MRI Glue demo

brain.py

# -*- coding: utf-8 -*-

"""
This script loads a Brain Tumor DICOM dataset into Glue.
The data comes from http://www.osirix-viewer.com/datasets/DATA/BRAINIX.zip

To run this locally, download and unzip that file, and run this script
from the directory that you dowloaded the ZIP file to

This requires the dicom library, which you can install via
pip install pydicom
"""

from glob import glob

from glue import qglue
from dicom import read_file
import numpy as np


def load(pth):
    ds = read_file(pth)
    shp = ds.Rows, ds.Columns
    return np.fromstring(ds.PixelData, dtype=np.short).reshape(shp)

datasets = {}

base = 'BRAINIX/BRAINIX/IRM cérébrale, neuro-crâne/'
subdirs = ['SOUS - 702',
           'T1-SE-extrp - 601',
           'T2W-FE-EPI - 501',
           'sT2W-FLAIR - 401',
           'T1-3D-FFE-C - 801',
           'T1-SE-extrp - 701',
           'sT2-TSE-T - 301'
           ]
for dir in subdirs:
    slices = glob(base + dir + '/*dcm')
    data = [load(s) for s in slices]  # read each slice
    data = np.dstack(data).transpose((2, 0, 1))  # assemble into cube
    datasets[dir] = {'value': data}

qglue(**datasets)