Error reading mhd files with SimpleITK in Python
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I'm here again with another question regarding SimpleITK in python. I want to plot a .mhd image but I don't know how. I'm trying the function described here Reading *.mhd/*.raw format in python:
load_itk('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
But it is not reading the image:
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/IO/Meta/src/itkMetaImageIO.cxx:483:
itk::ERROR: MetaImageIO(0x3a83730): File cannot be read: /home/bianca/Documents/PythonProcessing/result-Edep.mhd for reading.
Reason: Success
I have tried with scikit image too...
img = io.imread('/home/bianca/Documents/PythonProcessing/result-Edep.mhd', plugin='simpleitk')
but I'm also getting an error message
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/IO/Meta/src/itkMetaImageIO.cxx:483:
itk::ERROR: MetaImageIO(0x3a84280): File cannot be read: /home/bianca/Documents/PythonProcessing/result-Edep.mhd for reading.
Reason: Success
Even with medpy
from medpy.io import load
image_data, image_header = load('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
Traceback (most recent call last):
File "<pyshell#17>", line 1, in <module>
image_data, image_header = load('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
File "medpy/io/load.py", line 201, in load
raise err
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 itk.
But I do have SimpleITK now. I don't understand what's going on... =(
python image-processing computer-vision itk simpleitk
asked Jul 24 '17 at 20:04
user
378
add a comment |
up vote
1
down vote
favorite
I'm here again with another question regarding SimpleITK in python. I want to plot a .mhd image but I don't know how. I'm trying the function described here Reading *.mhd/*.raw format in python:
load_itk('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
But it is not reading the image:
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/IO/Meta/src/itkMetaImageIO.cxx:483:
itk::ERROR: MetaImageIO(0x3a83730): File cannot be read: /home/bianca/Documents/PythonProcessing/result-Edep.mhd for reading.
Reason: Success
I have tried with scikit image too...
img = io.imread('/home/bianca/Documents/PythonProcessing/result-Edep.mhd', plugin='simpleitk')
but I'm also getting an error message
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/IO/Meta/src/itkMetaImageIO.cxx:483:
itk::ERROR: MetaImageIO(0x3a84280): File cannot be read: /home/bianca/Documents/PythonProcessing/result-Edep.mhd for reading.
Reason: Success
Even with medpy
from medpy.io import load
image_data, image_header = load('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
Traceback (most recent call last):
File "<pyshell#17>", line 1, in <module>
image_data, image_header = load('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
File "medpy/io/load.py", line 201, in load
raise err
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 itk.
But I do have SimpleITK now. I don't understand what's going on... =(
python image-processing computer-vision itk simpleitk
asked Jul 24 '17 at 20:04
user
378
add a comment |
up vote
1
down vote
favorite
up vote
1
down vote
favorite
I'm here again with another question regarding SimpleITK in python. I want to plot a .mhd image but I don't know how. I'm trying the function described here Reading *.mhd/*.raw format in python:
load_itk('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
But it is not reading the image:
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/IO/Meta/src/itkMetaImageIO.cxx:483:
itk::ERROR: MetaImageIO(0x3a83730): File cannot be read: /home/bianca/Documents/PythonProcessing/result-Edep.mhd for reading.
Reason: Success
I have tried with scikit image too...
img = io.imread('/home/bianca/Documents/PythonProcessing/result-Edep.mhd', plugin='simpleitk')
but I'm also getting an error message
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/IO/Meta/src/itkMetaImageIO.cxx:483:
itk::ERROR: MetaImageIO(0x3a84280): File cannot be read: /home/bianca/Documents/PythonProcessing/result-Edep.mhd for reading.
Reason: Success
Even with medpy
from medpy.io import load
image_data, image_header = load('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
Traceback (most recent call last):
File "<pyshell#17>", line 1, in <module>
image_data, image_header = load('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
File "medpy/io/load.py", line 201, in load
raise err
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 itk.
But I do have SimpleITK now. I don't understand what's going on... =(
python image-processing computer-vision itk simpleitk
asked Jul 24 '17 at 20:04
user
378
I'm here again with another question regarding SimpleITK in python. I want to plot a .mhd image but I don't know how. I'm trying the function described here Reading *.mhd/*.raw format in python:
load_itk('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
But it is not reading the image:
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/IO/Meta/src/itkMetaImageIO.cxx:483:
itk::ERROR: MetaImageIO(0x3a83730): File cannot be read: /home/bianca/Documents/PythonProcessing/result-Edep.mhd for reading.
Reason: Success
I have tried with scikit image too...
img = io.imread('/home/bianca/Documents/PythonProcessing/result-Edep.mhd', plugin='simpleitk')
but I'm also getting an error message
RuntimeError: Exception thrown in SimpleITK ReadImage: /tmp/SimpleITK-build/ITK/Modules/IO/Meta/src/itkMetaImageIO.cxx:483:
itk::ERROR: MetaImageIO(0x3a84280): File cannot be read: /home/bianca/Documents/PythonProcessing/result-Edep.mhd for reading.
Reason: Success
Even with medpy
from medpy.io import load
image_data, image_header = load('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
Traceback (most recent call last):
File "<pyshell#17>", line 1, in <module>
image_data, image_header = load('/home/bianca/Documents/PythonProcessing/result-Edep.mhd')
File "medpy/io/load.py", line 201, in load
raise err
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 itk.
But I do have SimpleITK now. I don't understand what's going on... =(
python image-processing computer-vision itk simpleitk
python image-processing computer-vision itk simpleitk
asked Jul 24 '17 at 20:04
user
378
asked Jul 24 '17 at 20:04
user
378
asked Jul 24 '17 at 20:04
user
378
asked Jul 24 '17 at 20:04
user
378
asked Jul 24 '17 at 20:04
user
378
378
add a comment |
add a comment |
2 Answers
2
active
oldest
votes
up vote
1
down vote
Is the file you are trying to read valid? You can check that using some other image displaying tool, e.g. ITK-SNAP or 3D Slicer. If either of these tools can open it, please tell us the version of SimpleITK you are using.
answered Jul 24 '17 at 22:11
Dženan
1,59911930
3
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
– g.stevo
Jul 24 '17 at 23:34
Dzenan, thank you for your answer! Now it's reading the file thanks to g.stevo clue (it was missing the raw file). However, now I don't know how to display the image... (I believe you can guess that I'm just a beginner =/)
– user
Jul 25 '17 at 18:42
Have you seen this: insightsoftwareconsortium.github.io/SimpleITK-Notebooks
– Dženan
Jul 25 '17 at 20:19
If the above notebooks don't help try googling "SimpleITK Python tutorial" and following something.
– Dženan
Jul 25 '17 at 20:21
@g.stevo Your comment should be an answer, since that's what I missed in my case. All the best!
– Бојан Матовски
Nov 15 at 14:00
add a comment |
up vote
0
down vote
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
answered Nov 19 at 0:37
g.stevo
40728
add a comment |
2 Answers
2
active
oldest
votes
2 Answers
2
active
oldest
votes
active
oldest
votes
active
oldest
votes
up vote
1
down vote
Is the file you are trying to read valid? You can check that using some other image displaying tool, e.g. ITK-SNAP or 3D Slicer. If either of these tools can open it, please tell us the version of SimpleITK you are using.
answered Jul 24 '17 at 22:11
Dženan
1,59911930
3
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
– g.stevo
Jul 24 '17 at 23:34
Dzenan, thank you for your answer! Now it's reading the file thanks to g.stevo clue (it was missing the raw file). However, now I don't know how to display the image... (I believe you can guess that I'm just a beginner =/)
– user
Jul 25 '17 at 18:42
Have you seen this: insightsoftwareconsortium.github.io/SimpleITK-Notebooks
– Dženan
Jul 25 '17 at 20:19
If the above notebooks don't help try googling "SimpleITK Python tutorial" and following something.
– Dženan
Jul 25 '17 at 20:21
@g.stevo Your comment should be an answer, since that's what I missed in my case. All the best!
– Бојан Матовски
Nov 15 at 14:00
add a comment |
up vote
1
down vote
Is the file you are trying to read valid? You can check that using some other image displaying tool, e.g. ITK-SNAP or 3D Slicer. If either of these tools can open it, please tell us the version of SimpleITK you are using.
answered Jul 24 '17 at 22:11
Dženan
1,59911930
3
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
– g.stevo
Jul 24 '17 at 23:34
Dzenan, thank you for your answer! Now it's reading the file thanks to g.stevo clue (it was missing the raw file). However, now I don't know how to display the image... (I believe you can guess that I'm just a beginner =/)
– user
Jul 25 '17 at 18:42
Have you seen this: insightsoftwareconsortium.github.io/SimpleITK-Notebooks
– Dženan
Jul 25 '17 at 20:19
If the above notebooks don't help try googling "SimpleITK Python tutorial" and following something.
– Dženan
Jul 25 '17 at 20:21
@g.stevo Your comment should be an answer, since that's what I missed in my case. All the best!
– Бојан Матовски
Nov 15 at 14:00
add a comment |
up vote
1
down vote
up vote
1
down vote
Is the file you are trying to read valid? You can check that using some other image displaying tool, e.g. ITK-SNAP or 3D Slicer. If either of these tools can open it, please tell us the version of SimpleITK you are using.
answered Jul 24 '17 at 22:11
Dženan
1,59911930
Is the file you are trying to read valid? You can check that using some other image displaying tool, e.g. ITK-SNAP or 3D Slicer. If either of these tools can open it, please tell us the version of SimpleITK you are using.
answered Jul 24 '17 at 22:11
Dženan
1,59911930
answered Jul 24 '17 at 22:11
Dženan
1,59911930
answered Jul 24 '17 at 22:11
Dženan
1,59911930
answered Jul 24 '17 at 22:11
Dženan
1,59911930
1,59911930
3
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
– g.stevo
Jul 24 '17 at 23:34
Dzenan, thank you for your answer! Now it's reading the file thanks to g.stevo clue (it was missing the raw file). However, now I don't know how to display the image... (I believe you can guess that I'm just a beginner =/)
– user
Jul 25 '17 at 18:42
Have you seen this: insightsoftwareconsortium.github.io/SimpleITK-Notebooks
– Dženan
Jul 25 '17 at 20:19
If the above notebooks don't help try googling "SimpleITK Python tutorial" and following something.
– Dženan
Jul 25 '17 at 20:21
@g.stevo Your comment should be an answer, since that's what I missed in my case. All the best!
– Бојан Матовски
Nov 15 at 14:00
add a comment |
3
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
– g.stevo
Jul 24 '17 at 23:34
Dzenan, thank you for your answer! Now it's reading the file thanks to g.stevo clue (it was missing the raw file). However, now I don't know how to display the image... (I believe you can guess that I'm just a beginner =/)
– user
Jul 25 '17 at 18:42
Have you seen this: insightsoftwareconsortium.github.io/SimpleITK-Notebooks
– Dženan
Jul 25 '17 at 20:19
If the above notebooks don't help try googling "SimpleITK Python tutorial" and following something.
– Dženan
Jul 25 '17 at 20:21
@g.stevo Your comment should be an answer, since that's what I missed in my case. All the best!
– Бојан Матовски
Nov 15 at 14:00
3
3
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
– g.stevo
Jul 24 '17 at 23:34
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
– g.stevo
Jul 24 '17 at 23:34
Dzenan, thank you for your answer! Now it's reading the file thanks to g.stevo clue (it was missing the raw file). However, now I don't know how to display the image... (I believe you can guess that I'm just a beginner =/)
– user
Jul 25 '17 at 18:42
Dzenan, thank you for your answer! Now it's reading the file thanks to g.stevo clue (it was missing the raw file). However, now I don't know how to display the image... (I believe you can guess that I'm just a beginner =/)
– user
Jul 25 '17 at 18:42
Have you seen this: insightsoftwareconsortium.github.io/SimpleITK-Notebooks
– Dženan
Jul 25 '17 at 20:19
Have you seen this: insightsoftwareconsortium.github.io/SimpleITK-Notebooks
– Dženan
Jul 25 '17 at 20:19
If the above notebooks don't help try googling "SimpleITK Python tutorial" and following something.
– Dženan
Jul 25 '17 at 20:21
If the above notebooks don't help try googling "SimpleITK Python tutorial" and following something.
– Dženan
Jul 25 '17 at 20:21
@g.stevo Your comment should be an answer, since that's what I missed in my case. All the best!
– Бојан Матовски
Nov 15 at 14:00
@g.stevo Your comment should be an answer, since that's what I missed in my case. All the best!
– Бојан Матовски
Nov 15 at 14:00
add a comment |
up vote
0
down vote
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
answered Nov 19 at 0:37
g.stevo
40728
add a comment |
up vote
0
down vote
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
answered Nov 19 at 0:37
g.stevo
40728
add a comment |
up vote
0
down vote
up vote
0
down vote
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
answered Nov 19 at 0:37
g.stevo
40728
MHD Files typically require an mhd header and a raw file that contains the image data - do you have both in the same directory with the mhd header pointing to the data?
answered Nov 19 at 0:37
g.stevo
40728
answered Nov 19 at 0:37
g.stevo
40728
answered Nov 19 at 0:37
g.stevo
40728
answered Nov 19 at 0:37
g.stevo
40728
40728
add a comment |
add a comment |
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