Open mha image files in Python (2015 brats challenge dataset)

Question

I want to use deep learning for medical image segmentation as my graduation thesis, the data used is 2015 brats challenge.

for example: MHA file

but i don't how to open the .mha files by use python.I use the tensorflow framework, so it's more convenient to use python, and besides that, I need to do some preprocessing of the data graph.

from medpy.io import load
url = r'G:\path\to\mine.mha'
mage_data,image_header = load(url)

Then:

medpy.core.exceptions.DependencyError: Loading images of type Itk/Vtk MetaImage (.mhd, .mha/.raw) requires a third-party module that could not be encountered. Reason: No module named 'filter'.

---

The brats challenge is an international competition.But I don't know what network structure I'm supposed to use to train my network. If you have good advice, please let me know.

Answer 1

You can use MedPy package for this.

sudo apt-get install python-pip python-numpy python-scipy libboost-python-dev build-essential

Then:

sudo pip install nibabel pydicom medpy

And the Python usage:

from medpy.io import load
mage_data, image_header = load('/path/to/image.mha')

The library supports some useful preprocessing and analysis functions as well.

Good luck!