# Latest

**URL:** https://discourse.itk.org/latest.md?page=63

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

**Page:** 64

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## [Problem in extracting mnc file](https://discourse.itk.org/t/problem-in-extracting-mnc-file/3316)

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**Author:** [@Alsurayhi](https://discourse.itk.org/u/Alsurayhi)\
**Replies:** 2\
**Last updated:** [July 21, 2020, 7:50pm UTC](https://discourse.itk.org/t/problem-in-extracting-mnc-file/3316 "2020-07-21T19:50:24Z")

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Hi all, I am using the following code in order to convert MNC file to readable format for 3D slicer. But there are some errors in the code. for example in line 52 , it is mentioning qualified name is not allowed. I downl…

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## [Example vector images](https://discourse.itk.org/t/example-vector-images/3314)

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**Author:** [@bhb2048](https://discourse.itk.org/u/bhb2048)\
**Replies:** 2\
**Last updated:** [July 21, 2020, 7:13pm UTC](https://discourse.itk.org/t/example-vector-images/3314 "2020-07-21T19:13:15Z")

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In Examples/Data, which images are vector images? Thanks Barry

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## [(Just) isotropic scaling](https://discourse.itk.org/t/just-isotropic-scaling/3306)

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**Author:** [@david.russell](https://discourse.itk.org/u/david.russell)\
**Replies:** 3\
**Last updated:** [July 21, 2020, 1:36pm UTC](https://discourse.itk.org/t/just-isotropic-scaling/3306 "2020-07-21T13:36:54Z")

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I’m trying to do registration in 2D using only one scale parameter applied to to both axes. I believe this is called isotropic scaling. I’ve been struggling because the scale transform is ansiotropic. I was thinking that…

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## [Patches for ITK 4.13.3](https://discourse.itk.org/t/patches-for-itk-4-13-3/3304)

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**Author:** [@matt.mccormick](https://discourse.itk.org/u/matt.mccormick)\
**Replies:** 0\
**Last updated:** [July 20, 2020, 4:03pm UTC](https://discourse.itk.org/t/patches-for-itk-4-13-3/3304 "2020-07-20T16:03:15Z")

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Hi folks, For the next, likely final on the 4.X series, patch (bugfix) release, ITK 4.13.3, the currently staged commits on the Git release-4.13 branch are: Bradley Lowekamp (7): BUG: Patch missing const qualifie…

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## [how to use ReadImageDICOMFileSeries on a zipfile](https://discourse.itk.org/t/how-to-use-readimagedicomfileseries-on-a-zipfile/3277)

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**Author:** [@lonewolf](https://discourse.itk.org/u/lonewolf)\
**Replies:** 7\
**Last updated:** [July 20, 2020, 3:55pm UTC](https://discourse.itk.org/t/how-to-use-readimagedicomfileseries-on-a-zipfile/3277 "2020-07-20T15:55:53Z")

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Hi all, I am trying to unzip a file with CT series in it and I can only display one image. When I try passing multiple images, it fails. I am using itk.js 13.1.1. This is the error: message: “FS error” stack: “\<gener…

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## [Cropping a CT volume](https://discourse.itk.org/t/cropping-a-ct-volume/3302)

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**Author:** [@blizzardboi\_2020](https://discourse.itk.org/u/blizzardboi_2020)\
**Replies:** 2\
**Last updated:** [July 20, 2020, 3:28am UTC](https://discourse.itk.org/t/cropping-a-ct-volume/3302 "2020-07-20T03:28:24Z")

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Hello. I want to crop(28x28x50) all the dcm (CT) volumes(150x150x50) in a folder, any python script for that?

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## [Within-subject registration of an MRI image acquired at 1.5 Tesla to another image acquired at 3 Tesla](https://discourse.itk.org/t/within-subject-registration-of-an-mri-image-acquired-at-1-5-tesla-to-another-image-acquired-at-3-tesla/3299)

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**Author:** [@MSherafati74](https://discourse.itk.org/u/MSherafati74)\
**Replies:** 2\
**Last updated:** [July 18, 2020, 10:13pm UTC](https://discourse.itk.org/t/within-subject-registration-of-an-mri-image-acquired-at-1-5-tesla-to-another-image-acquired-at-3-tesla/3299 "2020-07-18T22:13:08Z")

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Hello, I have a presumably elementary registration task at hand. I am familiar with Python and have just learned the basics of the registration concept from some online resources. I intend to tackle the job using SimpleI…

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## [Working with large field medical images](https://discourse.itk.org/t/working-with-large-field-medical-images/3238)

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**Author:** [@juccapirama](https://discourse.itk.org/u/juccapirama)\
**Replies:** 8\
**Last updated:** [July 17, 2020, 11:51am UTC](https://discourse.itk.org/t/working-with-large-field-medical-images/3238 "2020-07-17T11:51:00Z")

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Hello, I’m working on a preprocessing and a segmentation pipeline for vessel extraction from micro-scan medical images. The image volumes are around 2048x2048x1400 and 2560x2560x1400, with 5,5 Gb and 8,5 Gb in 8 bits. I…

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## [Direction/Orientation matrix DICOM vs Nifti](https://discourse.itk.org/t/direction-orientation-matrix-dicom-vs-nifti/3289)

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**Author:** [@rcorredorj](https://discourse.itk.org/u/rcorredorj)\
**Replies:** 5\
**Last updated:** [July 16, 2020, 3:41pm UTC](https://discourse.itk.org/t/direction-orientation-matrix-dicom-vs-nifti/3289 "2020-07-16T15:41:50Z")

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Hi everyone, I’m having discrepancies between the orientation matrix read from DICOMs or from a Nifti generated from the same DICOM series. I’d like to understand what is going on. I have a DICOM series that I read in …

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## [Hi all, is there anyone known multi-modal medical image fusion project,like CT/PET, CT/MRI and so on?](https://discourse.itk.org/t/hi-all-is-there-anyone-known-multi-modal-medical-image-fusion-project-like-ct-pet-ct-mri-and-so-on/3292)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 1\
**Last updated:** [July 16, 2020, 2:39pm UTC](https://discourse.itk.org/t/hi-all-is-there-anyone-known-multi-modal-medical-image-fusion-project-like-ct-pet-ct-mri-and-so-on/3292 "2020-07-16T14:39:45Z")

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Now I want to reseach the multi-modal medical image fusion, i want to find an open source project as first.

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## [Which is the best one ITK c++ or simpleITK python?](https://discourse.itk.org/t/which-is-the-best-one-itk-c-or-simpleitk-python/3291)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 1\
**Last updated:** [July 16, 2020, 1:39pm UTC](https://discourse.itk.org/t/which-is-the-best-one-itk-c-or-simpleitk-python/3291 "2020-07-16T13:39:58Z")

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Which one do researchers generally use for medical image processing? Which one could be faster? Which one would be easy? What are the pros and cons?

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## [How to use ITK-SNAP for visualization instead of ImageJ in simpleITK python](https://discourse.itk.org/t/how-to-use-itk-snap-for-visualization-instead-of-imagej-in-simpleitk-python/3290)

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**Author:** [@unicorn](https://discourse.itk.org/u/unicorn)\
**Replies:** 3\
**Last updated:** [July 16, 2020, 1:33pm UTC](https://discourse.itk.org/t/how-to-use-itk-snap-for-visualization-instead-of-imagej-in-simpleitk-python/3290 "2020-07-16T13:33:34Z")

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I have been using ImageJ for visualization. Is there any way to use ITK SNAP or 3D slicer for this purpose?

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## [itkwidgets in Dash app](https://discourse.itk.org/t/itkwidgets-in-dash-app/3284)

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**Author:** [@darrent1974](https://discourse.itk.org/u/darrent1974)\
**Replies:** 4\
**Last updated:** [July 16, 2020, 11:57am UTC](https://discourse.itk.org/t/itkwidgets-in-dash-app/3284 "2020-07-16T11:57:23Z")

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Hi, I’m just wondering if it may be possible to host an itkwidgets control within a dash web app? This would be the perfect viz tool for my current work. I have only the most basic node.js experience but it appears tha…

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## [Adding custom metadata during a filtering pipeline](https://discourse.itk.org/t/adding-custom-metadata-during-a-filtering-pipeline/3261)

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**Author:** [@Steve\_Moore](https://discourse.itk.org/u/Steve_Moore)\
**Replies:** 2\
**Last updated:** [July 15, 2020, 2:59am UTC](https://discourse.itk.org/t/adding-custom-metadata-during-a-filtering-pipeline/3261 "2020-07-15T02:59:49Z")

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Hi I have a situation where I need to create some custom filters (derived from an itk::ImageToImageFilter) that modify an input image, but I also want to keep track of some metadata generated by one filter (e.g: a std::…

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## [reading dynamic or gated SPECT images](https://discourse.itk.org/t/reading-dynamic-or-gated-spect-images/3283)

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**Author:** [@KrisThielemans](https://discourse.itk.org/u/KrisThielemans)\
**Replies:** 1\
**Last updated:** [July 14, 2020, 7:45pm UTC](https://discourse.itk.org/t/reading-dynamic-or-gated-spect-images/3283 "2020-07-14T19:45:37Z")

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I need to read SPECT dynamic or gated images in DICOM format. In contrast to MR CT and PET where the data is spread over multiples files (with for each 2D slice), SPECT images are usually stored in a single file. For si…

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## [Compiler flags not passed down to external modules?](https://discourse.itk.org/t/compiler-flags-not-passed-down-to-external-modules/3249)

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**Author:** [@seanm](https://discourse.itk.org/u/seanm)\
**Replies:** 1\
**Last updated:** [July 14, 2020, 4:44pm UTC](https://discourse.itk.org/t/compiler-flags-not-passed-down-to-external-modules/3249 "2020-07-14T16:44:26Z")

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Hi all, My cdash submission here has some -Wmissing-braces warnings: https://open.cdash.org/viewBuildError.php?type=1&buildid=6624748 But that’s odd because I pass -Wno-missing-braces: https://open.cdash.org/viewNote…

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## [Registration/alignment of two images](https://discourse.itk.org/t/registration-alignment-of-two-images/3266)

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**Author:** [@markbuckup](https://discourse.itk.org/u/markbuckup)\
**Replies:** 2\
**Last updated:** [July 14, 2020, 4:36pm UTC](https://discourse.itk.org/t/registration-alignment-of-two-images/3266 "2020-07-14T16:36:09Z")

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Hello, I am trying to find the optimal registration process for these two images. They are of the same tissue across different stains, which means that they have different RGB qualities but are of the same basic size. T…

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## [ITK 4.13.2 build creates 4.13.1 libs](https://discourse.itk.org/t/itk-4-13-2-build-creates-4-13-1-libs/3270)

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**Author:** [@warfield](https://discourse.itk.org/u/warfield)\
**Replies:** 3\
**Last updated:** [July 14, 2020, 4:03pm UTC](https://discourse.itk.org/t/itk-4-13-2-build-creates-4-13-1-libs/3270 "2020-07-14T16:03:52Z")

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When I build the InsightToolkit 4.13.2 release, the libraries that are created are labelled version 4.13.1. Any idea what is going wrong ?

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## [python code for DiffeomorphicDemonsRegistration in SimpleITK](https://discourse.itk.org/t/python-code-for-diffeomorphicdemonsregistration-in-simpleitk/1937)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 6\
**Last updated:** [July 14, 2020, 1:36pm UTC](https://discourse.itk.org/t/python-code-for-diffeomorphicdemonsregistration-in-simpleitk/1937 "2020-07-14T13:36:26Z")

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I used a few methods for registration. Simple ITK in python looks very easy than using c++ for me. Is there any python code available for DiffeomorphicDemonsRegistration?

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## [Convert volume from voxels to mm^3 or cm^3](https://discourse.itk.org/t/convert-volume-from-voxels-to-mm-3-or-cm-3/3280)

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**Author:** [@agatadefr](https://discourse.itk.org/u/agatadefr)\
**Replies:** 3\
**Last updated:** [July 13, 2020, 1:47pm UTC](https://discourse.itk.org/t/convert-volume-from-voxels-to-mm-3-or-cm-3/3280 "2020-07-13T13:47:32Z")

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Hey Guys, I am quite new in ITK. I implemented using LabelGeometryImageFilter. I extracted label volumes. Output results are in voxels. I would like to convert to cc\`3 or mm^3. Could you help me how I can do that ? …

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## [How to apply composite affine matrix to a volume](https://discourse.itk.org/t/how-to-apply-composite-affine-matrix-to-a-volume/3182)

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**Author:** [@prms](https://discourse.itk.org/u/prms)\
**Replies:** 9\
**Last updated:** [June 21, 2020, 6:24pm UTC](https://discourse.itk.org/t/how-to-apply-composite-affine-matrix-to-a-volume/3182 "2020-06-21T18:24:04Z")

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I am performing affine transformation of image and have an affine matrix learned using PyTorch. I want to use the learned matrix to MR image and save the image to disk using SimpleITK. However, I am not able to apply the…

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## [How to get pixels within a radius from a specific pixel?](https://discourse.itk.org/t/how-to-get-pixels-within-a-radius-from-a-specific-pixel/3243)

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**Author:** [@aangelos28](https://discourse.itk.org/u/aangelos28)\
**Replies:** 5\
**Last updated:** [July 11, 2020, 9:29pm UTC](https://discourse.itk.org/t/how-to-get-pixels-within-a-radius-from-a-specific-pixel/3243 "2020-07-11T21:29:16Z")

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Hello, I was wondering if there is a way to get the indices of pixels within a certain radius from a center pixel with a specific ID. itk::NeighborhoodIterator was the closest thing I found to this, but how can I use it…

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## [AddObserver on DataObject](https://discourse.itk.org/t/addobserver-on-dataobject/3275)

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**Author:** [@Come](https://discourse.itk.org/u/Come)\
**Replies:** 3\
**Last updated:** [July 10, 2020, 5:51pm UTC](https://discourse.itk.org/t/addobserver-on-dataobject/3275 "2020-07-10T17:51:49Z")

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Hi, I want to add an observer to an image to know when it is modified. I tried the code below based on this example. #include \<itkImage.h\> #include \<itkRandomImageSource.h\> #include \<itkCommand.h\> class MyCommand : pu…

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## [Create image patches and reconstruct it back to the image](https://discourse.itk.org/t/create-image-patches-and-reconstruct-it-back-to-the-image/3274)

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**Author:** [@DL\_Begin](https://discourse.itk.org/u/DL_Begin)\
**Replies:** 6\
**Last updated:** [July 10, 2020, 12:54pm UTC](https://discourse.itk.org/t/create-image-patches-and-reconstruct-it-back-to-the-image/3274 "2020-07-10T12:54:28Z")

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Hello, I have 3D medical image of size \[284,143,143\] , 284 are the number of slices and I want to extract 2D image patches out of it and reconstruct the image back to patches. I want to have patches of shape 128\*128 .I…

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## [ITK octree](https://discourse.itk.org/t/itk-octree/3185)

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**Author:** [@rolof](https://discourse.itk.org/u/rolof)\
**Replies:** 7\
**Last updated:** [July 9, 2020, 1:16am UTC](https://discourse.itk.org/t/itk-octree/3185 "2020-07-09T01:16:42Z")

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Hi, I am trying to use Octrees on ITK, I saw that ITK have an Octree object. However, I can not find the methods of Octree to get the closest points. My problem is that I have a region of interest composed of several vo…

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## [No progress reporting in ITK5](https://discourse.itk.org/t/no-progress-reporting-in-itk5/2630)

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**Author:** [@lassoan](https://discourse.itk.org/u/lassoan)\
**Replies:** 37\
**Last updated:** [July 8, 2020, 5:08pm UTC](https://discourse.itk.org/t/no-progress-reporting-in-itk5/2630 "2020-07-08T17:08:06Z")

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ITK5 is great for many reasons but users started to complain that 3D Slicer hangs because all they see that image processing filters are stuck at 0% (e.g., https://discourse.slicer.org/t/bilateral-filter-not-working/9797…

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## [Update two dependent itk::DataObject](https://discourse.itk.org/t/update-two-dependent-itk-dataobject/3269)

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**Author:** [@Come](https://discourse.itk.org/u/Come)\
**Replies:** 3\
**Last updated:** [July 7, 2020, 2:21pm UTC](https://discourse.itk.org/t/update-two-dependent-itk-dataobject/3269 "2020-07-07T14:21:22Z")

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Hi, I created two itk::DataObject that are dependent and I would like to update both of them when any of the two is modified. I wonder if there is an easy way to do that (i.e. send a notification, from a DataObject, to …

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## [Generate Rotational Maximum Intensity Projections](https://discourse.itk.org/t/generate-rotational-maximum-intensity-projections/3226)

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**Author:** [@divya\_chou](https://discourse.itk.org/u/divya_chou)\
**Replies:** 11\
**Last updated:** [July 7, 2020, 6:38am UTC](https://discourse.itk.org/t/generate-rotational-maximum-intensity-projections/3226 "2020-07-07T06:38:20Z")

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I am very new to using ITK, and am working using SITK on Python. I have 3D PET scans. From each 3D matrix, I have generated 2 MIPs at 90 degrees - Sagittal and Coronal. This was easily achieved using the sitk.MaximumPro…

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## [ITK4 cannot read ITK5 .h5 transform files](https://discourse.itk.org/t/itk4-cannot-read-itk5-h5-transform-files/3264)

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**Author:** [@lassoan](https://discourse.itk.org/u/lassoan)\
**Replies:** 2\
**Last updated:** [July 4, 2020, 3:37pm UTC](https://discourse.itk.org/t/itk4-cannot-read-itk5-h5-transform-files/3264 "2020-07-04T15:37:47Z")

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It seems that simple AffineTransform\_double\_3\_3 saved with ITK 5.1 in HDF format cannot be loaded with ITK 4.13. Here is an example file: https://github.com/vinkirk/public/raw/master/Xfm\_acpc.h5 Is this intentional? Do…

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## [New Insight Toolkit (ITK) module for Structure Preserving Color Normalization](https://discourse.itk.org/t/new-insight-toolkit-itk-module-for-structure-preserving-color-normalization/3255)

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**Author:** [@Lee\_Newberg](https://discourse.itk.org/u/Lee_Newberg)\
**Replies:** 0\
**Last updated:** [July 2, 2020, 8:02pm UTC](https://discourse.itk.org/t/new-insight-toolkit-itk-module-for-structure-preserving-color-normalization/3255 "2020-07-02T20:02:23Z")

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Introduction We have added a new module to the Insight Toolkit (ITK) to perform Structure Preserving Color Normalization on an H & E image using a reference image. The software is available in C++ and is also …

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