https://github.com/natandrade/Tutorial-Medical-Image-Registration

Medical Image Registration
https://github.com/natandrade/Tutorial-Medical-Image-Registration

medical-image-analysis medical-image-processing medical-image-registration medical-imaging tutorial-medical-image-registration

Last synced: 3 days ago
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Medical Image Registration

• Host: GitHub
• URL: https://github.com/natandrade/Tutorial-Medical-Image-Registration
• Owner: natandrade
• Created: 2018-11-03T18:41:54.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2019-12-28T23:39:02.000Z (almost 5 years ago)
• Last Synced: 2024-08-03T01:15:03.744Z (3 months ago)
• Topics: medical-image-analysis, medical-image-processing, medical-image-registration, medical-imaging, tutorial-medical-image-registration
• Language: Jupyter Notebook
• Homepage:
• Size: 98.6 KB
• Stars: 205
• Watchers: 13
• Forks: 43
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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• awesome-image-alignment-and-stitching - [PDF&Slides

README

        
# This is a tutorial for anyone who wants to learn Medical Image Registration

![registrtation](https://user-images.githubusercontent.com/24567632/47958113-3b28e800-dfa3-11e8-8efb-205c9db8b3a6.png)

**The tutorial is divided into four parts:**

- **Pre / Pos - Processing:**

  - Intensity Normalization

  - Space Normalization

  - Brain Extraction

  - Validation

    

- **Registration with Classical Methodologies:**

  - [AIR](http://air.bmap.ucla.edu/AIR5/index.html)

  - [Demons Diffeomorfic](https://med.inria.fr/)

  - [DRAMMS](https://www.med.upenn.edu/sbia/dramms.html)

  - [DROP](http://www.mrf-registration.net/)

  - [Dartel](https://www.fil.ion.ucl.ac.uk/spm/)

  - [FLIRT](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)

  - [FNIRT](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)

  - [SyN](http://stnava.github.io/ANTs/)

  

- **Registration with Deep Learning**

  -  Learning to use Autoencoders (Autoencoder (shallow), Deep Autoencoder and Convolutional Autoencoder)

  

- **Interesting Platforms to Learn and Use**

  - [AFNI](https://afni.nimh.nih.gov/about_afni)

  - [ANTs](http://stnava.github.io/ANTs/)

  - [BIAL](https://github.com/GIBIS-UNIFESP/BIAL)

  - [FSL](https://fsl.fmrib.ox.ac.uk/fsl/fslwiki)

  - [Freesurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation)  

  - [3D Slicer](https://www.slicer.org/wiki/CitingSlicer)

  - [MedInria](https://med.inria.fr/) 

  - [Medpy](https://loli.github.io/medpy/)

  - [Nipype](https://nipype.readthedocs.io/en/latest/)

  - [NiftyReg](http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftyReg)

  

 

### Paper Sibgrapi (2018) -> A Practical Review on Medical Image Registration: from Rigid to Deep Learning based Approaches

http://sibgrapi.sid.inpe.br/col/sid.inpe.br/sibgrapi/2018/09.11.00.20/doc/Paper%20ID%20Tutorial-1.pdf

### Slides Tutorial: 

Part 1: http://www.imago.ufpr.br/sibgrapi2018/PART1-TUTORIAL_FUNDAMENTAL.pdf.pdf

Part 2 and 3: http://www.imago.ufpr.br/sibgrapi2018/tutorials.php

### Tutorial Videos: 

https://www.youtube.com/playlist?list=PLqoEuqQOzdkthOTuuXq4Ect4AS90lrsM5

### Coming soon: 

1) Undergraduate thesis: A Practical Review on Medical Image Registration

# Do not forget to cite the article and this content!:wink:

#### For more information visit: 

#### Group for Innovation Based on Images and Signals (GIBIS): http://gibis.unifesp.br/

#### Universidade Federal de São Paulo (UNIFESP) - Instituto de Ciência e Tecnologia (ICT) - BRASIL 

#### http://www.unifesp.br/campus/sjc/

#### AUTHOR: NaTaNdRaDe