Nifti Data Handeling Tutorial for PyTorch

Nifti Dataending is .nii or .nii.gz.

Installation on Linux

Download the repository.

git clone https://github.com/mfmezger/nifti-tutorial.git

Install the requirements.txt.

cd nifti-tutorial  
pip install -r requirements.txt

Nifti Inspector

You can use the Nifti Inspector to visualize the Nifti Files with the Batchviewer Libary. (https://github.com/FabianIsensee/BatchViewer)

Installation of Batch Viewer

git clone https://github.com/FabianIsensee/BatchViewer.git
cd BatchViewer
pip install . 

Visualize niftis using Fiji

It is also possible to inspect the images using Fiji.

https://imagej.net/software/fiji/

Just install Fiji, then you can open the images easily by choosing File -> Open. If you want to open Dicom Images you have to open it as File -> Import -> Image Sequence.

Nifti to Pytorch File Converter

You can use this script to convert a nifti image with or without mask to a pytorch file (.pt). Just run: python nifti-2-pt-conversion.py

Torch inspector

This script allows to visualize the data that was created with the
python nifti-2-pt-conversion.py.

Nifti2D

This script converts a 3D Volume in 2D slices and from there into PNG Images. python nifti2D.py