# Latest

**URL:** https://discourse.itk.org/latest.md?page=58

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

**Page:** 59

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## [particle swarm optimizer](https://discourse.itk.org/t/particle-swarm-optimizer/3504)

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**Author:** [@pierrectl](https://discourse.itk.org/u/pierrectl)\
**Replies:** 8\
**Last updated:** [November 26, 2020, 12:42pm UTC](https://discourse.itk.org/t/particle-swarm-optimizer/3504 "2020-11-26T12:42:36Z")

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Hello everyone, I was wondering if itk developers provided a registration example between two 3d images using particle swarm optimizer ? Thank you

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## [Extract surface mesh from 3D binary mask images](https://discourse.itk.org/t/extract-surface-mesh-from-3d-binary-mask-images/3646)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 1\
**Last updated:** [November 24, 2020, 4:47pm UTC](https://discourse.itk.org/t/extract-surface-mesh-from-3d-binary-mask-images/3646 "2020-11-24T16:47:15Z")

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I have generated a segmentation mask for a CT volume and and saved it as a nifti format. This image volume consists of below set of categories. 0: Background (None of the following organs) 1: Liver 2: Bladder 3: Lung…

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## [How to pass C++ itk::Image to Python](https://discourse.itk.org/t/how-to-pass-c-itk-image-to-python/3547)

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**Author:** [@cchriste](https://discourse.itk.org/u/cchriste)\
**Replies:** 8\
**Last updated:** [November 24, 2020, 4:07pm UTC](https://discourse.itk.org/t/how-to-pass-c-itk-image-to-python/3547 "2020-11-24T16:07:11Z")

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We have a C++ application-specific class that uses an ITK image under the hood. We also expose a Python interface to our class from which we want to provide access to its itk::Image member. Best guess at how this might …

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## [How to compare a slice and its next?](https://discourse.itk.org/t/how-to-compare-a-slice-and-its-next/3645)

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**Author:** [@Enr\_Brunetti](https://discourse.itk.org/u/Enr_Brunetti)\
**Replies:** 0\
**Last updated:** [November 23, 2020, 6:16pm UTC](https://discourse.itk.org/t/how-to-compare-a-slice-and-its-next/3645 "2020-11-23T18:16:35Z")

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I have a series of CT slice and I want to compare these ones in the axial view, because I want to delete elements in the slice, that not appear in the following slices. Is there any function in ITK or OpenCV, that can pe…

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## [affine transform followed by translation understanding](https://discourse.itk.org/t/affine-transform-followed-by-translation-understanding/3643)

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**Author:** [@prms](https://discourse.itk.org/u/prms)\
**Replies:** 1\
**Last updated:** [November 23, 2020, 1:08am UTC](https://discourse.itk.org/t/affine-transform-followed-by-translation-understanding/3643 "2020-11-23T01:08:34Z")

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I’ve been trying affine transform with translation. There are a few things I noticed while using them. It might be due to my limited understanding of the subject matter. Any help is highly appreciated. The notebook with …

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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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## [Save itk image with custom voxel spacing](https://discourse.itk.org/t/save-itk-image-with-custom-voxel-spacing/3634)

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**Author:** [@farhan\_009](https://discourse.itk.org/u/farhan_009)\
**Replies:** 7\
**Last updated:** [November 20, 2020, 3:15am UTC](https://discourse.itk.org/t/save-itk-image-with-custom-voxel-spacing/3634 "2020-11-20T03:15:51Z")

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Hello everyone! I got output from the model which is a NumPy array of shape \[128,448,448 \] .I converted to itkobject using itk.image\_view\_from\_array(predicted\_label) and save the image with itkwrite .But shape of inpu…

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## [Fixed Mask Not Working as Expected](https://discourse.itk.org/t/fixed-mask-not-working-as-expected/1238)

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**Author:** [@zivy](https://discourse.itk.org/u/zivy)\
**Replies:** 15\
**Last updated:** [November 19, 2020, 8:58pm UTC](https://discourse.itk.org/t/fixed-mask-not-working-as-expected/1238 "2020-11-19T20:58:46Z")

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Hi all, Is the following a “bug” which should be addressed or a “feature” which should be circumvented: When using the fixed image mask as part of registration I expect that only points that are inside the mask will be…

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## [SimpleITK cast 4D image](https://discourse.itk.org/t/simpleitk-cast-4d-image/3638)

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**Author:** [@jonasteuwen](https://discourse.itk.org/u/jonasteuwen)\
**Replies:** 1\
**Last updated:** [November 19, 2020, 8:32pm UTC](https://discourse.itk.org/t/simpleitk-cast-4d-image/3638 "2020-11-19T20:32:23Z")

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The question is inspired by this reply: https://discourse.itk.org/t/weighted-average-over-temporal-dimension/3636/5 Shortly: I have an external intercept parameter -1024 and a SimpleITK image (4D) with an unsigned data …

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## [Weighted average over temporal dimension](https://discourse.itk.org/t/weighted-average-over-temporal-dimension/3636)

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**Author:** [@jonasteuwen](https://discourse.itk.org/u/jonasteuwen)\
**Replies:** 5\
**Last updated:** [November 19, 2020, 8:22pm UTC](https://discourse.itk.org/t/weighted-average-over-temporal-dimension/3636 "2020-11-19T20:22:58Z")

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Hello all. I have a bunch of 3D scans of the same subject over time joined in a 4D scan using (by JoinSeries) and I have a vector with the phase weights. To create a 3D approximation of this 4D object you might want to m…

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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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## [How can I use GetBufferAsInt64 in c#](https://discourse.itk.org/t/how-can-i-use-getbufferasint64-in-c/3623)

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**Author:** [@Anders\_G](https://discourse.itk.org/u/Anders_G)\
**Replies:** 4\
**Last updated:** [November 19, 2020, 12:15pm UTC](https://discourse.itk.org/t/how-can-i-use-getbufferasint64-in-c/3623 "2020-11-19T12:15:14Z")

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I want to access the raw data pointer of an image in simpleITK c#. (It will be sent to another native library.) I understand how to do it for types like sitkFloat32 and sitkInt32 since the GetBufferAsXXX returns a IntPtr…

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## [Patch extraction](https://discourse.itk.org/t/patch-extraction/3630)

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**Author:** [@a10227](https://discourse.itk.org/u/a10227)\
**Replies:** 2\
**Last updated:** [November 19, 2020, 11:32am UTC](https://discourse.itk.org/t/patch-extraction/3630 "2020-11-19T11:32:41Z")

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Good day, Could you please tell me, how I can save extracted patched from 3D image, so their original coordinates are preserved? My goal is to select some patches, so those, being combined together, form the original im…

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## [NCI Imaging Data Commons is live!](https://discourse.itk.org/t/nci-imaging-data-commons-is-live/3557)

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**Author:** [@fedorov](https://discourse.itk.org/u/fedorov)\
**Replies:** 1\
**Last updated:** [November 18, 2020, 3:30pm UTC](https://discourse.itk.org/t/nci-imaging-data-commons-is-live/3557 "2020-11-18T15:30:54Z")

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Today we are happy to announce the public release of the NCI Imaging Data Commons! Learn more about IDC in this blog post: https://datascience.cancer.gov/news-events/blog/imaging-data-commons-brings-power-cloud-cancer-r…

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## [The usage of ITK patented code](https://discourse.itk.org/t/the-usage-of-itk-patented-code/3628)

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**Author:** [@Nayra\_Ahmed](https://discourse.itk.org/u/Nayra_Ahmed)\
**Replies:** 1\
**Last updated:** [November 17, 2020, 2:15pm UTC](https://discourse.itk.org/t/the-usage-of-itk-patented-code/3628 "2020-11-17T14:15:40Z")

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I am trying to build an old version of ITK to use the patented code in it. I am building ITK-3.20 and I enabled the generation of the patented code but I still cannot use it. So I have two questions here: First: Any a…

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## [Problems with running HelloWorld project from documentation](https://discourse.itk.org/t/problems-with-running-helloworld-project-from-documentation/3627)

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**Author:** [@Stefan\_Radonjic](https://discourse.itk.org/u/Stefan_Radonjic)\
**Replies:** 1\
**Last updated:** [November 16, 2020, 1:58pm UTC](https://discourse.itk.org/t/problems-with-running-helloworld-project-from-documentation/3627 "2020-11-16T13:58:52Z")

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Hi there! I am just starting to learn about ITK so I’ve decided to start scanning documentation and learn as much as possible. While following instructions specified in section 2.5.1. I ran into following error: stefan…

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## [Using fuzzy connectedness algorithm](https://discourse.itk.org/t/using-fuzzy-connectedness-algorithm/3625)

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**Author:** [@Nayra\_Ahmed](https://discourse.itk.org/u/Nayra_Ahmed)\
**Replies:** 1\
**Last updated:** [November 16, 2020, 1:56pm UTC](https://discourse.itk.org/t/using-fuzzy-connectedness-algorithm/3625 "2020-11-16T13:56:17Z")

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Hi there, I want to use fuzzy connectedness algorithm in my project and I didn’t find it in the latest version. So how can I use it? Thanks in advance. Best Regards, Nayra

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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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## [Can the spatial domain of the sampling point set be specified for registration?](https://discourse.itk.org/t/can-the-spatial-domain-of-the-sampling-point-set-be-specified-for-registration/3610)

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**Author:** [@spencermanwell](https://discourse.itk.org/u/spencermanwell)\
**Replies:** 5\
**Last updated:** [November 13, 2020, 8:01pm UTC](https://discourse.itk.org/t/can-the-spatial-domain-of-the-sampling-point-set-be-specified-for-registration/3610 "2020-11-13T20:01:42Z")

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Hi there, I am looking at registration of whole-body CT image volumes, repeat scans of the same individual over several month span. My primary concern is efficiency, secondary concern is accuracy and so I am tuning care…

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## [How to save the coordinates of ROI for ITK-SNAP](https://discourse.itk.org/t/how-to-save-the-coordinates-of-roi-for-itk-snap/3614)

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**Author:** [@nguyenhoa93](https://discourse.itk.org/u/nguyenhoa93)\
**Replies:** 1\
**Last updated:** [November 13, 2020, 4:33pm UTC](https://discourse.itk.org/t/how-to-save-the-coordinates-of-roi-for-itk-snap/3614 "2020-11-13T16:33:20Z")

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Hello, I am using ITK-SNAP for visualization and define the bounding box of the heart region for 3D CT scans. I found that the features in Snake are so cool. ROI can help me do that easily but I can’t save the coordinat…

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## [Advice on a workflow for copying of a region-of-interest across different DICOM series](https://discourse.itk.org/t/advice-on-a-workflow-for-copying-of-a-region-of-interest-across-different-dicom-series/3601)

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**Author:** [@ctorti](https://discourse.itk.org/u/ctorti)\
**Replies:** 5\
**Last updated:** [November 13, 2020, 10:55am UTC](https://discourse.itk.org/t/advice-on-a-workflow-for-copying-of-a-region-of-interest-across-different-dicom-series/3601 "2020-11-13T10:55:26Z")

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Hello everyone, I’m working on a medical image processing workflow in Python using SimpleITK and could benefit from the experience of others. The goal: To copy a segment from a “Source” DICOM SEG to a “Target” DICOM SE…

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## [Multistage Registration using itkRegistrationMethodV4](https://discourse.itk.org/t/multistage-registration-using-itkregistrationmethodv4/3608)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 0\
**Last updated:** [November 11, 2020, 7:07pm UTC](https://discourse.itk.org/t/multistage-registration-using-itkregistrationmethodv4/3608 "2020-11-11T19:07:50Z")

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Hello, everyone. I am using itkRegistrationMethodV4 to perform a multistage registration: 1st stage is a 3D rigid transform, and the 2nd stage is a BsplineTransform. The problem I am stucking happens when I try to conn…

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## [BSpline Multiresolution error while setting Transform](https://discourse.itk.org/t/bspline-multiresolution-error-while-setting-transform/3562)

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**Author:** [@machadoL](https://discourse.itk.org/u/machadoL)\
**Replies:** 8\
**Last updated:** [November 11, 2020, 6:54pm UTC](https://discourse.itk.org/t/bspline-multiresolution-error-while-setting-transform/3562 "2020-11-11T18:54:29Z")

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Hello, everyone. I am writing a MULTISTAGE registration pipeline. 1st Stage is a 3D rigid one; the output is added into CompositTransform object; Then I set the CompositTransform as the initial transform of the Defo…

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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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## [Conversion of dicom image format to jpeg or png or bmp](https://discourse.itk.org/t/conversion-of-dicom-image-format-to-jpeg-or-png-or-bmp/3473)

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**Author:** [@Jigabytes](https://discourse.itk.org/u/Jigabytes)\
**Replies:** 6\
**Last updated:** [November 10, 2020, 7:03pm UTC](https://discourse.itk.org/t/conversion-of-dicom-image-format-to-jpeg-or-png-or-bmp/3473 "2020-11-10T19:03:29Z")

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Hi, I am try to get convert a dicom image into jpeg, png or bmp. I would like to know if converting the image array from dicom to jpeg or any other format results loss in image data information? Thanks,Jiten

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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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## [3D registration results not consistent between two metrics](https://discourse.itk.org/t/3d-registration-results-not-consistent-between-two-metrics/3598)

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**Author:** [@Anesh](https://discourse.itk.org/u/Anesh)\
**Replies:** 6\
**Last updated:** [November 9, 2020, 4:02pm UTC](https://discourse.itk.org/t/3d-registration-results-not-consistent-between-two-metrics/3598 "2020-11-09T16:02:27Z")

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Hello, I recently started using ITKv3 for 3D registration based on ImageRegistraton8.cxx Note that ITK is interfaced to another software for image processing. For testing purpose, I started with the 3D images (brainwe…

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## [shrinkFactor causing weird artefacts with sitk.DisplacementFieldTransform](https://discourse.itk.org/t/shrinkfactor-causing-weird-artefacts-with-sitk-displacementfieldtransform/3574)

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**Author:** [@jingxuan](https://discourse.itk.org/u/jingxuan)\
**Replies:** 8\
**Last updated:** [November 7, 2020, 7:03pm UTC](https://discourse.itk.org/t/shrinkfactor-causing-weird-artefacts-with-sitk-displacementfieldtransform/3574 "2020-11-07T19:03:38Z")

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Hi everyone. I’m new to SimpleITK. It’s been great so far and I’m hoping to do more with it. I’m trying to perform a dense deformable registration between two 3D volumes, initialized with an affine registration performe…

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## [Creating an image mosaic in SimpleITK](https://discourse.itk.org/t/creating-an-image-mosaic-in-simpleitk/3582)

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**Author:** [@user1](https://discourse.itk.org/u/user1)\
**Replies:** 4\
**Last updated:** [November 6, 2020, 9:28pm UTC](https://discourse.itk.org/t/creating-an-image-mosaic-in-simpleitk/3582 "2020-11-06T21:28:07Z")

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I’m new to SimpleITK and am looking to create an image mosaic of a large number of grayscale images (probability maps from binary segmentation of blood vessels) through sequential image registration. Since I’m quite new …

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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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