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# Paste this code into the Slicer Python console

pip_install('highresnet')

import SampleData
from highresnet.inference import infer
from highresnet.cli.download_oasis import download_oasis

input_path = download_oasis()
loadVolume(input_path)

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import numpy as np
import matplotlib.pyplot as plt

def fourier_transform(array: np.ndarray):
    transformed = np.fft.fftn(array)
    fshift = np.fft.fftshift(transformed)
    return fshift

def inv_fourier_transform(fshift: np.ndarray):
    f_ishift = np.fft.ifftshift(fshift)

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import tempfile
from pathlib import Path
from subprocess import call

# pip install moviepy opencv-python scikit-image face_recognition

import cv2
import numpy as np
from PIL import Image
from tqdm import tqdm

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# Last modified on the 14th of May, 2018
mkdir -p ~/git
cd ~/git

# Replace fepegar by your username on Inria Forge. You’ll be asked your password
user="fepegar"
# To clone the master branch:
git clone https://[email protected]/authscm/$user/git/morpheme-privat/morpheme-privat.git --depth 1

# Install zlib1g-dev if Linux

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mkdir -p $HOME/git
cd $HOME/git
git clone https://github.com/KCL-BMEIS/niftyreg.git --depth 1
cd niftyreg
mkdir build install
cd build

# This gave me trouble on a DGX
## If cmake is run just once, make may not work. Might be related to https://stackoverflow.com/q/47684410/3956024
#cmake -DCMAKE_INSTALL_PREFIX:STRING=../install -DUSE_CUDA:BOOL=ON -DCMAKE_C_COMPILER:STRING=/usr/bin/gcc-6 ..

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Locally

ssh-keygen -t rsa -b 4096 -C "[email protected]"  # generate the SSH key
xclip -sel clip < ~/.ssh/id_rsa.pub  # send the key to che clipboard
ssh [email protected]  # SSH to storm
ssh-add

On storm

[Add the previous key to ~/.ssh/authorized_keys], then

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import numpy as np
import SampleData


def getSampleVolume():
    # Download MRHead
    sampleDataLogic = SampleData.SampleDataLogic()
    volumeNode = sampleDataLogic.downloadMRHead()
    return volumeNode

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