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# SlicerEISeg | ||
# SlicerEISegMed3D | ||
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3D slicer extension for interactive medical image segmentation | ||
A 3D slicer extension for performing **E**fficient **I**nteractive **Seg**mentation on **Med**ical image in **3D**. Users will guide a deep learning model to perform segmentation by providing positive and negative points. | ||
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## Install | ||
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EISegMed3D depends on pypi packages paddlepaddle and paddleseg. You would need to install them before using this plugin. | ||
If you are just trying out this plugin, there is no prior installation steps requred. You will be prompted to install required packages when the plugin loads. | ||
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Open up the python terminal inside 3D Slicer and run the following code. | ||
To achieve the best performance, it's advised to install the GPU version of paddlepaddle before running this plugin. Steps are as follows: | ||
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1. Check your CUDA driver version. Choose the first version that's lower than yours from the followings: 11.6, 11.2, 11.1, 10.2, 10.1 | ||
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2. Remove the dot in the chosen version, eg: 11.6 -> 116, and replace the [CHOSEN VERSION] part in the following code with it. | ||
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```python | ||
import sys | ||
import os | ||
os.system(f"'{sys.executable}' -m pip install paddlepaddle paddleseg") | ||
slicer.app.processEvents() | ||
os.system(f"'{sys.executable}' -m pip install paddlepaddle-gpu==2.3.1.post[CHOSEN VERSION] -f https://www.paddlepaddle.org.cn/whl/linux/mkl/avx/stable.html")) | ||
``` | ||
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You should see the terminal print out 0. Anything else indicates the installation failed. | ||
For CUDA 11.6, the code you run should be: | ||
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```python | ||
import sys | ||
import os | ||
slicer.app.processEvents() | ||
os.system(f"'{sys.executable}' -m pip install paddlepaddle-gpu==2.3.1.post116 -f https://www.paddlepaddle.org.cn/whl/linux/mkl/avx/stable.html")) | ||
``` | ||
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The final line will only show up after installation finshes. If you started 3D Slicer from a terminal, you should be able to see pip install progress there. | ||
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The final line should output 0. Anything else indicates the installation has failed. | ||
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# Usage | ||
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Model parameters: |