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% Rodent Brain-mask Segmentation tool

Detail description: The ‘RodentMRISkullStripping’ is a python module designed to provide an automatic rodent skull stripping. This module is a deep-learning-based framework, U-Net, to automatically identify the rodent brain boundaries in MR images. The whole framework is implemented using Keras with TensorFlow as the backend.

Plese install the following package before using RodentMRISkullStripping:

  1. numpy, tensorflow, and keras ex: conda install numpy tensorflow keras

  2. SimpleITK ex: conda install -c https://conda.anaconda.org/simpleitk SimpleITK

  3. scikit-image ex: conda install -c conda-forge scikit-image

Instruction:

  1. install RodentMRISKullStripping 'pip install rbm3==0.0.5'
  2. Give the input and output folder, you should put all the image in NIfTI format in the input folder . 'rbm3 -s 0.2 ' -s: image resolution, this option could resample the image resolution (i.e., 0.1, 0.2 isotropic resolution) in the UNet