pipeline_longitudinal.pl CAND001 V1 V2 \
  --model_dir /opt/minc/share/model --model icbm152

Process three visits with ages and nonlinear registration:

pipeline_longitudinal.pl CAND001 V1 V2 V3 \
  --ages 65,66,67 --gender M --nonlinear \
  --model_dir /opt/minc/share/model --model icbm152

Process with PCA normalization:

pipeline_longitudinal.pl CAND001 V1 V2 --pca --clobber

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

pipeline_mritotal.pl, pipeline_nlr.pl