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.regtools.flirt(in_file, ref_file, out, omat=None, init=None, cost='corratio', usesqform=False, displayinit=False, anglerep='euler', bins=256, interp='trilinear', dof=12, applyxfm=False, applyisoxfm=None, nosearch=False, wmseg=None, verbose=0)[source]¶

Affine registration with FSL flirt.

Parameters

in_file : str

input volume.

ref_file : str

reference volume.

out : str

output volume

omat : str, default None

matrix filename - output in 4x4 ascii format.

init : str, default None

input 4x4 affine matrix

cost : str, default ‘corratio’

choose the most appropriate option: ‘mutualinfo’, ‘corratio’, ‘normcorr’, ‘normmi’, ‘leastsq’, ‘labeldiff’, ‘bbr’.

usesqform : bool, default False

initialise using appropriate sform or qform.

displayinit : bool, default False

display initial matrix.

anglerep : str, default ‘euler’

choose the most appropriate option: ‘quaternion’, ‘euler’.

bins : int, default 256

number of histogram bins

interp : str, default ‘trilinear’

choose the most appropriate option: ‘trilinear’, ‘nearestneighbour’, ‘sinc’, ‘spline’.

dof : int, default 12

number of transform dofs.

applyxfm : bool, default False

ppplies transform (no optimisation) - requires -init.

applyisoxfm : float, default None

the integer defines the scale - as applyxfm but forces isotropic resampling.

verbose : int, default 0

0 is least and default.

nosearch : bool, default False

if set perform no search to initialize the optimization.

wmseg : str, default None

white matter segmentation volume needed by BBR cost function.

Returns

out : str

output volume.

omat : str

output matrix filename - output in 4x4 ascii format.