# Latest

**URL:** https://discourse.itk.org/latest.md?page=62

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

**Page:** 63

---

## [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)

<div class="topic-metadata">

**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")

</div>

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…

---

## [My first Image Registration Tutorial](https://discourse.itk.org/t/my-first-image-registration-tutorial/3371)

<div class="topic-metadata">

**Author:** [@ibr](https://discourse.itk.org/u/ibr)\
**Replies:** 0\
**Last updated:** [August 8, 2020, 5:36pm UTC](https://discourse.itk.org/t/my-first-image-registration-tutorial/3371 "2020-08-08T17:36:41Z")

</div>

Dear all, I wrote a tutorial bout image registration trying to simplify and to explain the math behind it. A simple python implementation is used. Ths result is compared to ITK implementation. The tutorial is written a…

---

## [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)

<div class="topic-metadata">

**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")

</div>

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…

---

## [Patches for ITK 5.1.1](https://discourse.itk.org/t/patches-for-itk-5-1-1/3365)

<div class="topic-metadata">

**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 2\
**Last updated:** [August 6, 2020, 2:14pm UTC](https://discourse.itk.org/t/patches-for-itk-5-1-1/3365 "2020-08-06T14:14:46Z")

</div>

Hi folks, The next patch (bugfix) release, ITK 5.1.1, is coming up. Patches currently staged on the Git release branch are: Antoine Robert (1): ENH: Use Numpy bridge with array of dimension 1 Bradley Lowekamp (…

---

## [Question about ImageType::Pointer](https://discourse.itk.org/t/question-about-imagetype-pointer/3364)

<div class="topic-metadata">

**Author:** [@totoro3y](https://discourse.itk.org/u/totoro3y)\
**Replies:** 4\
**Last updated:** [August 6, 2020, 9:33am UTC](https://discourse.itk.org/t/question-about-imagetype-pointer/3364 "2020-08-06T09:33:28Z")

</div>

I am using the c++ library of ITK and I am trying to fulfill my first script of reading images. I ref https://itk.org/ITKExamples/src/IO/ImageBase/ReadAnImage/Documentation.html?highlight=read%20image for my codes. And I…

---

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

<div class="topic-metadata">

**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")

</div>

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

---

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

<div class="topic-metadata">

**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")

</div>

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 …

---

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

<div class="topic-metadata">

**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")

</div>

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…

---

## [registration is too slow and changing sample rate seems not working](https://discourse.itk.org/t/registration-is-too-slow-and-changing-sample-rate-seems-not-working/3356)

<div class="topic-metadata">

**Author:** [@aweib](https://discourse.itk.org/u/aweib)\
**Replies:** 2\
**Last updated:** [August 4, 2020, 1:55am UTC](https://discourse.itk.org/t/registration-is-too-slow-and-changing-sample-rate-seems-not-working/3356 "2020-08-04T01:55:37Z")

</div>

Hello everyone, I’m using ITK for 3D brain image registration, but the registration is too slow. I try to change the sample rate but it seems not working, reducing sample rate does not affect the registration speed. It …

---

## [ITK 4.13.3 available for download](https://discourse.itk.org/t/itk-4-13-3-available-for-download/3359)

<div class="topic-metadata">

**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [August 3, 2020, 10:51pm UTC](https://discourse.itk.org/t/itk-4-13-3-available-for-download/3359 "2020-08-03T22:51:34Z")

</div>

On behalf of the Insight Toolkit (ITK) Community, we are happy to announce the release of ITK 4.13.3! ITK is an open-source, cross-platform toolkit for N-dimensional scientific image processing, segmentation, and registr…

---

## [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)

<div class="topic-metadata">

**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")

</div>

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…

---

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

<div class="topic-metadata">

**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")

</div>

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?

---

## [Stack images in bottom to top manner](https://discourse.itk.org/t/stack-images-in-bottom-to-top-manner/3352)

<div class="topic-metadata">

**Author:** [@Hasna\_R](https://discourse.itk.org/u/Hasna_R)\
**Replies:** 5\
**Last updated:** [August 3, 2020, 4:19pm UTC](https://discourse.itk.org/t/stack-images-in-bottom-to-top-manner/3352 "2020-08-03T16:19:21Z")

</div>

Hi, I have 500 y slices of size 500 X 1000. I want to generate a volume of size 500,500,1000 \[1000 images with size 500X500\]. When I used paste filter ,i was not able to paste these slices in y direction. But I was abl…

---

## [Registration and StreamingImageFilter](https://discourse.itk.org/t/registration-and-streamingimagefilter/3347)

<div class="topic-metadata">

**Author:** [@marvin67](https://discourse.itk.org/u/marvin67)\
**Replies:** 2\
**Last updated:** [August 3, 2020, 10:16am UTC](https://discourse.itk.org/t/registration-and-streamingimagefilter/3347 "2020-08-03T10:16:08Z")

</div>

Hello, I need to register multi GB 3D images and my workstation is running out of memory all the time. In the documentation I have found the class StreamingImageFilter that can be used to process large images piece by pi…

---

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

<div class="topic-metadata">

**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")

</div>

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 …

---

## [Non-rigid registration in simpleITK: please help](https://discourse.itk.org/t/non-rigid-registration-in-simpleitk-please-help/3344)

<div class="topic-metadata">

**Author:** [@nvladimus](https://discourse.itk.org/u/nvladimus)\
**Replies:** 10\
**Last updated:** [July 30, 2020, 9:33pm UTC](https://discourse.itk.org/t/non-rigid-registration-in-simpleitk-please-help/3344 "2020-07-30T21:33:23Z")

</div>

Hi, everyone, I am trying to register (non-rigidly) two volumes of microscopy images, a head of C.elegans worm imaged with lightsheet microscope from two different directions. I managed to register them rigidly, but any…

---

## [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")

</div>

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 .

---

## [resample the registered moving image](https://discourse.itk.org/t/resample-the-registered-moving-image/3323)

<div class="topic-metadata">

**Author:** [@TJH123456](https://discourse.itk.org/u/TJH123456)\
**Replies:** 8\
**Last updated:** [July 28, 2020, 9:01am UTC](https://discourse.itk.org/t/resample-the-registered-moving-image/3323 "2020-07-28T09:01:46Z")

</div>

Hello I want to resample the registered moving image, set the angle to and the translation amount remains unchanged, but I’m not sure if I’m right. Should I set the conversion parameter to (0,0,0,0,0) or (0,0,0, x, y, z…

---

## [setparameters](https://discourse.itk.org/t/setparameters/3331)

<div class="topic-metadata">

**Author:** [@TJH123456](https://discourse.itk.org/u/TJH123456)\
**Replies:** 2\
**Last updated:** [July 28, 2020, 7:50am UTC](https://discourse.itk.org/t/setparameters/3331 "2020-07-28T07:50:47Z")

</div>

Hello If I set the setparameters function in the simpleitk package to (1, 0, 0, 0, 0, 0), how many degrees does the image rotate? thank you.

---

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

<div class="topic-metadata">

**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")

</div>

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…

---

## [How to just flip an image about z axes?](https://discourse.itk.org/t/how-to-just-flip-an-image-about-z-axes/3333)

<div class="topic-metadata">

**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 2\
**Last updated:** [July 27, 2020, 2:20am UTC](https://discourse.itk.org/t/how-to-just-flip-an-image-about-z-axes/3333 "2020-07-27T02:20:23Z")

</div>

I am working on simple ITK python. can I use Image\[:,:,::-1\] as we do usually in python? But it is changing the origin of the image. I just want to flip my image.

---

## [Registration of large images](https://discourse.itk.org/t/registration-of-large-images/3335)

<div class="topic-metadata">

**Author:** [@Bleach665](https://discourse.itk.org/u/Bleach665)\
**Replies:** 1\
**Last updated:** [July 26, 2020, 11:51pm UTC](https://discourse.itk.org/t/registration-of-large-images/3335 "2020-07-26T23:51:14Z")

</div>

Hi guys. I register relatively large images (larger than 10000x10000). Everything works fine, but the registration time is about a few hours. I think it would be good to reduce the images size, register, scale the tran…

---

## [How to Color 2D Dicom Image and 3D volume image? like the following...](https://discourse.itk.org/t/how-to-color-2d-dicom-image-and-3d-volume-image-like-the-following/3327)

<div class="topic-metadata">

**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 4\
**Last updated:** [July 26, 2020, 6:48am UTC](https://discourse.itk.org/t/how-to-color-2d-dicom-image-and-3d-volume-image-like-the-following/3327 "2020-07-26T06:48:23Z")

</div>

---

## [Don't lose data with rotation?](https://discourse.itk.org/t/dont-lose-data-with-rotation/3325)

<div class="topic-metadata">

**Author:** [@radiplab](https://discourse.itk.org/u/radiplab)\
**Replies:** 2\
**Last updated:** [July 24, 2020, 7:21pm UTC](https://discourse.itk.org/t/dont-lose-data-with-rotation/3325 "2020-07-24T19:21:13Z")

</div>

Hello. I’m rotating CTs with a Euler3DTransform. Currently any data that rotates out of the image array is lost. I’ve compensated for this by adding blank columns/rows/slices before rotating, and then taking away blank d…

---

## [Question about CompositeTransform](https://discourse.itk.org/t/question-about-compositetransform/3326)

<div class="topic-metadata">

**Author:** [@ktsumura](https://discourse.itk.org/u/ktsumura)\
**Replies:** 0\
**Last updated:** [July 23, 2020, 9:25pm UTC](https://discourse.itk.org/t/question-about-compositetransform/3326 "2020-07-23T21:25:02Z")

</div>

Hi, I have a question on CompositeTransform. The description of CompositeTransform says " This class concatenates transforms in reverse queue order by means of composition". I am wondering why the reverse queue is us…

---

## [TubeTK hepatic vessel registration workflow](https://discourse.itk.org/t/tubetk-hepatic-vessel-registration-workflow/3294)

<div class="topic-metadata">

**Author:** [@Henco](https://discourse.itk.org/u/Henco)\
**Replies:** 4\
**Last updated:** [July 23, 2020, 8:24pm UTC](https://discourse.itk.org/t/tubetk-hepatic-vessel-registration-workflow/3294 "2020-07-23T20:24:52Z")

</div>

Hello all, I recently read the Alward et al. paper on their unique way of registering blood vessels to DSAs. I’d like to implement it an ITK project and I found that group had created TubeTK. I’d like use TubeTK to regi…

---

## [Registration to get rid of slices containing part of the body not found in other scan](https://discourse.itk.org/t/registration-to-get-rid-of-slices-containing-part-of-the-body-not-found-in-other-scan/3313)

<div class="topic-metadata">

**Author:** [@ibro45](https://discourse.itk.org/u/ibro45)\
**Replies:** 3\
**Last updated:** [July 22, 2020, 1:59pm UTC](https://discourse.itk.org/t/registration-to-get-rid-of-slices-containing-part-of-the-body-not-found-in-other-scan/3313 "2020-07-22T13:59:56Z")

</div>

\[SimpleITK, Python, Registration\] I have a dataset of CT and CBCT scans; CBCTs don’t have a limited FOV, but they do contain a smaller portion of body compared to CT, i.e. they have less slices than CT scans. What I wa…

---

## [Save a displacement field as a nifti image with SimpleITK in Python](https://discourse.itk.org/t/save-a-displacement-field-as-a-nifti-image-with-simpleitk-in-python/3320)

<div class="topic-metadata">

**Author:** [@CYY](https://discourse.itk.org/u/CYY)\
**Replies:** 3\
**Last updated:** [July 22, 2020, 1:45pm UTC](https://discourse.itk.org/t/save-a-displacement-field-as-a-nifti-image-with-simpleitk-in-python/3320 "2020-07-22T13:45:33Z")

</div>

Hello everyone, I am a beginner of SimpleITK in python. I’ve saw that SimpleITK could save a displacement field as an image but I didn’t find how to do it. So are there anyone can help me please? Thank you very much.

---

## [itk-vtkglue swig error](https://discourse.itk.org/t/itk-vtkglue-swig-error/3309)

<div class="topic-metadata">

**Author:** [@SiPyWiFi](https://discourse.itk.org/u/SiPyWiFi)\
**Replies:** 2\
**Last updated:** [July 22, 2020, 5:54am UTC](https://discourse.itk.org/t/itk-vtkglue-swig-error/3309 "2020-07-22T05:54:47Z")

</div>

Hi, If i import the itk.ImageToVTKFilter(), I get the error: AttributeError: module 'itk.ITKVtkGluePython' has no attribute 'swig' I am using: itk==5.1.0.post3 vtk==8.1.2 itk-vtkglue==0.3.0 How can i solve this er…

---

## [Registering with Rigid and a tiny bit of Affine transform](https://discourse.itk.org/t/registering-with-rigid-and-a-tiny-bit-of-affine-transform/3311)

<div class="topic-metadata">

**Author:** [@nvladimus](https://discourse.itk.org/u/nvladimus)\
**Replies:** 4\
**Last updated:** [July 21, 2020, 9:26pm UTC](https://discourse.itk.org/t/registering-with-rigid-and-a-tiny-bit-of-affine-transform/3311 "2020-07-21T21:26:17Z")

</div>

Hi, everyone, My first post here, please be merciful. I am using simpleITK for 3D microscopy image registration, and it generally works well for rigid transformations. My moving image is a bit skewed, so I’d like to add…

[Previous page](https://discourse.itk.org/latest.md?page=61)

[Next page](https://discourse.itk.org/latest.md?page=63)