Package that provides tools for brain MRI Deep Learning pre-processing.

Note

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

brainprep.cortical.recon_all(fsdir, anatfile, sid, reconstruction_stage='all', resume=False, t2file=None, flairfile=None)[source]¶

Performs all the FreeSurfer cortical reconstruction steps.

Note

This function is based on FreeSurfer.

Parameters:

fsdir : str

the FreeSurfer working directory with all the subjects.

anatfile : str

the input anatomical image to be segmented with FreeSurfer.

sid : str

the current subject identifier.

reconstruction_stage : str, default ‘all’

the FreeSurfer reconstruction stage that will be launched.

resume : bool, deafult False

if true, try to resume the recon-all. This option is also usefull if custom segmentation is used in recon-all.

t2file : str, default None

specify the path to a T2 image that will be used to improve the pial surfaces.

flairfile : str, default None

specify the path to a FLAIR image that will be used to improve the pial surfaces.

Returns:

subjfsdir : str

path to the resulting FreeSurfer segmentation.