Correct image and mask using command line

[Bassam]

Hi pyradiomics team,

kindly I imported DICOM images into 3D slicer and did segmentation and extract the features properly using 3D slicer, then I saved the image and the mask into file. now I wanna make sure that the same features I will get it If i used command line. Unfortunately, I did not get the features by command line using pyradiomics specifying the image and the mask and it showed me an error, here is the message I’ve got it:

C:\features>pyradiomics pancreas_image.nrrd pancreas_label.nrrd
[2019-12-04 22:13:22] E: radiomics.script: Feature extraction failed!
Traceback (most recent call last):
File “C:\Python27\lib\site-packages\pyradiomics-2.2.0.post35+g8da1db7-py2.7-win-amd64.egg\radiomics\scripts\segment.py”, line 70, in _extractFeatures
feature_vector.update(extractor.execute(imageFilepath, maskFilepath, label, label_channel))
File “C:\Python27\lib\site-packages\pyradiomics-2.2.0.post35+g8da1db7-py2.7-win-amd64.egg\radiomics\featureextractor.py”, line 273, in execute
boundingBox, correctedMask = imageoperations.checkMask(image, mask, **_settings)
File “C:\Python27\lib\site-packages\pyradiomics-2.2.0.post35+g8da1db7-py2.7-win-amd64.egg\radiomics\imageoperations.py”, line 239, in checkMask
raise ValueError('Image/Mask datatype or size mismatch. Potential fix: enable correctMask, see ’
ValueError: Image/Mask datatype or size mismatch. Potential fix: enable correctMask, see Documentation:Usage:Customizing the Extraction:Settings:correctMask for more information
Case-1_Image: C:\features\pancreas_image.nrrd
Case-1_Mask: C:\features\pancreas_label.nrrd

[pieper (Steve Pieper (Isomics, Inc.))]

You probably need to export to labelmap.

See:

The resolutions of segment and mri are different

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Aligning Segmentations and images using python

Dear all I have a problem to understand how to use Segmentations nrrd file with image files in Python. My problem is: I’m able to open a stack of images and its segmentations using pynrrd. However I can’t understand how to align the segmentation with the stack of images. Reading the header of the segmentation I can’t understand how to shift the segmentation to align with the original image. The same operation when performed in 3DSlicer is straightforward, and the alignment perfect. So, I …

[lassoan (Andras Lasso)]

To make things easier, we have made automated segmentation cropping optional. By default, extents of segmentation will match extents of master volume. Cropping can be enabled/disabled in the Save dialog’s additional options section. This feature is available in Slicer Preview Release that you download tomorrow or later.

[JoostJM (Joost Van Griethuysen)]

Alternatively, you can enable correctMask in the PyRadiomics configuration, which will resample the mask back to the image space.