I am trying to run hd-bet in a Jupyter Notebook. I have an anaconda environment and I go into its location and install HD-BET. Once I have activated the environment and run 'hd-bet' in the command line I get the below output. Do you have any idea how to fix this? It doesn't give an error if I do it when not in the anaconda environment.
File "/home/jmcn735/fsl/fslpython/bin/hd-bet", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/home/jmcn735/fsl/fslpython/HD-BET/HD_BET/hd-bet", line 4, in
from HD_BET.run import run_hd_bet
File "/home/jmcn735/fsl/fslpython/HD-BET/HD_BET/run.py", line 4, in
from HD_BET.data_loading import load_and_preprocess, save_segmentation_nifti
File "/home/jmcn735/fsl/fslpython/HD-BET/HD_BET/data_loading.py", line 3, in
from skimage.transform import resize
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/skimage/transform/init.py", line 4, in
from .radon_transform import (radon, iradon, iradon_sart,
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/skimage/transform/radon_transform.py", line 5, in
from scipy.fft import fft, ifft, fftfreq, fftshift
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/init.py", line 91, in
from ._helper import next_fast_len
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/_helper.py", line 3, in
from ._pocketfft import helper as _helper
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/_pocketfft/init.py", line 3, in
from .basic import *
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/_pocketfft/basic.py", line 6, in
from . import pypocketfft as pfft
ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-39-x86_64-linux-gnu.so)
Hello,
I am trying to run hd-bet in a Jupyter Notebook. I have an anaconda environment and I go into its location and install HD-BET. Once I have activated the environment and run 'hd-bet' in the command line I get the below output. Do you have any idea how to fix this? It doesn't give an error if I do it when not in the anaconda environment.
File "/home/jmcn735/fsl/fslpython/bin/hd-bet", line 7, in
exec(compile(f.read(), file, 'exec'))
File "/home/jmcn735/fsl/fslpython/HD-BET/HD_BET/hd-bet", line 4, in
from HD_BET.run import run_hd_bet
File "/home/jmcn735/fsl/fslpython/HD-BET/HD_BET/run.py", line 4, in
from HD_BET.data_loading import load_and_preprocess, save_segmentation_nifti
File "/home/jmcn735/fsl/fslpython/HD-BET/HD_BET/data_loading.py", line 3, in
from skimage.transform import resize
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/skimage/transform/init.py", line 4, in
from .radon_transform import (radon, iradon, iradon_sart,
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/skimage/transform/radon_transform.py", line 5, in
from scipy.fft import fft, ifft, fftfreq, fftshift
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/init.py", line 91, in
from ._helper import next_fast_len
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/_helper.py", line 3, in
from ._pocketfft import helper as _helper
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/_pocketfft/init.py", line 3, in
from .basic import *
File "/home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/_pocketfft/basic.py", line 6, in
from . import pypocketfft as pfft
ImportError: /lib/x86_64-linux-gnu/libstdc++.so.6: version `GLIBCXX_3.4.30' not found (required by /home/jmcn735/fsl/fslpython/lib/python3.9/site-packages/scipy/fft/_pocketfft/pypocketfft.cpython-39-x86_64-linux-gnu.so)