Change entire images slices of NIFTI in Python 3.7

问题

I'm actually work on MRI images using Python. The image format is the NIFTI format I get how to visualise slices on x, y or z axe, but now, I want tu use Sobel filtering on each of them and create a new NIFTI image with those slices.

For that:

I load the main .nii.gz image (img = nib.load(im_path))
I load again the main .nii.gz image with a new name "img_sobel" (img_sobel = nib.load(im_path))
Create a loop for each slice
Sobel filtering the slice
Replace this slice on the corresponding slice of img_sobel ("img_sobel_data[:, :, sl] == np.hypot(sx, sy)")
After the loop, save the img_sobel with the name "image_XXX_Sobel"

Using subplot, I see the sobel filtering work on each slice, but it seems the line "img_sobel_data[:, :, sl] == np.hypot(sx, sy)" don't work, why ?

Here's the lopp section :

    # Name the interested data
    img_data = img.get_fdata()
    img_sobel_data = img_sobel.get_fdata()

    header = img.header
    nb_img = header.get_data_shape()
    nb_img_h = nb_img[2] #Hauteur

    for sl in range(0,nb_img_h):
            slice_h = img_data[:, :, sl]
            #Sobel
            sx = ndimage.sobel(slice_h, axis=0, mode='constant')
            sy = ndimage.sobel(slice_h, axis=1, mode='constant')
            sobel_h = np.hypot(sx, sy)

            img_sobel_data[:, :, sl] = sobel_h #Change the image slice to the sobel one
# Save Sobel:
nib.save(img_sobel,imSobel_path)

What's wrong ? Can't we replace an image slice from another one in Python ? Is there a trick to solve this problem ?

Thank you !

EDIT : OK I get a bit more why I can't do taht so easily : I extracted the slices of the NIFTI image, filtered them, but I wasn't change the NIFTI image itself !!! So my question now : How to change the NIFTI image get from img_sobel.get_fdata() ?

回答1:

simply because you didn't save your img_sobel_data, with affine and header properly, if you want save Nifti image you have to provide header and affine before to save it img_sobel = nib.Nifti1Image(img_sobel_data, affine=img_sobel_affine, header=header) otherwise you can save the image on other formats using cv2 library with cv2.imwrite to save your image in JPG or PNG extension.

#======================================
# Importing Necessary Libs
#======================================
import nibabel as nib
import numpy as np 
from scipy import ndimage, misc
import matplotlib.pyplot as plt
#==============================
img  = nib.load(Nifti_img_path)
img_sobel  = nib.load(Nifti_img_sobel_path)
#==============================
if True: 
    # Name the interested data  
    img_data = img.get_fdata()
    img_sobel_data = img_sobel.get_fdata()
    img_sobel_affine = img_sobel.affine
    header = img.header
    nb_img = header.get_data_shape()
    nb_img_h = nb_img[2] #Hauteur

    for sl in range(0,nb_img_h):
            slice_h = img_data[:, :, sl]
            #Sobel
            sx = ndimage.sobel(slice_h, axis=0, mode='constant')
            sy = ndimage.sobel(slice_h, axis=1, mode='constant')
            sobel_h = np.hypot(sx, sy)

            img_sobel_data[:, :, sl] = sobel_h #Change the image slice to the sobel one
# Save Sobel:
img_sobel = nib.Nifti1Image(img_sobel_data, affine=img_sobel_affine, header=header)
nib.save(img_sobel,imSobel_path)
#==============================

来源：https://stackoverflow.com/questions/60489418/change-entire-images-slices-of-nifti-in-python-3-7

标签

python

python-3.x

image-processing

nifti

mri