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synthflair

Synthetic FLAIR generation software

https://github.com/neurosainteanne/synthflair

Science Score: 44.0%

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    Scientific vocabulary similarity
    Low similarity (7.5%) to scientific vocabulary

Keywords

deep-learning generative-model mri mri-brain tensorflow
Last synced: 6 months ago · JSON representation ·

Repository

Synthetic FLAIR generation software

Basic Info
  • Host: GitHub
  • Owner: NeuroSainteAnne
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 2.03 MB
Statistics
  • Stars: 7
  • Watchers: 5
  • Forks: 2
  • Open Issues: 0
  • Releases: 0
Topics
deep-learning generative-model mri mri-brain tensorflow
Created about 5 years ago · Last pushed 10 months ago
Metadata Files
Readme License Citation

README.md

synthFLAIR

Software designed to convert MRI diffusion-weighted sequences into FLAIR sequences

Prerequisites

Python 3.8

Usage

First, clone the git directory :

git clone https://github.com/NeuroSainteAnne/synthFLAIR.git cd synthFLAIR/

Then install required modules:

pip install -r requirements.txt pip install jupyterlab

Open the jupyter notebook

jupyter notebook

Data preparation

Open the synthFLAIR-Dataprep in order to convert you NIFTI files in a Memmap format for model training

Model training

Open the synthFLAIR-Train notebook and follow instructions to train and save your model.

Alternatively, download the pre-trained weights available here.

Inference

Once the model is trained and saved, you can convert 4D NIFTI DWI volumes into synthFLAIR volumes with the synthFLAIR-Convert tool.

Orthanc module

Once the model is trained and saved, you can use the Orthanc module to automatically convert DWI volumes into FLAIR using a lightweight DICOM server. Follow the intructions at Orthanc Module Readme

Owner

  • Name: NeuroSainteAnne
  • Login: NeuroSainteAnne
  • Kind: organization

Citation (CITATION.cff) 

cff-version: 1.2.0
authors:
- family-names: "Benzakoun"
  given-names: "Joseph"
- family-names: "Deslys"
  given-names: "Marc-Antoine"
- family-names: "Legrand"
  given-names: "Laurence"
- family-names: "Hmeydia"
  given-names: "Ghazi"
- family-names: "Turc"
  given-names: "Guilaume"
- family-names: "Ben Hassen"
  given-names: "Wagih"
- family-names: "Charron"
  given-names: "Sylvain"
- family-names: "Debacker"
  given-names: "Clément"
- family-names: "Naggara"
  given-names: "Olivier"
- family-names: "Baron"
  given-names: "Jean-Claude"
- family-names: "Thirion"
  given-names: "Bertrand"
- family-names: "Oppenheim"
  given-names: "Catherine"
title: "Synthetic FLAIR as a Substitute for FLAIR Sequence in Acute Ischemic Stroke"
url: "https://github.com/NeuroSainteAnne/synthFLAIR"

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