janalipkova / s3 Goto Github PK
View Code? Open in Web Editor NEWSkull stripping and brain tissue segmentation
License: GNU General Public License v3.0
Skull stripping and brain tissue segmentation
License: GNU General Public License v3.0
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
Hi! Thanks sharing code, I just wanna know how to use gpu accelerate speed in batch processing?
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?
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.