Coronal, sagittal, axial and oblique

This examples illustrates how vreg can be used to slice 3D volumes in different ways.

Setup

import numpy as np
import vreg
import vreg.plot as plt

Get data

The starting point of this example is a 3D coronal volume of the abdomen. For visual reference we’ll also load a 3D coronal mask of the kidneys.

# 3D coronal volume of the abdomen
cor = vreg.fetch('Dixon_out_phase')

# 3D coronal mask of the kidneys
mask = vreg.fetch('kidneys')

# Show the data
plt.overlay_2d(cor, mask, alpha=1.0, width=6)

Coronal -> Axial

We reslice the coronal volume in the axial plane using an isotropic 1mm voxel size. Since 1mm is the default spacing, we do not have to specify it explicitly.

# Reslice isotropically in the axial plane
axial = cor.reslice(orient='axial')

# Show the result
plt.overlay_2d(axial, mask, alpha=1.0, width=6)

Axial -> Sagittal

Since vreg keeps track of the position in space, we can keep reslicing the result. Let’s reslice the axial volume sagitally:

# Reslice isotropically in the sagittal plane
sagit = axial.reslice(orient='sagittal')

# Show the result
plt.overlay_2d(sagit, mask, alpha=1.0, width=6)

Sagittal -> Coronal

As a consistency check, we can reslice the sagittal volume coronally again and check against the original

# Sagittal to coronal
cor = sagit.reslice(orient='coronal')

# Compare result to the original
plt.overlay_2d(cor, mask, alpha=1.0, width=6)

As expected, this looks visually the same as the original coronal image. The number of slices is increased because this now has a 1mm isotropic voxel size, whereas the original had 1.5mm slice thickness.

Oblique

The oblique orientation refers to any that is not in one of the standard plances (coronal, sagittal or axial). A volume can be reslice to any oblique orientation by specifying a rotation vector.

As an example, let’s reslice the coronal volume obliquely along the principle axis of the kidneys. The sagittal images shows that the kidneys make an angle of approximately 30 degrees with the vertical (z-axis).

If we reslice the coronal volume using a rotation of -30 degrees around the x-axis, we get a coronal-oblique view through the kidneys:

obl = cor.reslice(rotation=[-np.radians(30), 0, 0])

# Show the oblique reslice:
plt.overlay_2d(obl, mask, alpha=1.0, width=6)

Oblique in the sagittal plane

The oblique image above cuts along the natural axis of the kidneys. We can verify this visually by looking at this oblique section in the sagittal plane:

obl = cor.reslice(orient='sagittal', rotation=[-np.radians(30), 0, 0])

# Show the sagittal-oblique view
plt.overlay_2d(obl, mask, alpha=1.0, width=6)