koriavinash1 / deepbrainseg Goto Github PK

Fully automatic brain tumour segmentation using Deep 3-D convolutional neural networks

License: MIT License

Python 90.11% Tcl 9.89%

artificial-intelligence biomedical-image-analysis brain-segmentation brain-tumor brain-tumor-segmentation brats deep-convolutional-neural-networks deep-learning ensemble-learning medical-image-analysis segmentation

deepbrainseg's Introduction

Hi there, I'm Avinash 👋

🔭 I’m currently working on Interpretability and Causality research.
🌱 I love to code and contribute to Open Source.
💬 Ask me anything regarding my work, code and research here.
📫 How to reach me: [email protected]

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deepbrainseg's Issues

Related Import Error of deepseg

Describe the bug
While installing using git also facing the same issue.

To Reproduce
from DeepBrainSeg import deepSeg

ImportError: cannot import name 'deepSeg'

Please help!

UI improvements

Planning to shift to web-based or electron-based UI for brain tumor segmentation tool

Could you provide the docker?

These codes are very useful.
However, there are issues to install the older libraries.
Could you provide the docker for this code?
It will help to use without compbility issue of versions.

[Self-resolved, after a week] Unable to run on windows.

After running through a long cycle of installation on my Windows 10 machine, including trying either torch cpu or gpu, I finally got rid of all installation errors, apparently.

Afterward, upon invoking DeepBrainSegUI.py, via python 3, I get the following error:

Is it possible to state precisely what version of the main modules you use pertaining to this repository/pypi distribution?

**Despite having the latest pip installed, which is said to automatically install required versions, I am not sure that is the case here.

interpretability and uncertainty pipeline integration

pip install of DeepBrainSeg fails

Describe the bug
pip install DeepBrainSeg
Collecting DeepBrainSeg
Downloading DeepBrainSeg-0.2.1.tar.gz (37 kB)
ERROR: Could not find a version that satisfies the requirement torch==1.5.1 (from DeepBrainSeg) (from versions: 0.1.2, 0.1.2.post1, 0.1.2.post2)
ERROR: No matching distribution found for torch==1.5.1 (from DeepBrainSeg)

_pickle.UnpicklingError: invalid load key, '<'.

Hi! sorry, I'm not very good in python.
When i run "python DeepBrainSegUI.py" I have this error

invalid load key, '<'.
or
_pickle.UnpicklingError: invalid load key, '<'.

Deep Learning based skull stripping tool addition, to replace ANTs usage

Radiomic feature extraction pipeline

Pipeline implemented using pyradiomics: commit d66b4ce

Installation problem

Dear developer,

I'm trying to utilize this automatic tumor segmentation function in your toolbox.
Here I met some problem related to installation.
As you described,
I ran this commands:

git clone https://github.com/koriavinash1/DeepBrainSeg.git
cd DeepBrainSeg

So far so good, but after I ran:
python3 setup.py install
I received the error:

Installed /Users/ziqianwanglive.cn/opt/miniconda3/lib/python3.7/site-packages/pyradiomics-2.2.0-py3.7-macosx-10.9-x86_64.egg
Searching for scipypydensecrf
Reading https://pypi.org/simple/scipypydensecrf/
Couldn't find index page for 'scipypydensecrf' (maybe misspelled?)
Scanning index of all packages (this may take a while)
Reading https://pypi.org/simple/
No local packages or working download links found for scipypydensecrf
error: Could not find suitable distribution for Requirement.parse('scipypydensecrf').

The laptop I am using is Mac. The python version is 3.7.4
Do you have any idea about how to solve this problem?
Looking forward to your reply!

Best regards,
Ziqian