问题
I downloaded the BraTS dataset for my summer project.
The dataset consisted of nii.gz files which I was able to open using nibabel library in Python. I used the following code:
import os
import numpy as np
import nibabel as nib
import matplotlib.pyplot as plat
examplefile=os.path.join("mydatapath","BraTS19_2013_5_1_flair.nii.gz")
img=nib.load(examplefile)
print(img)
this gave me the following output:
<class 'nibabel.nifti1.Nifti1Image'>
data shape (240, 240, 155)
affine:
[[ -1. 0. 0. -0.]
[ 0. -1. 0. 239.]
[ 0. 0. 1. 0.]
[ 0. 0. 0. 1.]]
metadata:
<class 'nibabel.nifti1.Nifti1Header'> object, endian='<'
sizeof_hdr : 348
data_type : b''
db_name : b''
extents : 0
session_error : 0
regular : b'r'
dim_info : 0
dim : [ 3 240 240 155 1 1 1 1]
intent_p1 : 0.0
intent_p2 : 0.0
intent_p3 : 0.0
intent_code : none
datatype : int16
bitpix : 16
slice_start : 0
pixdim : [1. 1. 1. 1. 0. 0. 0. 0.]
vox_offset : 0.0
scl_slope : nan
scl_inter : nan
slice_end : 0
slice_code : unknown
xyzt_units : 2
cal_max : 0.0
cal_min : 0.0
slice_duration : 0.0
toffset : 0.0
glmax : 0
glmin : 0
descrip : b''
aux_file : b''
qform_code : aligned
sform_code : scanner
quatern_b : 0.0
quatern_c : 0.0
quatern_d : 1.0
qoffset_x : -0.0
qoffset_y : 239.0
qoffset_z : 0.0
srow_x : [-1. 0. 0. -0.]
srow_y : [ 0. -1. 0. 239.]
srow_z : [0. 0. 1. 0.]
intent_name : b''
magic : b'n+1'
Can someone please walk me through this. I know it's a lot of data if someone could just tell me how to get the image from this data it would be wonderful.
Thank You.
回答1:
Have you looked at nibabel's documentation? It's excellent and has the answer to your question. https://nipy.org/nibabel/gettingstarted.html
In your question, you are looking at the header of the Nifti file. Use the following to get the image data as a numpy array.
import nibabel as nib
img = nib.load("image.nii.gz")
data = img.get_fdata()
来源：https://stackoverflow.com/questions/62100928/clarification-regarding-brats-dataset