python

Python Helper Fuction for the MASMAT toolbox

Main functions

Main functions are stored in segmentatiom_propagation.py:

reg_aladin:

affine registration using NiftyReg package

reg_resample:

resample nifti image using NiftyReg package

reorient

reorient nifti image using nibabel library

N4_correction

N4 Bias Field Correction using nipype

N4_correction_slicer

N4 Bias Field Correction using 3D Slicer

N4_correction_itk

N4 Bias Field Correction using SimpleITK

mas_quickcheck

generate quickcheck files using FSL

affine_mask_propagation

generate slurm sbatch file for affine mask mask propagation

affine_label_fusion

[SLURM] affine label fusion (after slurm_affine_mask_propagation)

nonrigid_label_propagation

[SLURM] nonrigid label fusion

nonrigid_label_fusion

[SLURM] nonrigid label/brain-mask fusion (after slurm_nonrigid_label_propagation)

extract_label_volumes

extract label volumes from nifti files of segmentation labels