ndreg

ndreg.imgMetamorphosis(inImg, refImg, alpha=0.02, beta=0.05, scale=1.0, iterations=1000, epsilon=None, minEpsilon=None, sigma=0.0001, useNearest=False, useBias=False, useMI=False, verbose=False, debug=False, inMask=None, refMask=None, outDirPath='')

Performs Metamorphic LDDMM between input and reference images

ndreg.imgMetamorphosisComposite(inImg, refImg, alphaList=0.02, betaList=0.05, scaleList=1.0, iterations=1000, epsilonList=None, minEpsilonList=None, sigma=0.0001, useNearest=False, useBias=False, useMI=False, inMask=None, refMask=None, verbose=True, debug=False, outDirPath='')

Performs Metamorphic LDDMM between input and reference images

ndreg.register_affine(atlas, img, learning_rate=0.01, iters=200, min_step=1e-10, shrink_factors=[1], sigmas=[0.15], use_mi=False, grad_tol=1e-06, verbose=False)

Performs affine registration between an atlas an an image given that they have the same spacing.

ndreg.register_brain(atlas, img, modality, outdir=None)

Register 3D mouse brain to the Allen Reference atlas using affine and deformable registration.

atlas : {SimpleITK.SimpleITK.Image}

Allen reference atlas or other atlas to register data to.

img : {SimpleITK.SimpleITK.Image}

Input observed 3D mouse brain volume

modality : {str}

Can be ‘lavision’ or ‘colm’ for either modality.

outdir : {str}, optional

Path to output directory to store intermediates. (the default is None, which will store all outputs in ‘./’)

Returns:

SimpleITK.SimpleITK.Image

The atlas deformed to fit the input image.

ndreg.register_lddmm(affine_img, target_img, alpha_list=0.05, scale_list=[0.0625, 0.125, 0.25, 0.5, 1.0], epsilon_list=0.0001, min_epsilon_list=1e-10, sigma=0.1, use_mi=False, iterations=200, inMask=None, refMask=None, verbose=True, out_dir='')

ndreg.register_rigid(atlas, img, learning_rate=0.01, iters=200, min_step=1e-10, shrink_factors=[1], sigmas=[0.15], use_mi=False, grad_tol=1e-06, verbose=False)

Performs affine registration between an atlas an an image given that they have the same spacing.