Note

This page is a reference documentation. It only explains the function signature, and not how to use it. Please refer to the user guide for the big picture.

brainprep.interfaces.reconall_longitudinal

brainprep.interfaces.reconall_longitudinal(workspace_dir, output_dir, entities)[source]

Longitudinal brain parcellation using FreeSurfer’s recon-all.

Assuming you have run recon-all for all timepoints of a given subject, and that the results are stored in one subject directory per timepoint, this function will:

  1. generate a template for this subject using recon-all.

  2. parcellation refinements using recon-all and the new generated template.

Parameters:
workspace_dir: Directory

Working directory where FreeSurfer outputs are reorganized to run longitudinal commands.

output_dirDirectory

FreeSurfer working directory containing all the subject

entitiesdict

A dictionary of parsed BIDS entities including modality.

Returns:
commandlist[str]

Brain parcellation command-line.

outputstuple[File | list[File]]

  • log_template_file : File - Generated log file for the template creation step.

  • log_files : list[File] - Generated log files for the parcellation refinements.

Raises:
ValueError

If a cross-sectional recon-all is not available or if multiple subjects are passed as inputs.