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volumevoxelmedicalniftinibabel
Carlao
Carlao

Reputation: 70

How to compute the volume of a single voxel of nifti medical image?

I have loaded a nifti image file using nibabel tool and I have played with some properties. But I don’t have idea how to compute the volume (in mm³) of a single voxel.

Upvotes: 2

Views: 7996

Answers (2)

fepegar
fepegar

Reputation: 693

Here's the answer using NiBabel, as OP asked:

import nibabel as nib
nii = nib.load('t1.nii.gz')
sx, sy, sz = nii.header.get_zooms()
volume = sx * sy * sz

Upvotes: 9

HockeyStick
HockeyStick

Reputation: 73

I am not a NiBabel expert, but I can instead recommend the SimpleITK package for Python. I often use it for reading NifTi image files. It has a method GetSpacing() which returns the pixel spacing in mm.

import SimpleITK as sitk

# read image
im = sitk.ReadImage("/path/to/input/image.nii")

# get voxel spacing (for 3-D image)
spacing = im.GetSpacing()
spacing_x = spacing[0]
spacing_y = spacing[1]
spacing_z = spacing[2]

# determine volume of a single voxel
voxel_volume = spacing_x * spacing_y * spacing_z

Upvotes: 1

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