SimpleITK is a simplified, open-source interface to the United States National Library of Medicine’s Insight Segmentation and Registration Toolkit. The SimpleITK image analysis library is available in multiple programming languages including C++, Python, R, Java, C#, Lua, Ruby and Tcl.
Questions tagged [simpleitk]
221 questions
2
votes
1 answer
Install SimpleElastix for Python3 on macOS
I am using macOS Sierra 10.12.6, trying to install the SimpleElastix extension of SimpleITK. I have been following the instructions here. After I got it to work, it turned out the extension seems to be only included in SimpleITK when I use Python…
TomD
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- 2
2
votes
3 answers
Compute symmetric surface distances [Python]
I want to compute surface distance metrics between 2 binary objects, aka segmentations of liver tumors. I am looking to compute:
Average symmetric surface distance
Root mean square symmetric distance
Hausdorff distance (also known as maximum…
RMS
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2
votes
1 answer
sitk.GetArrayFromImage returns empty numpy array?
I am working with 3D MR image data. In order to calculate the histogram, I converted from sitk.Image to an numpy arrray of dimension 3. While I am able to display each axial slice using matplotlib, the numpy array is completely empty in all three…
DottedGlass
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2
votes
2 answers
Error reading mhd files with SimpleITK in Python
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…
user
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2
votes
1 answer
sudo easy_install for SimpleITK not that easy
So... I've tried several ways to download SimpleITK (pip install) on Python but it's not working at all! (Here: SimpleITK python 2.7.12 installation issue) Now I'm using easy_install and I get this error:
Searching for simpleitk
Reading…
user
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2
votes
2 answers
SimpleITK Selectively Alter Pixels / Slicing
I've loaded a CT scan in SimpleITK. I'd like to do a few things that are pretty simple in NumPy, but haven't figured out how to do them in SimpleITK. I'd like to do them in SimpleITK for speed.
# NumPy: Changes all values of 100 to now become…
Authman Apatira
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1
vote
0 answers
SimpleITK ImportError with fresh conda env
I have been having an issue installing SimpleITK>2.2. Fully reinstalled miniconda and I am still having issues. However, it works for SimpleITK<=2.1.1.1
Not sure what the issue is, but I’ve never had this sort of issue before. Not sure if it’s a…
krolic
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1
vote
1 answer
Images sizes not matched when downsampling then upsampling images
I am trying to downsample an image (for speed), run prediction, then upsample it back. Due to rounding, I get mismatches with the original image size for some pixel dimensions/voxel sizes. What is the best way to handle this?
Forward…
illan
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1
vote
2 answers
SimpleITK Filtering with sitk.ConnectedThresholdImageFilter() wrong output
I have tried many things to segment gray_matter, white_matter and cs_fluid images using sitk.ConnectedThresholdImageFilter(). unfortunately, I couldn't. Please, let me know what I am doing wrong.
Here is the example code:
data_dir = "
Burak
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1
vote
2 answers
read nifti files 3d slicer vs other methods
I have some nii.gz files which, when I open using imajeJ , or any python library such as SimpleITK or Monai I get a stack of MRI images, as if taken from top to bottom. That being said, when I open the same file with slicer, I also get a stack of…
Iliasp
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1
vote
1 answer
SimpleITK Python apply BinaryMorphologicalClosingImageFilter to a TIFF image
I am trying to apply a BinaryMorphologicalClosingImageFilter to a binary TIFF image to fill empty spaces between structures (where ImageJ Fill Holes doesn't help). Here is the code I use:
import SimpleITK as sitk
#Import TIFF image
image =…
Chris
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- 4
1
vote
0 answers
How to read a Multiframe Dicom file and display it as video using an UI
I am looking to find a way to read a DICOM file and display the multi frame DICOM file as a video in an UI, I tried reading the multi frame DICOM file using pydicom and I was able to get each frame and appended it into a list and I created a gif out…
RonKing
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1
vote
1 answer
3D Image co-registration between multiple subjects
When preforming image co-registration of multiple subjects, how should we select the reference image?
Can a randomly selected image form one dataset could be the reference image for an image from the other dataset?
If we do that, should all the…
Dushi Fdz
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1
vote
1 answer
SimpleITK.Show() generates error in ImageJ on Macbook
I'm struggling with imagej on Jupyter. This is part of the code that i'm running:
def ImageGen(a,b,x_0,y_0, sigma_x, sigma_y, theta ):
g=GaussianFunc(x_0,y_0,sigma_x,sigma_y,theta)
g2=sitk.GetImageFromArray(g)
res=a*g2+b
if…
zahra ameli
- 11
- 1
1
vote
2 answers
Skull stripping with python/simpleITK
I'm trying to perform a skull stripping with simpleITK in python.
I'm using the StripTsImageFilter function as follows:
#upload data
# Path of nii img
path = r'C:\Users\Kate\Jupyter\DataThesis\PROGRESSION\0003\fet.nii.gz'
# Read the .nii image with…
Kate
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