How can i get deformation field？

[domadaaaa]

HI，I want to save deformation field to NIFTY format, what should i do?

[ntustison]

How did you produce the deformation field?

[domadaaaa]

How did you produce the deformation field?

That's exactly what I want to know too LOL

[cookpa]

Are you asking how to do image registration? Start with the script antsRegistrationSyNQuick.sh

[domadaaaa]

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

[cookpa]

I'm a little confused, running the registration script with its default parameters will produce a deformation field in NIFTI format.

[domadaaaa]

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')
`

[cookpa]

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