How can i get deformation field?
domadaaaa opened this issue · comments
HI,I want to save deformation field to NIFTY format, what should i do?
How did you produce the deformation field?
How did you produce the deformation field?
That's exactly what I want to know too LOL
Are you asking how to do image registration? Start with the script antsRegistrationSyNQuick.sh
Are you asking how to do image registration? Start with the script
antsRegistrationSyNQuick.sh
No... I would like to obtain a deformation field file generated during the registration process
I'm a little confused, running the registration script with its default parameters will produce a deformation field in NIFTI format.
I'm a little confused, running the registration script with its default parameters will produce a deformation field in NIFTI format.
sry,there is something wrong with my expression. I registrat with python package antspy running in linux
my code is as follows, can i modify code to obtain the deformation field?
`
import ants
from scipy.ndimage import zoom
import nibabel as nib
import numpy as np
fixed = ants.image_read("MRI.nii.gz")
img = nib.load('CT.nii.gz')
moving = img.get_fdata()
scale = (0.9375, 0.9375, 0.6)
moving = zoom(moving, scale)
moving = nib.Nifti1Image(moving, img.affine, img.header)
nib.save(moving, 're_CT.nii.gz')
moving = ants.image_read("re_CT.nii.gz")
SyN = ants.registration(fixed=fixed, moving=moving, save_state=True)
result = ants.apply_transforms(fixed=fixed, moving=moving, transformlist=SyN['fwdtransforms'])
ants.image_write(result, 'moved.nii.gz')
`
Ok I think I understand now
SyN['fwdtransforms']
This should be a list of strings, they are file names. The first one will be the deformation field, in NIFTI format.
They can be read with the read_transform
function