NifTK/NiftyNet issues and pull requests

#489 - Segmentation classes description not available

Issue - State: open - Opened by AkhilaPhenomx over 3 years ago

#488 - dense-vnet to Monai

Issue - State: open - Opened by lroyer-star about 4 years ago - 1 comment

#487 - How to train a model with one input and multi-output?

Issue - State: open - Opened by amir-sanaat about 4 years ago

#486 - using other DL framework

Issue - State: open - Opened by szhang963 over 4 years ago

#485 - Niftynet window aggregator function for inferens - explaination needed

Issue - State: open - Opened by jamtheim over 4 years ago

#484 - NiftiNet Roadmap

Issue - State: closed - Opened by hjmjohnson over 4 years ago - 2 comments

#483 - Using NiftyNet to do segmentation of MRI scans(in .nii extension) to grey matter,white matter and csf

Issue - State: open - Opened by natli-think over 4 years ago

#482 - Segmentation configuration file fix

Pull Request - State: closed - Opened by eschnider over 4 years ago

#481 - Feature: Rewrite NiftyNet to use TensorFlow 2.0

Issue - State: open - Opened by snorrealm over 4 years ago - 1 comment

#480 - TensorRT frozen graphs - integration with NiftyNet

Issue - State: open - Opened by carlpe over 4 years ago

#479 - AdamW optimizer

Issue - State: open - Opened by bcdarwin almost 5 years ago

#478 - Sections containing `csv_data_file` are not loaded

Issue - State: open - Opened by javierbg almost 5 years ago

#477 - Added GAN parameter for logging generated images to Tensorboard

Pull Request - State: open - Opened by javierbg almost 5 years ago

#476 - Handle SimpleITK's lack of thread safety

Issue - State: open - Opened by bcdarwin almost 5 years ago

#475 - Fixed bug when logging discriminator loss for tensorboard in GAN application

Pull Request - State: closed - Opened by javierbg almost 5 years ago

#474 - Change file name in niftyreg_image_resampling: setup --> setup.py

Pull Request - State: closed - Opened by RafaelPalomar almost 5 years ago

#473 - Build and use niftyreg_image_resampling module

Pull Request - State: closed - Opened by RafaelPalomar almost 5 years ago

#472 - Float comparison in histogram normalisation layer

Issue - State: open - Opened by fepegar almost 5 years ago

#471 - Default values for the bias field layer might be too large

Issue - State: open - Opened by fepegar almost 5 years ago

#470 - Remove unconnected islands

Issue - State: open - Opened by carlpe almost 5 years ago

#469 - If Niftynet supports Xavier initialization?

Issue - State: open - Opened by lixin14222 almost 5 years ago

#468 - fixes #454

Pull Request - State: closed - Opened by wyli almost 5 years ago

#467 - Fixes #331 https://github.com/NifTK/NiftyNet/issues/331

Pull Request - State: closed - Opened by wyli almost 5 years ago

#466 - upgrade to support TF 1.15

Pull Request - State: closed - Opened by wyli almost 5 years ago

#465 - upgrade to support tensorflow 1.15

Issue - State: closed - Opened by wyli almost 5 years ago

#464 - Using GANs without conditioning

Issue - State: open - Opened by hasansari almost 5 years ago

#463 - Provided indices are out-of-bounds w.r.t. dense side with broadcasted shape. Histogram error?

Issue - State: closed - Opened by EndritPJ almost 5 years ago - 1 comment

#462 - Expected size of adding custom dataset for classification task on MR dataset?

Issue - State: open - Opened by Aliktk almost 5 years ago

#461 - Multi-GPU initialisation issue

Issue - State: closed - Opened by danieltudosiu about 5 years ago

#460 - Implement FixUp Layer

Issue - State: open - Opened by danieltudosiu about 5 years ago

#459 - Support for tensorflow 1.15

Issue - State: closed - Opened by tvercaut about 5 years ago - 1 comment

#458 - 457 subpixel convolution upgrade

Pull Request - State: closed - Opened by danieltudosiu about 5 years ago - 1 comment

#457 - SubPixel Convolution Upgrade

Issue - State: open - Opened by danieltudosiu about 5 years ago - 1 comment

#456 - Merge pull request #1 from NifTK/master

Pull Request - State: closed - Opened by zhanghaoyue about 5 years ago

#455 - How do I use 'vars_to_restore' and 'vars_to_freeze'

Issue - State: open - Opened by Endousan about 5 years ago

#454 - KeyError: 'total_loss' in deep_boosted_regression application

Issue - State: closed - Opened by hasansari about 5 years ago - 1 comment

#453 - fixes pip install dependencies

Pull Request - State: closed - Opened by wyli about 5 years ago

#452 - Add a warning about not using CI-skip syntax in commit message

Pull Request - State: closed - Opened by dzhoshkun about 5 years ago

#451 - Add changelog release notes for v0.6.0

Pull Request - State: closed - Opened by dzhoshkun about 5 years ago

#450 - update requirements

Pull Request - State: closed - Opened by wyli about 5 years ago

#449 - Getting High Error between the Patch in Generated images

Issue - State: open - Opened by IsaacLord about 5 years ago

#448 - FEATURE: different padding modes for different inputs

Issue - State: open - Opened by brynolff about 5 years ago

#447 - Problem with Installation of Niftynet (incompatible version of numpy and tensorbord between tensorflow and Niftynet)

Issue - State: closed - Opened by IsaacLord about 5 years ago - 8 comments

#446 - problems to run niftynet

Issue - State: open - Opened by yuniorcf about 5 years ago - 7 comments

#445 - GPU->CPU Memcpy failed (pip version of tensorflow)

Issue - State: closed - Opened by IsaacLord about 5 years ago - 3 comments

#444 - Fix weighted sampler

Pull Request - State: closed - Opened by fepegar about 5 years ago

#443 - CRITICAL:niftynet: Don't know how to generate sampling locations: Spatial dimensions of the grouped input sources are not consistent. {(512, 512, 102), (512, 512, 92)} 2019-09-27 17:21:51.189240: W tensorflow/core/framework/op_kernel.cc:1261] Unimplemented: NotImplementedError:

Issue - State: closed - Opened by zhaoxiaoqian666 about 5 years ago - 7 comments

#442 - fixes customised config parameters

Pull Request - State: closed - Opened by wyli about 5 years ago

#441 - How does the mask operation work? Train with Image/Label/Mask and test only with "image".

Issue - State: closed - Opened by maz369 about 5 years ago - 1 comment

#440 - Fix misleading error message

Pull Request - State: closed - Opened by eschnider about 5 years ago

#439 - Fix spatial dims error message

Pull Request - State: closed - Opened by eschnider about 5 years ago - 1 comment

#438 - what does iteration mean in the configuration file?

Issue - State: open - Opened by 12neurotool about 5 years ago - 1 comment
Labels: question, documentation

#437 - Overlap in window outputs with border parameter

Issue - State: open - Opened by manuel-lincbiotech about 5 years ago

#436 - GPU->CPU Memcpy failed

Issue - State: closed - Opened by talmazov about 5 years ago - 6 comments
Labels: bug

#435 - Control the GPU memory allocation

Issue - State: closed - Opened by carlpe about 5 years ago - 6 comments

#434 - fixes https://github.com/NifTK/NiftyNet/issues/245

Pull Request - State: closed - Opened by wyli about 5 years ago

#433 - Segmentation evaluation creates accumulative n_pos_ref across all labels.

Issue - State: closed - Opened by carlpe about 5 years ago - 1 comment

#432 - Unexpected behaviour of weighted sampler

Issue - State: closed - Opened by fepegar about 5 years ago - 2 comments
Labels: bug, work in progress

#431 - Merging GitHub PR 430

Pull Request - State: closed - Opened by wyli over 5 years ago

#430 - ENH: Squeeze internal 5d representation back to 2d or 3d

Pull Request - State: closed - Opened by hjmjohnson over 5 years ago

#429 - Classification task

Issue - State: closed - Opened by ProofOC over 5 years ago
Labels: help wanted

#428 - Why are the preprocessing layers deepcopied?

Issue - State: closed - Opened by fepegar over 5 years ago - 3 comments
Labels: help wanted

#427 - Segmentation loss

Issue - State: closed - Opened by poorneshwaran over 5 years ago - 4 comments

#426 - custom optimization

Issue - State: open - Opened by poorneshwaran over 5 years ago - 2 comments

#426 - custom optimization

Issue - State: open - Opened by poorneshwaran over 5 years ago - 2 comments

#425 - Fix dead links

Pull Request - State: closed - Opened by fepegar over 5 years ago

#425 - Fix dead links

Pull Request - State: closed - Opened by fepegar over 5 years ago

#424 - Links to papers on https://niftynet.io/ not working

Issue - State: closed - Opened by fepegar over 5 years ago - 2 comments

#423 - Fixes model zoo unit tests

Pull Request - State: closed - Opened by wyli over 5 years ago - 2 comments

#423 - Fixes model zoo unit tests

Pull Request - State: closed - Opened by wyli over 5 years ago - 2 comments

#422 - mixup and mixmatch added

Pull Request - State: closed - Opened by Zach-ER over 5 years ago

#417 - Inference produces dotted segmentation output [deepmedic]

Issue - State: open - Opened by andreasstefani over 5 years ago - 3 comments

#412 - Training with images of different sizes

Issue - State: closed - Opened by bsc0001 over 5 years ago - 2 comments

#412 - Training with images of different sizes

Issue - State: closed - Opened by bsc0001 over 5 years ago - 2 comments

#405 - 142 csv reader nnhack

Pull Request - State: closed - Opened by csudre over 5 years ago

#394 - Feature: Provide input group functionality for NiftyNet

Issue - State: open - Opened by atbenmurray over 5 years ago
Labels: enhancement

#394 - Feature: Provide input group functionality for NiftyNet

Issue - State: open - Opened by atbenmurray over 5 years ago
Labels: enhancement

#393 - fixes aggregators output folder

Pull Request - State: closed - Opened by wyli over 5 years ago

#393 - fixes aggregators output folder

Pull Request - State: closed - Opened by wyli over 5 years ago

#390 - Refactor: Move image preprocessing fields that can vary by input to '[input_x]' section

Issue - State: open - Opened by atbenmurray over 5 years ago
Labels: enhancement

#390 - Refactor: Move image preprocessing fields that can vary by input to '[input_x]' section

Issue - State: open - Opened by atbenmurray over 5 years ago
Labels: enhancement

#384 - Go through all the ToDo and see/implement what is missing

Issue - State: closed - Opened by csudre over 5 years ago
Labels: enhancement

#381 - TensorflowTestCase makes our tests to be skipped in TF 1.13.1>=

Issue - State: closed - Opened by danieltudosiu over 5 years ago
Labels: bug

#381 - TensorflowTestCase makes our tests to be skipped in TF 1.13.1>=

Issue - State: closed - Opened by danieltudosiu over 5 years ago
Labels: bug

#367 - Consider switching to GitHub Pages to host the niftynet website

Issue - State: closed - Opened by tvercaut over 5 years ago - 6 comments
Labels: documentation

#367 - Consider switching to GitHub Pages to host the niftynet website

Issue - State: closed - Opened by tvercaut over 5 years ago - 6 comments
Labels: documentation

#365 - Upgrading Requirements to be compatible with Tensorflow 1.14.0rc0

Issue - State: closed - Opened by danieltudosiu over 5 years ago
Labels: work in progress

#365 - Upgrading Requirements to be compatible with Tensorflow 1.14.0rc0

Issue - State: closed - Opened by danieltudosiu over 5 years ago
Labels: work in progress

#352 - Feature Request: CONDA, Jupyter, Docker

Issue - State: open - Opened by agrawal123 over 5 years ago - 4 comments
Labels: enhancement

#350 - Loss stuck in DenseVnet training

Issue - State: open - Opened by KathrynSch over 5 years ago - 1 comment
Labels: help wanted

#349 - 124 apps as modules

Pull Request - State: open - Opened by stian-johnsen over 5 years ago - 1 comment
Labels: enhancement, work in progress

#333 - Self-generated data split file doesn't work properly

Issue - State: open - Opened by kwang-greenhand over 5 years ago - 2 comments

#331 - Classification using resnet cannot run through cifar10 dataset

Issue - State: closed - Opened by SouthMemory over 5 years ago - 9 comments
Labels: help wanted

#330 - How Do I Run a Simple GAN without any conditioning?

Issue - State: open - Opened by enochkan over 5 years ago - 3 comments
Labels: help wanted

#326 - cannot share and inference niftynet trained model

Issue - State: open - Opened by yuanpeng5 over 5 years ago - 7 comments
Labels: enhancement

#326 - cannot share and inference niftynet trained model

Issue - State: open - Opened by yuanpeng5 over 5 years ago - 7 comments
Labels: enhancement

#296 - DenseVnet Dice loss remains and does not fall

Issue - State: open - Opened by kye9216789 almost 6 years ago - 6 comments
Labels: help wanted

#289 - Evaluation doesn't consider save_seg_dir of Inference and compares lables to labels

Issue - State: open - Opened by C-nit almost 6 years ago - 1 comment
Labels: documentation

#275 - Vnet 3D segmentation: Train loss remains 0.99 all the time

Issue - State: open - Opened by qianjiangcn about 6 years ago - 2 comments
Labels: help wanted

#261 - batch() missing 1 required positional argument: 'self'

Issue - State: closed - Opened by soodee about 6 years ago - 2 comments

GitHub / NifTK/NiftyNet issues and pull requests