Open mha image files in Python (2015 brats challenge dataset)
I want to use deep learning for medical image segmentation as my graduation thesis, the data used is 2015 brats challenge.
for example:
MHA file
but i don't how to open the .mha files by use python.I use the tensorflow framework, so it's more convenient to use python, and besides that, I need to do some preprocessing of the data graph.
from medpy.io import load
url = r'G:pathtomine.mha'
mage_data,image_header = load(url)
Then:
medpy.core.exceptions.DependencyError: Loading images of type Itk/Vtk MetaImage (.mhd, .mha/.raw) requires a third-party module that could not be encountered. Reason: No module named 'filter'.
The brats challenge is an international competition.But I don't know what network structure I'm supposed to use to train my network. If you have good advice, please let me know.
python tensorflow deep-learning
asked Nov 7 '17 at 6:45
hey6775hey6775
218
add a comment |
I want to use deep learning for medical image segmentation as my graduation thesis, the data used is 2015 brats challenge.
for example:
MHA file
but i don't how to open the .mha files by use python.I use the tensorflow framework, so it's more convenient to use python, and besides that, I need to do some preprocessing of the data graph.
from medpy.io import load
url = r'G:pathtomine.mha'
mage_data,image_header = load(url)
Then:
medpy.core.exceptions.DependencyError: Loading images of type Itk/Vtk MetaImage (.mhd, .mha/.raw) requires a third-party module that could not be encountered. Reason: No module named 'filter'.
The brats challenge is an international competition.But I don't know what network structure I'm supposed to use to train my network. If you have good advice, please let me know.
python tensorflow deep-learning
asked Nov 7 '17 at 6:45
hey6775hey6775
218
add a comment |
I want to use deep learning for medical image segmentation as my graduation thesis, the data used is 2015 brats challenge.
for example:
MHA file
but i don't how to open the .mha files by use python.I use the tensorflow framework, so it's more convenient to use python, and besides that, I need to do some preprocessing of the data graph.
from medpy.io import load
url = r'G:pathtomine.mha'
mage_data,image_header = load(url)
Then:
medpy.core.exceptions.DependencyError: Loading images of type Itk/Vtk MetaImage (.mhd, .mha/.raw) requires a third-party module that could not be encountered. Reason: No module named 'filter'.
The brats challenge is an international competition.But I don't know what network structure I'm supposed to use to train my network. If you have good advice, please let me know.
python tensorflow deep-learning
asked Nov 7 '17 at 6:45
hey6775hey6775
218
I want to use deep learning for medical image segmentation as my graduation thesis, the data used is 2015 brats challenge.
for example:
MHA file
but i don't how to open the .mha files by use python.I use the tensorflow framework, so it's more convenient to use python, and besides that, I need to do some preprocessing of the data graph.
from medpy.io import load
url = r'G:pathtomine.mha'
mage_data,image_header = load(url)
Then:
medpy.core.exceptions.DependencyError: Loading images of type Itk/Vtk MetaImage (.mhd, .mha/.raw) requires a third-party module that could not be encountered. Reason: No module named 'filter'.
The brats challenge is an international competition.But I don't know what network structure I'm supposed to use to train my network. If you have good advice, please let me know.
python tensorflow deep-learning
python tensorflow deep-learning
asked Nov 7 '17 at 6:45
hey6775hey6775
218
asked Nov 7 '17 at 6:45
hey6775hey6775
218
edited Nov 7 '17 at 15:11
hey6775
asked Nov 7 '17 at 6:45
hey6775hey6775
218
asked Nov 7 '17 at 6:45
hey6775hey6775
218
asked Nov 7 '17 at 6:45
hey6775hey6775
218
218
add a comment |
add a comment |
1 Answer
1
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oldest
votes
You can use MedPy package for this.
sudo apt-get install python-pip python-numpy python-scipy libboost-python-dev build-essential
Then:
sudo pip install nibabel pydicom medpy
And the Python usage:
from medpy.io import load
mage_data, image_header = load('/path/to/image.mha')
The library supports some useful preprocessing and analysis functions as well.
Good luck!
answered Nov 7 '17 at 11:51
rkellermrkellerm
3,22463878
,sorry,It seems that there have been some mistakes.
– hey6775
Nov 7 '17 at 15:08
add a comment |
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1 Answer
1
active
oldest
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1 Answer
1
active
oldest
votes
active
oldest
votes
active
oldest
votes
You can use MedPy package for this.
sudo apt-get install python-pip python-numpy python-scipy libboost-python-dev build-essential
Then:
sudo pip install nibabel pydicom medpy
And the Python usage:
from medpy.io import load
mage_data, image_header = load('/path/to/image.mha')
The library supports some useful preprocessing and analysis functions as well.
Good luck!
answered Nov 7 '17 at 11:51
rkellermrkellerm
3,22463878
,sorry,It seems that there have been some mistakes.
– hey6775
Nov 7 '17 at 15:08
add a comment |
You can use MedPy package for this.
sudo apt-get install python-pip python-numpy python-scipy libboost-python-dev build-essential
Then:
sudo pip install nibabel pydicom medpy
And the Python usage:
from medpy.io import load
mage_data, image_header = load('/path/to/image.mha')
The library supports some useful preprocessing and analysis functions as well.
Good luck!
answered Nov 7 '17 at 11:51
rkellermrkellerm
3,22463878
,sorry,It seems that there have been some mistakes.
– hey6775
Nov 7 '17 at 15:08
add a comment |
You can use MedPy package for this.
sudo apt-get install python-pip python-numpy python-scipy libboost-python-dev build-essential
Then:
sudo pip install nibabel pydicom medpy
And the Python usage:
from medpy.io import load
mage_data, image_header = load('/path/to/image.mha')
The library supports some useful preprocessing and analysis functions as well.
Good luck!
answered Nov 7 '17 at 11:51
rkellermrkellerm
3,22463878
You can use MedPy package for this.
sudo apt-get install python-pip python-numpy python-scipy libboost-python-dev build-essential
Then:
sudo pip install nibabel pydicom medpy
And the Python usage:
from medpy.io import load
mage_data, image_header = load('/path/to/image.mha')
The library supports some useful preprocessing and analysis functions as well.
Good luck!
answered Nov 7 '17 at 11:51
rkellermrkellerm
3,22463878
answered Nov 7 '17 at 11:51
rkellermrkellerm
3,22463878
answered Nov 7 '17 at 11:51
rkellermrkellerm
3,22463878
answered Nov 7 '17 at 11:51
rkellermrkellerm
3,22463878
3,22463878
,sorry,It seems that there have been some mistakes.
– hey6775
Nov 7 '17 at 15:08
add a comment |
,sorry,It seems that there have been some mistakes.
– hey6775
Nov 7 '17 at 15:08
,sorry,It seems that there have been some mistakes.
– hey6775
Nov 7 '17 at 15:08
,sorry,It seems that there have been some mistakes.
– hey6775
Nov 7 '17 at 15:08
add a comment |
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