The s3's discuss from janalipkova

How to generate atlas mask?

Thanks for sharing it. I have a question about atlas mask. It mentioned that

atlas_mask = binary mask of the atlas brain, the mask was created as a sum of segmented atlas anatomies

However, I opened it and it does not look likes probability map. Because different subject has different size of brain mask, so I expected the output must be a smooth probability. In my opinion, the mask that you gave us likes mask of a subject instead of a combination of multiple subjects

If I have ten raw image and its brain mask. Do you know how to create probability brain mask?

How to use gpu accelerate speed

Hi! Thanks sharing code, I just wanna know how to use gpu accelerate speed in batch processing?

Problems with types

I get this error when I try to execute the main example.

$ python3 s3.py -i example/T1.nii
Traceback (most recent call last):
  File "s3.py", line 1, in <module>
    from src.skull import SkullStripper
  File "/home/user/Programas/Skull-Stripping/src/skull.py", line 19, in <module>
    from nilearn.image import math_img
  File "/home/user/anaconda3/lib/python3.8/site-packages/nilearn/__init__.py", line 54, in <module>
    _check_module_dependencies()
  File "/home/user/anaconda3/lib/python3.8/site-packages/nilearn/version.py", line 111, in _check_module_dependencies
    _import_module_with_version_check(
  File "/home/user/anaconda3/lib/python3.8/site-packages/nilearn/version.py", line 60, in _import_module_with_version_check
    module = __import__(module_name)
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/__init__.py", line 64, in <module>
    from .base import clone
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/base.py", line 14, in <module>
    from .utils.fixes import signature
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/utils/__init__.py", line 14, in <module>
    from . import _joblib
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/utils/_joblib.py", line 22, in <module>
    from ..externals import joblib
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/__init__.py", line 119, in <module>
    from .parallel import Parallel
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/parallel.py", line 28, in <module>
    from ._parallel_backends import (FallbackToBackend, MultiprocessingBackend,
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/_parallel_backends.py", line 22, in <module>
    from .executor import get_memmapping_executor
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/executor.py", line 14, in <module>
    from .externals.loky.reusable_executor import get_reusable_executor
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/externals/loky/__init__.py", line 12, in <module>
    from .backend.reduction import set_loky_pickler
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/externals/loky/backend/reduction.py", line 125, in <module>
    from sklearn.externals.joblib.externals import cloudpickle  # noqa: F401
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/externals/cloudpickle/__init__.py", line 3, in <module>
    from .cloudpickle import *
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/externals/cloudpickle/cloudpickle.py", line 167, in <module>
    _cell_set_template_code = _make_cell_set_template_code()
  File "/home/user/anaconda3/lib/python3.8/site-packages/sklearn/externals/joblib/externals/cloudpickle/cloudpickle.py", line 148, in _make_cell_set_template_code
    return types.CodeType(
TypeError: an integer is required (got type bytes)

I found out that it may be due to the scikit-learn version (0.20.3).
I solved it by installing scikit-learn 0.22

janalipkova / s3 Goto Github PK

s3's Issues

How to generate atlas mask?

How to use gpu accelerate speed

Problems with types

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