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

brainprep.interfaces.reconall(t1_file, output_dir, entities, t2_file=None, flair_file=None, resume=False)[source]

Brain parcellation using FreeSurfer’s recon-all.

In FreeSurfer, recon-all is the main command used to perform automated cortical reconstruction and volumetric segmentation from structural MRI data. It includes multiple processing steps such as skull stripping, surface reconstruction, and anatomical labeling [1].

Parameters:
t1_fileFile

Path to the input T1w image file.

output_dirDirectory

FreeSurfer working directory containing all the subjects.

entitiesdict

A dictionary of parsed BIDS entities including modality.

t2_fileFile | None

Path to the input T2w image file - used to improve the pial surface. Default None.

flair_fileFile | None

Path to the input FLAIR image file - used to improve the pial surface. Default None.

resumebool

If True, try to resume recon-all. This option is particularly useful when a custom segmentation is used in recon-all. Default False.

Returns:
commandlist[str]

Brain parcellation command-line.

outputstuple[File]

  • log_file : File - Generated log file.

References