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DeepParcellation: fast and accurate brain MRI parcellation by deep learning

Project description

DeepParcellation Package

DeepParcellation: fast and accurate brain MRI parcellation by deep learning

Contributions

  • The project was initiated by Dr. Lim (abysslover) and Dr. Choi (yooha1003).
  • The code is written by Dr. Lim at Gwangju Alzheimer's & Related Dementias (GARD) Cohort Research Center (GARD CRC), Chosun University.
  • This research was conducted in collaborations with the following people: Eun-Cheon Lim1, Uk-Su Choi1, Yul-Wan Sung2, Kun-Ho Lee1 and Jungsoo Gim1.
  1. Gwangju Alzheimer's & Related Dementias (GARD) Cohort Research Center, Chosun University, Gwangju, Republic of Korea
  2. Kansei Fukushi Research Institute, Tohoku Fukushi University, Sendai, Miyagi, Japan
  • The manuscript will be available in the future.

Getting Started

A step-by-step tutorial is provided in the following sections.

Prerequisites

You should install CUDA-enabled GPU cards with at least 8GB GPU memory manufactured by nVidia, e.g., Titan XP.

Prepare T1-weighted MR images

  1. Convert MR images to Neuroimaging Informatics Technology Initiative (NIfTI) format.
  2. The parent directory name of a NIfTI file path will be used as Subject Id during prediction.
  3. You can specify either an input path of the NIfTI file or input direcotry of many NIfTI files.

Install DeepParcellation

  1. Install Anaconda
    • Download an Anaconda distribution: Link
  2. Create a Conda environment
	conda create -n deepparc python=3.8 -y
  1. Install DeepParcellation (CPU mode)
	conda activate deepparc
	pip install deepparcellation
  1. Install DeepParcellation (GPU mode)
	conda activate deepparc
	pip install deepparcellation
	conda install cudnn=7.6.5 -c anaconda -y
	conda install cudatoolkit=10.1.243 -c conda-forge -y
	pip uninstall tensorflow -y
	pip install tensorflow-gpu==2.2.0
	pip uninstall keras -y
	conda install keras-gpu=2.4.3 -c anaconda -y
  1. Install DeepParcellation (Force)
	conda activate deepparc
	pip install --force --no-dependencies deepparcellation
  1. Run DeepParcellation
	conda activate deepparc
	deepparcellation -o=/tmp/test --i=./subject-0-0000/test.nii.gz
	or
	deepparcellation -o=/tmp/test --i=./

NOTE:

  1. You must always activate the conda enviroment before running DeepParcellation if you opened a new console.
  2. You should install DeepParcellation with force parameter when all the other dependencies were manually met, i.e., you have installed tensorflow-macos, tensorflow-metal dependencies for Apple M1 chips.

Contact

Please contact abysslover@gmail.com if you have any questions about DeepParcellation.

Project details


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