# Uncategorized

**URL:** https://discourse.itk.org/c/uncategorized/1.md?no_subcategories=false&page=8

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

**Page:** 9

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## [How to set non-uniform spacing](https://discourse.itk.org/t/how-to-set-non-uniform-spacing/3715)

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**Author:** [@Anesh](https://discourse.itk.org/u/Anesh)\
**Replies:** 2\
**Last updated:** [December 21, 2020, 3:06pm UTC](https://discourse.itk.org/t/how-to-set-non-uniform-spacing/3715 "2020-12-21T15:06:47Z")

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Hello, I am reading in 2D multislice MRI data which contains e.g. 3 slices using the SetImportPointer for registration. The Z-slices are positioned at -101.25, -33.75 and -18.75 mm. I am confused on how to use the image…

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## [using the itk : GeodesicActiveContour](https://discourse.itk.org/t/using-the-itk-geodesicactivecontour/3642)

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**Author:** [@abir](https://discourse.itk.org/u/abir)\
**Replies:** 5\
**Last updated:** [November 30, 2020, 5:32pm UTC](https://discourse.itk.org/t/using-the-itk-geodesicactivecontour/3642 "2020-11-30T17:32:31Z")

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I used the MRI dataset provided by Left Atrial Segmentation Challenge 2013which was part of the STACOM’13 workshop this is the data I used test\_data training\_data I am suppose to segment the left atrium wall (epicrdi…

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## [Slice to Volume registration](https://discourse.itk.org/t/slice-to-volume-registration/3659)

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**Author:** [@aabbcc](https://discourse.itk.org/u/aabbcc)\
**Replies:** 3\
**Last updated:** [November 28, 2020, 2:06pm UTC](https://discourse.itk.org/t/slice-to-volume-registration/3659 "2020-11-28T14:06:35Z")

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I have a 3D microCT image about a tissue sample. And I use a ultramicrotome to get some ultrathin sections(slices) of the tissue. Then I get these slices’ 2D images using electron microscope. How can I use itk to registe…

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## [3D Image Registration with DICOM Series](https://discourse.itk.org/t/3d-image-registration-with-dicom-series/3641)

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**Author:** [@Jennsoo](https://discourse.itk.org/u/Jennsoo)\
**Replies:** 5\
**Last updated:** [November 22, 2020, 2:13pm UTC](https://discourse.itk.org/t/3d-image-registration-with-dicom-series/3641 "2020-11-22T14:13:26Z")

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Hello, I was performing registration between two modalities of brain and got weird results. It is hard to describe. It looks like some of the edges are highlighted. Is that normal? Here is my code.

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## [NumFocus ITK page](https://discourse.itk.org/t/numfocus-itk-page/3300)

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**Author:** [@dchen](https://discourse.itk.org/u/dchen)\
**Replies:** 7\
**Last updated:** [November 19, 2020, 7:26pm UTC](https://discourse.itk.org/t/numfocus-itk-page/3300 "2020-11-19T19:26:04Z")

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I was clicking around on the NumFocus ITK project page (https://numfocus.org/project/itk), and I noticed that the website link at the bottom of the page points to https://scikit-image.org/. Presumably it should point to…

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## [itkSimpleFuzzyConnectednessScalarImageFilter.h](https://discourse.itk.org/t/itksimplefuzzyconnectednessscalarimagefilter-h/1634)

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**Author:** [@zandarina](https://discourse.itk.org/u/zandarina)\
**Replies:** 6\
**Last updated:** [November 16, 2020, 9:28am UTC](https://discourse.itk.org/t/itksimplefuzzyconnectednessscalarimagefilter-h/1634 "2020-11-16T09:28:53Z")

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Dear all, I installed the itk and i found that this file is not installed itkSimpleFuzzyConnectednessScalarImageFilter.h I read that it is a patented algorithm and there migh be a directory for patented algorithms bu…

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## [Imaging Data Commons Webinar: November 16 @ 1pm Eastern](https://discourse.itk.org/t/imaging-data-commons-webinar-november-16-1pm-eastern/3607)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 0\
**Last updated:** [November 11, 2020, 1:41am UTC](https://discourse.itk.org/t/imaging-data-commons-webinar-november-16-1pm-eastern/3607 "2020-11-11T01:41:06Z")

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We will hold a webinar introducing NCI Imaging Data Commons this coming Monday Nov 16 at 1pm. Please see details at the event page below:

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## [CT patient bed and clothing removal from dicom files](https://discourse.itk.org/t/ct-patient-bed-and-clothing-removal-from-dicom-files/3278)

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**Author:** [@Gokce\_Guven](https://discourse.itk.org/u/Gokce_Guven)\
**Replies:** 6\
**Last updated:** [November 10, 2020, 6:35pm UTC](https://discourse.itk.org/t/ct-patient-bed-and-clothing-removal-from-dicom-files/3278 "2020-11-10T18:35:42Z")

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Hi, I need to remove patient bed, clothing etc. from CT (dicom file) but could not find a code and I am really new in medical analysis. I couldn’t find any HU value for bed, clothing etc as well to use as a threshold va…

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## [I read a stl file and want to convert it to image, How can i do using ITK?](https://discourse.itk.org/t/i-read-a-stl-file-and-want-to-convert-it-to-image-how-can-i-do-using-itk/3600)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 1\
**Last updated:** [November 5, 2020, 1:53pm UTC](https://discourse.itk.org/t/i-read-a-stl-file-and-want-to-convert-it-to-image-how-can-i-do-using-itk/3600 "2020-11-05T13:53:10Z")

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this is the stl 3D PolyData.

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## [How to create an image(like a line) and fused with 3D dicom images ?](https://discourse.itk.org/t/how-to-create-an-image-like-a-line-and-fused-with-3d-dicom-images/3579)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 4\
**Last updated:** [November 2, 2020, 2:24pm UTC](https://discourse.itk.org/t/how-to-create-an-image-like-a-line-and-fused-with-3d-dicom-images/3579 "2020-11-02T14:24:08Z")

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like the title, In fact, I want to create an image and fused with vtkImageData.

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## [Does SimpleITK image read from dicom series reflect the view of a 3D-object (axial, coronal and sagital)?](https://discourse.itk.org/t/does-simpleitk-image-read-from-dicom-series-reflect-the-view-of-a-3d-object-axial-coronal-and-sagital/3569)

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**Author:** [@nguyenhoa93](https://discourse.itk.org/u/nguyenhoa93)\
**Replies:** 3\
**Last updated:** [October 24, 2020, 1:53pm UTC](https://discourse.itk.org/t/does-simpleitk-image-read-from-dicom-series-reflect-the-view-of-a-3d-object-axial-coronal-and-sagital/3569 "2020-10-24T13:53:36Z")

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Hi, I am using SimpleITK to read 3D-CT scans from DICOM folders. My scans can belong to any of 3 views: axial, coronal, and sagittal. I did like this: import SimpleITK as sitk dicom\_names = sitk.ImageSeriesReader().Get…

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## [IO DLLs not found](https://discourse.itk.org/t/io-dlls-not-found/3464)

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**Author:** [@simon.rit](https://discourse.itk.org/u/simon.rit)\
**Replies:** 7\
**Last updated:** [October 23, 2020, 7:39pm UTC](https://discourse.itk.org/t/io-dlls-not-found/3464 "2020-10-23T19:39:04Z")

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I am trying to setup the new CI infrastructure in RTK but the windows “build-test-cxx” fails, see When doing the same compilation locally, it turns out that the IO DLLs (ITKIOGDCM-5.2.dll, ITKIOTIFF-5.2.dll, ITKIOMe…

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## [\[sitk.ImageFileWriter()\] Unable to read a saved image when moved to a different location](https://discourse.itk.org/t/sitk-imagefilewriter-unable-to-read-a-saved-image-when-moved-to-a-different-location/3560)

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**Author:** [@pmody](https://discourse.itk.org/u/pmody)\
**Replies:** 1\
**Last updated:** [October 22, 2020, 1:31pm UTC](https://discourse.itk.org/t/sitk-imagefilewriter-unable-to-read-a-saved-image-when-moved-to-a-different-location/3560 "2020-10-22T13:31:01Z")

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Hi, I save a file with .mha extension as follows. writer = sitk.ImageFileWriter() writer.SetFileName(filepath) writer.SetUseCompression(compression) writer.Execute(data) Problem I am able to read the file via s…

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## [How to process CT images one by one and save these images of one series in memory?](https://discourse.itk.org/t/how-to-process-ct-images-one-by-one-and-save-these-images-of-one-series-in-memory/3489)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 12\
**Last updated:** [October 10, 2020, 9:42pm UTC](https://discourse.itk.org/t/how-to-process-ct-images-one-by-one-and-save-these-images-of-one-series-in-memory/3489 "2020-10-10T21:42:42Z")

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I have a series of CT images, now I want to process these images one by one, and save these images processed in memory as a 3D data? Then , I can convert this ITK 3D data to VTK image and visual.

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## [how to use itk c++ in jupiter notebooks?](https://discourse.itk.org/t/how-to-use-itk-c-in-jupiter-notebooks/3511)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [October 5, 2020, 9:15am UTC](https://discourse.itk.org/t/how-to-use-itk-c-in-jupiter-notebooks/3511 "2020-10-05T09:15:57Z")

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I have recently got to know that, we can use jupyter notebooks for running c++ codes also. How can we import ITK into it?

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## [How to print and stretch CT data value(the gray value)?](https://discourse.itk.org/t/how-to-print-and-stretch-ct-data-value-the-gray-value/3488)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 2\
**Last updated:** [September 28, 2020, 8:29pm UTC](https://discourse.itk.org/t/how-to-print-and-stretch-ct-data-value-the-gray-value/3488 "2020-09-28T20:29:36Z")

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How to print and stretch CT data value(the gray value)?

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## [converting 3d .zraw image into 2d .png](https://discourse.itk.org/t/converting-3d-zraw-image-into-2d-png/3476)

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**Author:** [@abir](https://discourse.itk.org/u/abir)\
**Replies:** 2\
**Last updated:** [September 22, 2020, 5:30am UTC](https://discourse.itk.org/t/converting-3d-zraw-image-into-2d-png/3476 "2020-09-22T05:30:08Z")

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I used a python code to convert my 3d image into png images but an error occured. Someone suggested me to use Simple itk. for every 3d image I should get 3 2d images (axial,coronal and sagittal vue ) Can any one help m…

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## [How to store certain indices in point set or a matrix?](https://discourse.itk.org/t/how-to-store-certain-indices-in-point-set-or-a-matrix/3459)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [September 14, 2020, 4:40pm UTC](https://discourse.itk.org/t/how-to-store-certain-indices-in-point-set-or-a-matrix/3459 "2020-09-14T16:40:05Z")

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I want to extract certain indices of segmentation from each slice of the image and store it in a point set or a matrix(I’m not sure which one to use). Upon that, I would like to perform singular value decomposition. How…

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## [convert rgb to rgba](https://discourse.itk.org/t/convert-rgb-to-rgba/3414)

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**Author:** [@Henco](https://discourse.itk.org/u/Henco)\
**Replies:** 4\
**Last updated:** [August 28, 2020, 5:29pm UTC](https://discourse.itk.org/t/convert-rgb-to-rgba/3414 "2020-08-28T17:29:03Z")

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Hi all, I’m attempting to convert an RGB pixel type image to a RGBA pixel type image, as I would like to be able to overlay it on another image and therefore need it to be slightly transparent. I tried to cast using itk…

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## [ITK in the Arctic Vault as part of the GitHub Archive Program](https://discourse.itk.org/t/itk-in-the-arctic-vault-as-part-of-the-github-archive-program/3412)

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**Author:** [@agirault](https://discourse.itk.org/u/agirault)\
**Replies:** 1\
**Last updated:** [August 26, 2020, 11:16pm UTC](https://discourse.itk.org/t/itk-in-the-arctic-vault-as-part-of-the-github-archive-program/3412 "2020-08-26T23:16:58Z")

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Note: I’m basically posting a duplicate of this post for VTK/vtk.js I got a notification today on my GitHub profile that I was an :snowflake:Artic Code Vault Contributor : This links to the GitHub Archive Prog…

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## [Create and save mesh inside of another mesh in .ply format](https://discourse.itk.org/t/create-and-save-mesh-inside-of-another-mesh-in-ply-format/3381)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 1\
**Last updated:** [August 17, 2020, 11:07pm UTC](https://discourse.itk.org/t/create-and-save-mesh-inside-of-another-mesh-in-ply-format/3381 "2020-08-17T23:07:10Z")

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I want to create and save a mesh inside of another mesh. I just create and render it as below using VTK, but how I can save this as to a single .ply file? If so how can I do that? On the other hand, I can give opacity …

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## [I want to rotate my image by a given angle.](https://discourse.itk.org/t/i-want-to-rotate-my-image-by-a-given-angle/3370)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [August 10, 2020, 1:03pm UTC](https://discourse.itk.org/t/i-want-to-rotate-my-image-by-a-given-angle/3370 "2020-08-10T13:03:52Z")

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I don’t actually get this concept of rotation. Does it happen about the origin? or about the centre of the image? Which coordinates? Which transform should I use for rotation when I have only angle of rotation. and my i…

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## [Software Guide download links are broken](https://discourse.itk.org/t/software-guide-download-links-are-broken/3367)

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**Author:** [@opoplawski](https://discourse.itk.org/u/opoplawski)\
**Replies:** 1\
**Last updated:** [August 6, 2020, 3:15am UTC](https://discourse.itk.org/t/software-guide-download-links-are-broken/3367 "2020-08-06T03:15:41Z")

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The download links for the SoftwareGuide for the 4.13.3 release are broken.

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## [how can i use iterators in simpleITK python?](https://discourse.itk.org/t/how-can-i-use-iterators-in-simpleitk-python/3363)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [August 5, 2020, 1:03pm UTC](https://discourse.itk.org/t/how-can-i-use-iterators-in-simpleitk-python/3363 "2020-08-05T13:03:35Z")

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I worked on iterators in ITK. I wonder if there is any way to use them in simpleITK? If not, what is the alternative? For example, I want to write compare two images and compute some similarity measure(in my case it is …

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## [rotate the image](https://discourse.itk.org/t/rotate-the-image/3340)

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**Author:** [@TJH123456](https://discourse.itk.org/u/TJH123456)\
**Replies:** 5\
**Last updated:** [August 5, 2020, 12:48pm UTC](https://discourse.itk.org/t/rotate-the-image/3340 "2020-08-05T12:48:57Z")

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Hello I have a problem that I can’t think about. I rotate the image with setparameters() function by 1 radian on the Z axis, and then calculate the mutual information value A between the graph and the fixed image. The m…

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## [Extract list of non zero pixels of a binary image](https://discourse.itk.org/t/extract-list-of-non-zero-pixels-of-a-binary-image/3355)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [August 3, 2020, 6:50pm UTC](https://discourse.itk.org/t/extract-list-of-non-zero-pixels-of-a-binary-image/3355 "2020-08-03T18:50:17Z")

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i want to extract non-zero pixels into a separate array. and later I want to find covariance matrix, followed by eigen values and vectors to find the direction . How can I do this using simple itk? Can I just transform…

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## [CT brain extraction](https://discourse.itk.org/t/ct-brain-extraction/3086)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 5\
**Last updated:** [August 3, 2020, 6:31pm UTC](https://discourse.itk.org/t/ct-brain-extraction/3086 "2020-08-03T18:31:22Z")

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I want to remove the skull from CT images. I have been through SkullStripping.cxx code. I do not have a brain mask. Instead, I have skull mask. Is there any other resource that I could look into?

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## [Metric to Compare two images using SimpleITK](https://discourse.itk.org/t/metric-to-compare-two-images-using-simpleitk/3351)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [August 2, 2020, 9:37pm UTC](https://discourse.itk.org/t/metric-to-compare-two-images-using-simpleitk/3351 "2020-08-02T21:37:46Z")

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Im currently using sitk and using conversions to numpy, I am able to perform few operations. I want to know the metrics that are available to compare two image. Is there any direct metric to find correlation between two …

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## [Can I use other packages like openCV and scikitimage along with simpleitk ?](https://discourse.itk.org/t/can-i-use-other-packages-like-opencv-and-scikitimage-along-with-simpleitk/3343)

<div class="topic-metadata">

**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [July 29, 2020, 12:44pm UTC](https://discourse.itk.org/t/can-i-use-other-packages-like-opencv-and-scikitimage-along-with-simpleitk/3343 "2020-07-29T12:44:53Z")

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How can I use other packages like openCV and scikitimage along with simpleitk? When dealing with 2D slices, I want to implement few algorithms like houghtransform etc .

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## [CT resampling, padding issue](https://discourse.itk.org/t/ct-resampling-padding-issue/3308)

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**Author:** [@Gokce\_Guven](https://discourse.itk.org/u/Gokce_Guven)\
**Replies:** 5\
**Last updated:** [July 27, 2020, 9:50am UTC](https://discourse.itk.org/t/ct-resampling-padding-issue/3308 "2020-07-27T09:50:05Z")

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Hi, I need to resample my list of CT mhd files to a pixel spacing 1x1x1mm, and constant size such as (256x256x256) with the same origin and direction. I need to shift the origin as well. My main issue right now, is to h…

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