Questions tagged [niftynet]

NiftyNet is a TensorFlow-based open-source convolutional neural networks (CNNs) platform for research in medical image analysis and image-guided therapy.

NiftyNet is a TensorFlow-based open-source convolutional neural networks (CNNs) platform for research in medical image analysis and image-guided therapy.

The code is available via GitLab, or you can quickly get started with the PyPI module available here.

Features

NiftyNet currently supports medical image segmentation and generative adversarial networks. NiftyNet is not intended for clinical use. Other features of NiftyNet include:

  • Easy-to-customise interfaces of network components
  • Sharing networks and pre-trained models
  • Support for 2-D, 2.5-D, 3-D, 4-D inputs
  • Efficient discriminative training with multiple-GPU support
  • Implementation of recent networks (HighRes3DNet, 3D U-net, V-net, DeepMedic)
  • Comprehensive evaluation metrics for medical image segmentation

NiftyNet is released under the Apache License, Version 2.0. Please see the LICENSE file in the NiftyNet source code repository for details.

If you use NiftyNet in your work, please cite Gibson, Li et al. 2017. The NiftyNet platform originated in software developed for Li et. al. 2017.

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NiftyNet label_normalization for segmentation

I was using NiftyNet to do some segmentation project. For the Label_normalization option in Segmentation section, in my understanding it's converting the labels into "0,1,...", right? I may be wrong. So my questions are: How does this affect my…
Kai Wang
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Niftynet: autocontext_mr_ct_model_zoo error: Unknown keywords in config file

I have just started exploring NiftyNet.I am getting the following error when I try to run the autocontext_mr_ct_model_zoo. When I run the following command: python net_regress.py train \ -c…
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Promise12 Demo Inference Error

I am getting the following error when I try to run the inference part of the NiftyNet Promise12 Demo in Jupyter Notebook. AttributeError Traceback (most recent call last) in () …
YChen
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Dice_loss for validation set

I'm using NiftyNet to process MRI images. It seems that the main program has only two options: train, to update weights based on training set; inference, to predict. I want to adjust my hyperparameters using validation set, is there any…
Kai Wang
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Niftynet: error: argument --axcodes: list of strings expected

I have just started exploring NiftyNet, which I think will help me in my project. I am trying to train a network for segmentation using the segmentation_application. However I built my own config.ini file and when running net_run.py I receive the…
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BRATS17 arguments for net_run

Good evening, I am trying to reproduce the results from Wang et al. using their cascaded convoloutional network with NiftyNet. Nevertheless when trying to train the CNN with : net_run train -c train_whole_tumor_sagittal.ini --app…
Paulbd
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where is the default initilizer in the code?

I've tried find the default initilizer in the code but the framework is complicated, so I decided to directly ask here. Where can I find the default initializer? Is there any configuarable parameter in the 'ini' file?
John Kexul
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NiftyNet: How to load own data?

I spend some time read doc, but still don't understand: 1. how to load my own data 2. how the image - label are mapped 3. whether exist standard data format
LiFeiteng
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NIftyNet data organization

I want to use NiftyNet to implement Deep Learning on medical image processing. However, there is one thing I haven't figured out regarding the data input: how does it join the multi-modality images? I saw the demo of BRATS2017, they seems to use 4…
Kai Wang
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ZeroDivisionError: float division by zero during net_segment inference patch aggregation

I ran (on Ubuntu 16.04 in a Google Cloud VM Instance): net_segment inference -c for a binary segmentation problem using unet_2d with softmax and a (96,96,1) spatial window. This was after I trained my model for 10 epochs and saved…
jxc
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