How to visualize MRI data?

from polpo.plot.mri import MriPlotter, MriSlicer, SlicesPlotter
from polpo.preprocessing.load.pregnancy import FigsharePregnancyDataLoader
from polpo.preprocessing.mri import MriImageLoader
from polpo.preprocessing.path import FileFinder, FileRule

Loading data

We’ll create a pipeline that:

• downloads data from figshare

• finds nii file in folder

• loads image as an array

SESSION_ID = 1

folder_name = f"ses-{str(SESSION_ID).zfill(2)}"

loader = FigsharePregnancyDataLoader(
    data_dir="~/.herbrain/data/pregnancy/mri",
    remote_path=f"mri/{folder_name}",
)

finder = FileFinder(
    rules=[
        FileRule(value="BrainNormalized", func="startswith"),
        FileRule(value=".nii.gz", func="endswith"),
    ]
)

pipe = loader + finder + MriImageLoader()

img_fdata = pipe()

Visualization

MriSlicer slices the MRI image. SlicesPlotter takes care of plotting slices. By default, it plots side, front and top views.

slices_plotter = SlicesPlotter()
slicer = MriSlicer()

slices_plotter.plot(slicer.slice(img_fdata, (35, 70, 105)));

For convenience, there’s also MriPlotter.

mri_plotter = MriPlotter()

mri_plotter.plot(img_fdata, [val // 2 for val in img_fdata.shape]);

Further reading

• How to get a mesh from an MRI image?