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.

5.4.1. sammba.segmentation.brain_extraction_report

sammba.segmentation.brain_extraction_report(head_file, brain_volume, write_dir=None, clipping_fractions=[0.2, None], use_rats_tool=True, caching=False, verbose=False, digits=2)

Parameters

head_file : str

Path to the image to mask.

brain_volume : int

Volume of the brain in mm3 used for brain extraction. Typically 400 for mouse and 1800 for rat.

write_dir : str or None, optional

Path to the folder to save the output file to. If None, the folder of the head file is used.

clipping_fractions : list. Elements can be floats between 0. and .9

or None, optional Clip level fractions to explore. Each value is passed to nipype.interfaces.afni.Unifize, to tune the bias correction step done prior to brain mask segmentation. Smaller fractions tend to make the mask larger. If None, no unifization is done for brain mask computation.

caching : bool, optional

Wether or not to use caching.

digits : int, optional

Number of digits for formating output floating point values.

Returns

path to brain extracted image.