Package that provides tools for brain Lithium MRI 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.

limri.normtools.fast(input_file, out_fileroot, klass=3, im_type=1, segments=False, bias_field=True, bias_corrected_im=True, probabilities=False)[source]¶

FAST (FMRIB’s Automated Segmentation Tool) segments a 3D image of the brain into different tissue types (Grey Matter, White Matter, CSF, etc.), whilst also correcting for spatial intensity variations (also known as bias field or RF inhomogeneities).

Parameters

input_file : str

the image to be segmented.

out_fileroot : str

output basename.

klass : int, default 3

number of tissue-type classes.

im_type : int, default 1

type of image 1=T1, 2=T2, 3=PD.

segments : bool, default False

outputs a separate binary image for each tissue type.

bias_field, default True

output estimated bias field.

bias_corrected_im : bool, default True

output bias-corrected image.

probabilities : bool, default False

outputs individual probability maps.

Returns

biascorrected_file : str

the bias corrected input image.