Decompress nifti medical image in gz format using python

Question

I want to decompress a butch of nii.gz files in python so that they could be processed in sitk later on. When I decompress a single file manually by right-clicking the file and choosing 'Extract..', this file is then correctly interpreted by sitk (I do sitk.ReadImage(unzipped)). But when I try to decompress it in python using following code:

with gzip.open(segmentation_zipped, "rb") as f:
    bindata = f.read()
segmentation_unzipped = os.path.join(segmentation_zipped.replace(".gz", ""))
with gzip.open(segmentation_unzipped, "wb") as f:
    f.write(bindata)

I get error when sitk tries to read the file: RuntimeError: Exception thrown in SimpleITK ReadImage: C:\d\VS14-Win64-pkg\SimpleITK\Code\IO\src\sitkImageReaderBase.cxx:82: sitk::ERROR: Unable to determine ImageIO reader for "E:\BraTS19_2013_10_1_seg.nii"

Also when trying to do it a little differently:

input = gzip.GzipFile(segmentation_zipped, 'rb')
s = input.read()
input.close()

segmentation_unzipped = os.path.join(segmentation_zipped.replace(".gz", ""))
output = open(segmentation_unzipped, 'wb')
output.write(s)
output.close()

I get: RuntimeError: Exception thrown in SimpleITK ReadImage: C:\d\VS14-Win64-pkg\SimpleITK-build\ITK\Modules\IO\PNG\src\itkPNGImageIO.cxx:101: itk::ERROR: PNGImageIO(0000022E3AF2C0C0): PNGImageIO failed to read header for file: Reason: fread read only 0 instead of 8

can anyone help?

It's weird that you're getting errors from SimpleITK, since you're not reading the image with SimpleITK (at least in the code you show). Note that SimpleITK.ReadImage can read a '.nii.gz' file without decompressing it. — Dave Chen

Bilal Bilal · Accepted Answer · 2020-06-05T17:52:56

No need to unzip the Nifti images, libraries such as Nibabel can handle it without decompression.

#==================================
import nibabel as nib
import numpy as np
import matplotlib.pyplot as plt
#==================================
# load image (4D) [X,Y,Z_slice,time]
nii_img  = nib.load('path_to_file.nii.gz')
nii_data = nii_img.get_fdata()

fig, ax = plt.subplots(number_of_frames, number_of_slices,constrained_layout=True)
fig.canvas.set_window_title('4D Nifti Image')
fig.suptitle('4D_Nifti 10 slices 30 time Frames', fontsize=16)
#-------------------------------------------------------------------------------
mng = plt.get_current_fig_manager()
mng.full_screen_toggle()

for slice in range(number_of_slices):
    # if your data in 4D, otherwise remove this loop
    for frame in range(number_of_frames):
        ax[frame, slice].imshow(nii_data[:,:,slice,frame],cmap='gray', interpolation=None)
        ax[frame, slice].set_title("layer {} / frame {}".format(slice, frame))
        ax[frame, slice].axis('off')

plt.show()

Or you can Use SimpleITK as following:

import SimpleITK as sitk
import numpy as np

# A path to a T1-weighted brain .nii image:
t1_fn = 'path_to_file.nii'

# Read the .nii image containing the volume with SimpleITK:
sitk_t1 = sitk.ReadImage(t1_fn)

# and access the numpy array:
t1 = sitk.GetArrayFromImage(sitk_t1)

Decompress nifti medical image in gz format using python

1 Answers