# \#ct

**URL:** https://discourse.itk.org/tag/ct/143.md

[Latest](https://discourse.itk.org/latest.md) · [Categories](https://discourse.itk.org/categories.md) · [Tags](https://discourse.itk.org/tags.md)

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## [Is it possible to convert to Hounsfield Units in Sitk?](https://discourse.itk.org/t/is-it-possible-to-convert-to-hounsfield-units-in-sitk/5061)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 5\
**Last updated:** [August 14, 2023, 12:56pm UTC](https://discourse.itk.org/t/is-it-possible-to-convert-to-hounsfield-units-in-sitk/5061 "2023-08-14T12:56:09Z")

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Hi, Is there a function in SITK to convert the pixel values in dicom CT images to Hounsfield Units (HU) ? This is what I currently do: def transform\_to\_hu(slices): images = np.stack(\[file.pixel\_array for file in …

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## [Pre-processing segmentation mask](https://discourse.itk.org/t/pre-processing-segmentation-mask/5530)

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**Author:** [@DushiFdo](https://discourse.itk.org/u/DushiFdo)\
**Replies:** 9\
**Last updated:** [December 6, 2022, 7:31pm UTC](https://discourse.itk.org/t/pre-processing-segmentation-mask/5530 "2022-12-06T19:31:30Z")

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I am working with 3D CT images (Dicoms), and I performed several pre-processing steps on the input images such as resampling, normalizing, removing noise, crop image, resizing, crop center and reshaping to (128, 128, 128…

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## [How to remove the CT scanning bed with SimpleITK](https://discourse.itk.org/t/how-to-remove-the-ct-scanning-bed-with-simpleitk/5392)

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**Author:** [@kleingeo](https://discourse.itk.org/u/kleingeo)\
**Replies:** 8\
**Last updated:** [October 14, 2022, 12:25am UTC](https://discourse.itk.org/t/how-to-remove-the-ct-scanning-bed-with-simpleitk/5392 "2022-10-14T00:25:23Z")

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I currently have CT scans that have the scanner bed in the image. I was wondering if someone knew of a method to crop out the bed from the images with SimpleITK. I have seen some work using 3D Slicer, but as this is part…

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## [Reading in .ima 3D image files from CBCT](https://discourse.itk.org/t/reading-in-ima-3d-image-files-from-cbct/5184)

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**Author:** [@gmm9uf](https://discourse.itk.org/u/gmm9uf)\
**Replies:** 1\
**Last updated:** [July 14, 2022, 10:32pm UTC](https://discourse.itk.org/t/reading-in-ima-3d-image-files-from-cbct/5184 "2022-07-14T22:32:07Z")

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I have 3D CBCT images to analyze but am not sure how to read in these image files. Each image consists of about 400 .ima files (which I am assuming are 2D slices that together form the 3D image). I am able to read in eac…

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## [Spine CT and MRI images registration](https://discourse.itk.org/t/spine-ct-and-mri-images-registration/5146)

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**Author:** [@ainor](https://discourse.itk.org/u/ainor)\
**Replies:** 5\
**Last updated:** [July 5, 2022, 9:06am UTC](https://discourse.itk.org/t/spine-ct-and-mri-images-registration/5146 "2022-07-05T09:06:32Z")

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Hello, I am trying to make an automatic registration between CT and MRI images of the spine with ITK, the images are of the same person but they can have different sizes as the example that I show in the attached images. …

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## [Extract Overlapping Patches from a 3D Medical image and reconstruct the patches back to an Image](https://discourse.itk.org/t/extract-overlapping-patches-from-a-3d-medical-image-and-reconstruct-the-patches-back-to-an-image/3368)

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**Author:** [@DL\_Begin](https://discourse.itk.org/u/DL_Begin)\
**Replies:** 3\
**Last updated:** [August 7, 2020, 6:33pm UTC](https://discourse.itk.org/t/extract-overlapping-patches-from-a-3d-medical-image-and-reconstruct-the-patches-back-to-an-image/3368 "2020-08-07T18:33:30Z")

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Hello, I have a 3D CT image size of shape 284,143,143 and I want to extract 3D patches of size 64x64x64. Is there a way I can extract the patches from this volumetric image and reconstruct patches back. I have been usi…

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## [Resampling depth in 3D datasets](https://discourse.itk.org/t/resampling-depth-in-3d-datasets/2733)

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**Author:** [@TanjaIvanovska](https://discourse.itk.org/u/TanjaIvanovska)\
**Replies:** 2\
**Last updated:** [February 18, 2020, 8:16am UTC](https://discourse.itk.org/t/resampling-depth-in-3d-datasets/2733 "2020-02-18T08:16:13Z")

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Dear All, i want to resample a 3D dataset with original spacing (X\_o,Y\_o,Z\_o) to a new spacing, which differs from the original one only in depth (X\_o,Y\_o, Z\_new). This will result in the same spatial dimensions of imag…