How to get a mesh from an MRI image?#

[1]:

import pyvista as pv

import polpo.preprocessing.dict as ppdict
from polpo.preprocessing.load.pregnancy.pilot import (
    HippocampalSubfieldsSegmentationsLoader,
    MriLoader,
)
from polpo.preprocessing.mesh.conversion import PvFromData
from polpo.preprocessing.mri import (
    MeshExtractorFromSegmentedImage,
    SkimageMarchingCubes,
)

[KeOps] Warning : cuda was detected, but driver API could not be initialized. Switching to cpu only.

[2]:

STATIC_VIZ = True

if STATIC_VIZ:
    pv.set_jupyter_backend("static")

Loading data#

Following How to visualize MRI data?, we start by getting the image data.

[3]:

SESSION_ID = 1

[4]:

loader = MriLoader(subset=[SESSION_ID], as_image=True)

pipe = loader + ppdict.ExtractUniqueKey()

[5]:

img_fdata = pipe()

INFO: Data has already been downloaded... using cached file ('/home/luisfpereira/.herbrain/data/pregnancy/raw/mri').

Marching cubes#

We now use marching cubes and transform the output to pyvista.PolyData for visualization.

[6]:

mesh_from_image = SkimageMarchingCubes()

[7]:

mesh = (mesh_from_image + PvFromData())(img_fdata)

Visualization#

[8]:

pl = pv.Plotter(border=False)

pl.show_axes()
pl.add_mesh(mesh, show_edges=True)
pl.show()
../../../_images/_notebooks_how_to_all_mri2mesh_13_0.png

Segmented data#

Load the segmented data.

[9]:

pipe = (
    HippocampalSubfieldsSegmentationsLoader(subset=[SESSION_ID], as_image=True)
    + ppdict.ExtractUniqueKey()
)

[10]:

img_fdata = pipe()

INFO: Data has already been downloaded... using cached file ('/home/luisfpereira/.herbrain/data/pregnancy/derivatives/segmentations').

The process changes only slightly when the data is segmented. (NB: encoding informs about the tool used for segmentation, which matters to map ids to tool ids and colors.)

[11]:

img2mesh = (
    MeshExtractorFromSegmentedImage(
        return_colors=True,
        encoding="ashs",
    )
    + PvFromData()
)

mesh = img2mesh(img_fdata)

[12]:

pl = pv.Plotter(border=False)

pl.show_axes()
pl.add_mesh(mesh, show_edges=True)
pl.show()
../../../_images/_notebooks_how_to_all_mri2mesh_20_0.png

For example, we can select a particular subfield of the hippocampus.

[13]:

img2mesh = (
    MeshExtractorFromSegmentedImage(
        struct_id="PostHipp", return_colors=False, encoding="ashs"
    )
    + PvFromData()
)

mesh = img2mesh(img_fdata)

[14]:

pl = pv.Plotter(border=False)

pl.show_axes()
pl.add_mesh(mesh, show_edges=True)
pl.show()
../../../_images/_notebooks_how_to_all_mri2mesh_23_0.png

Further reading#