ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject

[gionanide]

Commands to reproduce

1. conda create --name myenv python=3.10
2. conda activate myenv
3. pip install --upgrade pip setuptools wheel (tried with and without)
4. pip install fastMONAI

Python -> Python 3.10.0

#######################################################################################
pip list
Package Version

---

aiofiles 23.2.1
annotated-types 0.7.0
anyio 4.6.2.post1
asttokens 2.4.1
beautifulsoup4 4.12.3
blis 1.0.1
catalogue 2.0.10
certifi 2024.8.30
charset-normalizer 3.4.0
click 8.1.7
click-option-group 0.5.6
cloudpathlib 0.20.0
cmake 3.31.0.1
comm 0.2.2
confection 0.1.5
contourpy 1.3.1
cycler 0.12.1
cymem 2.0.8
debugpy 1.8.9
decorator 5.1.1
Deprecated 1.2.15
distro 1.9.0
exceptiongroup 1.2.2
executing 2.1.0
fastai 2.7.12
fastapi 0.115.5
fastcore 1.5.55
fastdownload 0.0.7
fastMONAI 0.4.0.2
fastprogress 1.0.3
ffmpy 0.4.0
filelock 3.16.1
fonttools 4.55.0
fsspec 2024.10.0
gdown 5.2.0
gradio 5.6.0
gradio_client 1.4.3
h11 0.14.0
httpcore 1.0.7
httpx 0.27.2
huggingface-hub 0.26.2
humanize 4.11.0
idna 3.10
imagedata 2.1.3
imageio 2.36.0
importlib-metadata 6.11.0
importlib_resources 6.4.5
ipykernel 6.29.5
ipython 8.29.0
isodate 0.7.2
itk-core 5.4.0
itk-io 5.4.0
jedi 0.19.2
Jinja2 3.1.4
joblib 1.4.2
jupyter_client 8.6.3
jupyter_core 5.7.2
kiwisolver 1.4.7
langcodes 3.5.0
language_data 1.3.0
lit 18.1.8
marisa-trie 1.2.1
markdown-it-py 3.0.0
MarkupSafe 2.1.5
matplotlib 3.9.2
matplotlib-inline 0.1.7
mdurl 0.1.2
monai 1.2.0
mpmath 1.3.0
murmurhash 1.0.10
nest_asyncio 1.6.0
networkx 3.4.2
nibabel 5.3.2
numpy 2.0.2
nvidia-cublas-cu11 11.10.3.66
nvidia-cuda-cupti-cu11 11.7.101
nvidia-cuda-nvrtc-cu11 11.7.99
nvidia-cuda-runtime-cu11 11.7.99
nvidia-cudnn-cu11 8.5.0.96
nvidia-cufft-cu11 10.9.0.58
nvidia-curand-cu11 10.2.10.91
nvidia-cusolver-cu11 11.4.0.1
nvidia-cusparse-cu11 11.7.4.91
nvidia-nccl-cu11 2.14.3
nvidia-nvtx-cu11 11.7.91
opencv-python 4.10.0.84
orjson 3.10.11
packaging 24.2
pandas 2.2.3
parso 0.8.4
pexpect 4.9.0
pickleshare 0.7.5
pillow 11.0.0
pip 24.3.1
platformdirs 4.3.6
preshed 3.0.9
progressbar2 4.5.0
prompt_toolkit 3.0.48
psutil 6.1.0
ptyprocess 0.7.0
pure_eval 0.2.3
pydantic 2.10.1
pydantic_core 2.27.1
pydicom 2.4.4
pydub 0.25.1
Pygments 2.18.0
pynetdicom 1.5.7
pyparsing 3.2.0
PySocks 1.7.1
python-dateutil 2.8.2
python-magic 0.4.27
python-multipart 0.0.12
python-utils 3.9.0
pytz 2024.2
PyWavelets 1.7.0
PyYAML 6.0.2
pyzmq 26.2.0
requests 2.32.3
rich 13.9.4
ruff 0.8.0
safehttpx 0.1.1
scikit-build 0.18.1
scikit-image 0.19.3
scikit-learn 1.5.2
scipy 1.14.1
semantic-version 2.10.0
setuptools 75.6.0
shellingham 1.5.4
SimpleITK 2.4.0
six 1.16.0
smart-open 7.0.5
sniffio 1.3.1
sortedcontainers 2.4.0
soupsieve 2.6
spacy 3.8.2
spacy-legacy 3.0.12
spacy-loggers 1.0.5
srsly 2.4.8
stack-data 0.6.2
starlette 0.41.3
sympy 1.13.3
thinc 8.3.2
threadpoolctl 3.5.0
tifffile 2024.9.20
tomli 2.1.0
tomlkit 0.12.0
torch 2.0.1
torchio 0.18.91
torchvision 0.15.2
tornado 6.4.1
tqdm 4.67.0
traitlets 5.14.3
triton 2.0.0
typer 0.13.1
typing_extensions 4.12.2
tzdata 2024.2
urllib3 2.2.3
uvicorn 0.32.1
wasabi 1.1.3
wcwidth 0.2.13
weasel 0.4.1
websockets 12.0
wheel 0.45.0
wrapt 1.17.0
xlrd 2.0.1
xnat 0.6.2
zipp 3.21.0

#######################################################################################
conda list

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
aiofiles 23.2.1 pypi_0 pypi
annotated-types 0.7.0 pypi_0 pypi
anyio 4.6.2.post1 pypi_0 pypi
asttokens 2.4.1 pyhd8ed1ab_0 conda-forge
beautifulsoup4 4.12.3 pypi_0 pypi
blis 1.0.1 pypi_0 pypi
bzip2 1.0.8 h4bc722e_7 conda-forge
ca-certificates 2024.8.30 hbcca054_0 conda-forge
catalogue 2.0.10 pypi_0 pypi
certifi 2024.8.30 pypi_0 pypi
charset-normalizer 3.4.0 pypi_0 pypi
click 8.1.7 pypi_0 pypi
click-option-group 0.5.6 pypi_0 pypi
cloudpathlib 0.20.0 pypi_0 pypi
cmake 3.31.0.1 pypi_0 pypi
comm 0.2.2 pyhd8ed1ab_0 conda-forge
confection 0.1.5 pypi_0 pypi
contourpy 1.3.1 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
cymem 2.0.8 pypi_0 pypi
debugpy 1.8.9 py310hf71b8c6_0 conda-forge
decorator 5.1.1 pyhd8ed1ab_0 conda-forge
deprecated 1.2.15 pypi_0 pypi
distro 1.9.0 pypi_0 pypi
exceptiongroup 1.2.2 pyhd8ed1ab_0 conda-forge
executing 2.1.0 pyhd8ed1ab_0 conda-forge
fastai 2.7.12 pypi_0 pypi
fastapi 0.115.5 pypi_0 pypi
fastcore 1.5.55 pypi_0 pypi
fastdownload 0.0.7 pypi_0 pypi
fastmonai 0.4.0.2 pypi_0 pypi
fastprogress 1.0.3 pypi_0 pypi
ffmpy 0.4.0 pypi_0 pypi
filelock 3.16.1 pypi_0 pypi
fonttools 4.55.0 pypi_0 pypi
fsspec 2024.10.0 pypi_0 pypi
gdown 5.2.0 pypi_0 pypi
gradio 5.6.0 pypi_0 pypi
gradio-client 1.4.3 pypi_0 pypi
h11 0.14.0 pypi_0 pypi
httpcore 1.0.7 pypi_0 pypi
httpx 0.27.2 pypi_0 pypi
huggingface-hub 0.26.2 pypi_0 pypi
humanize 4.11.0 pypi_0 pypi
idna 3.10 pypi_0 pypi
imagedata 2.1.3 pypi_0 pypi
imageio 2.36.0 pypi_0 pypi
importlib-metadata 6.11.0 pypi_0 pypi
importlib-resources 6.4.5 pypi_0 pypi
ipykernel 6.29.5 pyh3099207_0 conda-forge
ipython 8.29.0 pyh707e725_0 conda-forge
isodate 0.7.2 pypi_0 pypi
itk-core 5.4.0 pypi_0 pypi
itk-io 5.4.0 pypi_0 pypi
jedi 0.19.2 pyhff2d567_0 conda-forge
jinja2 3.1.4 pypi_0 pypi
joblib 1.4.2 pypi_0 pypi
jupyter_client 8.6.3 pyhd8ed1ab_0 conda-forge
jupyter_core 5.7.2 pyh31011fe_1 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
kiwisolver 1.4.7 pypi_0 pypi
krb5 1.21.3 h659f571_0 conda-forge
langcodes 3.5.0 pypi_0 pypi
language-data 1.3.0 pypi_0 pypi
ld_impl_linux-64 2.43 h712a8e2_2 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 14.2.0 h77fa898_1 conda-forge
libgcc-ng 14.2.0 h69a702a_1 conda-forge
libgomp 14.2.0 h77fa898_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libsodium 1.0.20 h4ab18f5_0 conda-forge
libsqlite 3.47.0 hadc24fc_1 conda-forge
libstdcxx 14.2.0 hc0a3c3a_1 conda-forge
libstdcxx-ng 14.2.0 h4852527_1 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libzlib 1.3.1 hb9d3cd8_2 conda-forge
lit 18.1.8 pypi_0 pypi
marisa-trie 1.2.1 pypi_0 pypi
markdown-it-py 3.0.0 pypi_0 pypi
markupsafe 2.1.5 pypi_0 pypi
matplotlib 3.9.2 pypi_0 pypi
matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge
mdurl 0.1.2 pypi_0 pypi
monai 1.2.0 pypi_0 pypi
mpmath 1.3.0 pypi_0 pypi
murmurhash 1.0.10 pypi_0 pypi
ncurses 6.5 he02047a_1 conda-forge
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge
networkx 3.4.2 pypi_0 pypi
nibabel 5.3.2 pypi_0 pypi
numpy 2.0.2 pypi_0 pypi
nvidia-cublas-cu11 11.10.3.66 pypi_0 pypi
nvidia-cuda-cupti-cu11 11.7.101 pypi_0 pypi
nvidia-cuda-nvrtc-cu11 11.7.99 pypi_0 pypi
nvidia-cuda-runtime-cu11 11.7.99 pypi_0 pypi
nvidia-cudnn-cu11 8.5.0.96 pypi_0 pypi
nvidia-cufft-cu11 10.9.0.58 pypi_0 pypi
nvidia-curand-cu11 10.2.10.91 pypi_0 pypi
nvidia-cusolver-cu11 11.4.0.1 pypi_0 pypi
nvidia-cusparse-cu11 11.7.4.91 pypi_0 pypi
nvidia-nccl-cu11 2.14.3 pypi_0 pypi
nvidia-nvtx-cu11 11.7.91 pypi_0 pypi
opencv-python 4.10.0.84 pypi_0 pypi
openssl 3.4.0 hb9d3cd8_0 conda-forge
orjson 3.10.11 pypi_0 pypi
packaging 24.2 pyhff2d567_1 conda-forge
pandas 2.2.3 pypi_0 pypi
parso 0.8.4 pyhd8ed1ab_0 conda-forge
pexpect 4.9.0 pyhd8ed1ab_0 conda-forge
pickleshare 0.7.5 py_1003 conda-forge
pillow 11.0.0 pypi_0 pypi
pip 24.3.1 pyh8b19718_0 conda-forge
platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge
preshed 3.0.9 pypi_0 pypi
progressbar2 4.5.0 pypi_0 pypi
prompt-toolkit 3.0.48 pyha770c72_0 conda-forge
psutil 6.1.0 py310ha75aee5_0 conda-forge
ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge
pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge
pydantic 2.10.1 pypi_0 pypi
pydantic-core 2.27.1 pypi_0 pypi
pydicom 2.4.4 pypi_0 pypi
pydub 0.25.1 pypi_0 pypi
pygments 2.18.0 pyhd8ed1ab_0 conda-forge
pynetdicom 1.5.7 pypi_0 pypi
pyparsing 3.2.0 pypi_0 pypi
pysocks 1.7.1 pypi_0 pypi
python 3.10.0 h543edf9_3_cpython conda-forge
python-dateutil 2.8.2 pypi_0 pypi
python-magic 0.4.27 pypi_0 pypi
python-multipart 0.0.12 pypi_0 pypi
python-utils 3.9.0 pypi_0 pypi
python_abi 3.10 5_cp310 conda-forge
pytz 2024.2 pypi_0 pypi
pywavelets 1.7.0 pypi_0 pypi
pyyaml 6.0.2 pypi_0 pypi
pyzmq 26.2.0 py310h71f11fc_3 conda-forge
readline 8.2 h8228510_1 conda-forge
requests 2.32.3 pypi_0 pypi
rich 13.9.4 pypi_0 pypi
ruff 0.8.0 pypi_0 pypi
safehttpx 0.1.1 pypi_0 pypi
scikit-build 0.18.1 pypi_0 pypi
scikit-image 0.19.3 pypi_0 pypi
scikit-learn 1.5.2 pypi_0 pypi
scipy 1.14.1 pypi_0 pypi
semantic-version 2.10.0 pypi_0 pypi
setuptools 75.6.0 pyhff2d567_0 conda-forge
shellingham 1.5.4 pypi_0 pypi
simpleitk 2.4.0 pypi_0 pypi
six 1.16.0 pyh6c4a22f_0 conda-forge
smart-open 7.0.5 pypi_0 pypi
sniffio 1.3.1 pypi_0 pypi
sortedcontainers 2.4.0 pypi_0 pypi
soupsieve 2.6 pypi_0 pypi
spacy 3.8.2 pypi_0 pypi
spacy-legacy 3.0.12 pypi_0 pypi
spacy-loggers 1.0.5 pypi_0 pypi
sqlite 3.47.0 h9eae976_1 conda-forge
srsly 2.4.8 pypi_0 pypi
stack_data 0.6.2 pyhd8ed1ab_0 conda-forge
starlette 0.41.3 pypi_0 pypi
sympy 1.13.3 pypi_0 pypi
thinc 8.3.2 pypi_0 pypi
threadpoolctl 3.5.0 pypi_0 pypi
tifffile 2024.9.20 pypi_0 pypi
tk 8.6.13 noxft_h4845f30_101 conda-forge
tomli 2.1.0 pypi_0 pypi
tomlkit 0.12.0 pypi_0 pypi
torch 2.0.1 pypi_0 pypi
torchio 0.18.91 pypi_0 pypi
torchvision 0.15.2 pypi_0 pypi
tornado 6.4.1 py310ha75aee5_1 conda-forge
tqdm 4.67.0 pypi_0 pypi
traitlets 5.14.3 pyhd8ed1ab_0 conda-forge
triton 2.0.0 pypi_0 pypi
typer 0.13.1 pypi_0 pypi
typing_extensions 4.12.2 pyha770c72_0 conda-forge
tzdata 2024.2 pypi_0 pypi
urllib3 2.2.3 pypi_0 pypi
uvicorn 0.32.1 pypi_0 pypi
wasabi 1.1.3 pypi_0 pypi
wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge
weasel 0.4.1 pypi_0 pypi
websockets 12.0 pypi_0 pypi
wheel 0.45.0 pyhd8ed1ab_0 conda-forge
wrapt 1.17.0 pypi_0 pypi
xlrd 2.0.1 pypi_0 pypi
xnat 0.6.2 pypi_0 pypi
xz 5.2.6 h166bdaf_0 conda-forge
zeromq 4.3.5 h3b0a872_7 conda-forge
zipp 3.21.0 pyhd8ed1ab_0 conda-forge

#######################################################################################
ERROR
#######################################################################################
from fastMONAI.vision_all import *
#######################################################################################

ValueError Traceback (most recent call last)
Cell In[2], line 1
----> 1 from fastMONAI.vision_all import *

File ~/anaconda3/envs/fastmonai/lib/python3.10/site-packages/fastMONAI/vision_all.py:7
5 from .vision_loss import *
6 from .vision_metrics import *
----> 7 from .vision_inference import *
8 from .utils import *
9 from .external_data import *

File ~/anaconda3/envs/fastmonai/lib/python3.10/site-packages/fastMONAI/vision_inference.py:13
11 import numpy as np
12 from scipy.ndimage import label
---> 13 from skimage.morphology import remove_small_objects
14 from SimpleITK import DICOMOrient, GetArrayFromImage
15 from torchio import Resize, Image

File ~/anaconda3/envs/fastmonai/lib/python3.10/site-packages/skimage/init.py:151
147 # We are not importing the rest of the scikit during the build
148 # process, as it may not be compiled yet
149 else:
150 try:
--> 151 from ._shared import geometry
152 del geometry
153 except ImportError as e:

File ~/anaconda3/envs/fastmonai/lib/python3.10/site-packages/skimage/_shared/geometry.pyx:1, in init skimage._shared.geometry()

ValueError: numpy.dtype size changed, may indicate binary incompatibility. Expected 96 from C header, got 88 from PyObject