# Beginner Questions

**URL:** https://discourse.itk.org/c/beginner-questions/9.md?no_subcategories=false&page=6

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

**Page:** 7

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## [How do you compose transforms after registration to perform resampling?](https://discourse.itk.org/t/how-do-you-compose-transforms-after-registration-to-perform-resampling/6401)

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**Author:** [@sdiebolt](https://discourse.itk.org/u/sdiebolt)\
**Replies:** 6\
**Last updated:** [January 23, 2024, 4:10pm UTC](https://discourse.itk.org/t/how-do-you-compose-transforms-after-registration-to-perform-resampling/6401 "2024-01-23T16:10:11Z")

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I have a question that has already been asked at least twice (here and here) but got no explicit answer. Like their original authors, I’m struggling to understand how to compose the fixed initial, moving initial, and opt…

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## [Coordinate conversion](https://discourse.itk.org/t/coordinate-conversion/6393)

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**Author:** [@Ellen-D216](https://discourse.itk.org/u/Ellen-D216)\
**Replies:** 7\
**Last updated:** [January 23, 2024, 3:45pm UTC](https://discourse.itk.org/t/coordinate-conversion/6393 "2024-01-23T15:45:53Z")

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I want to convert the image to a polar coordinate system, process it, and then convert it back to the Cartesian coordinate system. How can I do it with itkCartesianToPolarTransform and itkPolarToCartesianTransform? With …

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## [DICOMOrientImageFilter in C#](https://discourse.itk.org/t/dicomorientimagefilter-in-c/6400)

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**Author:** [@Toru\_Hironaka](https://discourse.itk.org/u/Toru_Hironaka)\
**Replies:** 2\
**Last updated:** [January 18, 2024, 12:01am UTC](https://discourse.itk.org/t/dicomorientimagefilter-in-c/6400 "2024-01-18T00:01:35Z")

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I installed SimpleITK-1.2.4-CSharp-win64-x64, but I could not find DICOMOrientImageFilter. Is this class only available in C++? or Do I have to build SimpleITK source to install?

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## [How to change the values in the sitk.ForwardFFTImageFilter](https://discourse.itk.org/t/how-to-change-the-values-in-the-sitk-forwardfftimagefilter/6379)

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**Author:** [@gfunkalea](https://discourse.itk.org/u/gfunkalea)\
**Replies:** 1\
**Last updated:** [January 3, 2024, 2:43pm UTC](https://discourse.itk.org/t/how-to-change-the-values-in-the-sitk-forwardfftimagefilter/6379 "2024-01-03T14:43:30Z")

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I want to take the discreet FFT of an image and then zero out the high spatial frequency values and then use the inverse FFT to see the result. My problem is that I get an error trying to use SetPixel on the Fourier tran…

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## [Is information lost when converting dicom to png 16 bit?](https://discourse.itk.org/t/is-information-lost-when-converting-dicom-to-png-16-bit/6375)

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**Author:** [@Wallesss](https://discourse.itk.org/u/Wallesss)\
**Replies:** 5\
**Last updated:** [January 3, 2024, 1:35pm UTC](https://discourse.itk.org/t/is-information-lost-when-converting-dicom-to-png-16-bit/6375 "2024-01-03T13:35:35Z")

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Hello, is there any loss of information when converting a dicom file to a 16 bit png image? We are, of course, not talking about metadata in dicom. My comrade is reluctant to convert dicom files into images, claiming tha…

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## [SmoothingRecursiveGaussian vs DiscreteGaussian](https://discourse.itk.org/t/smoothingrecursivegaussian-vs-discretegaussian/6370)

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**Author:** [@reox](https://discourse.itk.org/u/reox)\
**Replies:** 4\
**Last updated:** [December 21, 2023, 3:24pm UTC](https://discourse.itk.org/t/smoothingrecursivegaussian-vs-discretegaussian/6370 "2023-12-21T15:24:50Z")

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Here is a small example using both SmoothingRecursiveGaussian and DiscreteGaussian to smooth an image. Both filter should use the same σ of 0.8 - as far as I understood the documentation, the Recursive filter has the sta…

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## [How to get oblique 2d slice from volume (simpleITK)](https://discourse.itk.org/t/how-to-get-oblique-2d-slice-from-volume-simpleitk/6028)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 8\
**Last updated:** [December 20, 2023, 8:53pm UTC](https://discourse.itk.org/t/how-to-get-oblique-2d-slice-from-volume-simpleitk/6028 "2023-12-20T20:53:36Z")

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Hello, I’m searching for code example of oblique 2d slice. Asking chatgpt and bard I was able to understand the underlying geometry: plane center point, plane normal vector, rotation matrix, translation matrix. They ev…

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## [What are the valid input parameters of the different optimization algorithms available in SimpleITK?](https://discourse.itk.org/t/what-are-the-valid-input-parameters-of-the-different-optimization-algorithms-available-in-simpleitk/6314)

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**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 8\
**Last updated:** [December 18, 2023, 1:50pm UTC](https://discourse.itk.org/t/what-are-the-valid-input-parameters-of-the-different-optimization-algorithms-available-in-simpleitk/6314 "2023-12-18T13:50:54Z")

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Hello, I want to compare the performance of different optimization algorithms while registering two images. For this purpose, I want to know what are the valid input parameters (step size, function tolerance, number of …

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## [Does non-rigid registration changes the real Geometry?](https://discourse.itk.org/t/does-non-rigid-registration-changes-the-real-geometry/6359)

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**Author:** [@Faramarz-bagherzadeh](https://discourse.itk.org/u/Faramarz-bagherzadeh)\
**Replies:** 2\
**Last updated:** [December 16, 2023, 5:42am UTC](https://discourse.itk.org/t/does-non-rigid-registration-changes-the-real-geometry/6359 "2023-12-16T05:42:25Z")

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Hello all, I have 2 sets of micro CT images (3D): with the 12-micrometer resolution taken in Axial mode with the 120-micrometer resolution taken in Helical mode We can consider the high-res image displays the reality…

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## [Torch import time](https://discourse.itk.org/t/torch-import-time/6354)

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**Author:** [@tbaudier](https://discourse.itk.org/u/tbaudier)\
**Replies:** 2\
**Last updated:** [December 14, 2023, 5:07pm UTC](https://discourse.itk.org/t/torch-import-time/6354 "2023-12-14T17:07:24Z")

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Hi, In a new virtual environment, I installed itk with pypi and I tested the import time: ITK is fast to import. But now, I installed torch with pypi: The import time is huge now, due to torch. I do not need tor…

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## [deformable PointSet to PointSet registration with python](https://discourse.itk.org/t/deformable-pointset-to-pointset-registration-with-python/6351)

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**Author:** [@HnHd](https://discourse.itk.org/u/HnHd)\
**Replies:** 2\
**Last updated:** [December 11, 2023, 7:38pm UTC](https://discourse.itk.org/t/deformable-pointset-to-pointset-registration-with-python/6351 "2023-12-11T19:38:39Z")

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Hello all, I am trying to implement a deformable registration for two pointsets in python-itk. Being a newbie I started with the itk.PointSetToPointSetRegistrationMethod, but got stuck when trying to set the metric for…

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## [where is the origin of image position?](https://discourse.itk.org/t/where-is-the-origin-of-image-position/6344)

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**Author:** [@zhang-qiang-github](https://discourse.itk.org/u/zhang-qiang-github)\
**Replies:** 2\
**Last updated:** [December 11, 2023, 6:11pm UTC](https://discourse.itk.org/t/where-is-the-origin-of-image-position/6344 "2023-12-11T18:11:53Z")

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For tag: 0020|0032 (image position patient), 0020|0037 (image orientation patient), where is the origin point (0, 0, 0). Is it a point of scanner? If one scanner give two dcm data, whether the origion point (0,0,0) are …

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## [Multiprocessing LabelMap](https://discourse.itk.org/t/multiprocessing-labelmap/6339)

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**Author:** [@chlee](https://discourse.itk.org/u/chlee)\
**Replies:** 1\
**Last updated:** [December 5, 2023, 9:39pm UTC](https://discourse.itk.org/t/multiprocessing-labelmap/6339 "2023-12-05T21:39:20Z")

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Dear ITK community, I am dealing with LabelMap, where for each label (and corresponding main image) I want to do image operations, say otsu-thresholding and subsequent filtering to obtain a blob (in itself a label - the…

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## [Simple ITK with Elastix has earlier version of N4BiasFieldCorrectionImageFilter](https://discourse.itk.org/t/simple-itk-with-elastix-has-earlier-version-of-n4biasfieldcorrectionimagefilter/6336)

<div class="topic-metadata">

**Author:** [@J\_B](https://discourse.itk.org/u/J_B)\
**Replies:** 2\
**Last updated:** [December 4, 2023, 2:00pm UTC](https://discourse.itk.org/t/simple-itk-with-elastix-has-earlier-version-of-n4biasfieldcorrectionimagefilter/6336 "2023-12-04T14:00:54Z")

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Hello, I have used SimpleITK.N4BiasFieldCorrectionImageFilter() successfully, and SimpleITK.ElastixImageFilter() successfully to do a registration, but when SimpleITK-SimpleElastix is pip installed into a python virtual …

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## [how to determine the orientation of a two-dimensional Image?](https://discourse.itk.org/t/how-to-determine-the-orientation-of-a-two-dimensional-image/6329)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 0\
**Last updated:** [December 1, 2023, 6:05pm UTC](https://discourse.itk.org/t/how-to-determine-the-orientation-of-a-two-dimensional-image/6329 "2023-12-01T18:05:05Z")

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i’m using SimpleITK.extract(image, size\[\], index\[x\]) to extract a cross section from a series. And I need to determine the orientation of this cross section with: posterior, anterior, right, left, inferior and superior. …

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## [Checking simpleitk.Image Equality](https://discourse.itk.org/t/checking-simpleitk-image-equality/6323)

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**Author:** [@Franciska](https://discourse.itk.org/u/Franciska)\
**Replies:** 5\
**Last updated:** [November 29, 2023, 3:37pm UTC](https://discourse.itk.org/t/checking-simpleitk-image-equality/6323 "2023-11-29T15:37:19Z")

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Hi! I have two methods to the same task. I’d like to check, whether the result of the two methods gives equal outcomes. The files are nifti Images. I can check if their numpy part is the same easily: output1=sitk.Read…

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## [How to convert 4D fMRI images to a series of 3D images?](https://discourse.itk.org/t/how-to-convert-4d-fmri-images-to-a-series-of-3d-images/6322)

<div class="topic-metadata">

**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 1\
**Last updated:** [November 27, 2023, 2:08pm UTC](https://discourse.itk.org/t/how-to-convert-4d-fmri-images-to-a-series-of-3d-images/6322 "2023-11-27T14:08:55Z")

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Hello, I am working with the ADHD200 dataset. It consists of anatomical and resting state fMRI images in NIFTI (nii.gz) format. The fMRI images are 4D images. These represent 3D image of the brain over a period of time…

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## [Registration mask and rigidity penalty](https://discourse.itk.org/t/registration-mask-and-rigidity-penalty/6311)

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**Author:** [@calici](https://discourse.itk.org/u/calici)\
**Replies:** 0\
**Last updated:** [November 20, 2023, 2:47am UTC](https://discourse.itk.org/t/registration-mask-and-rigidity-penalty/6311 "2023-11-20T02:47:36Z")

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My questions is actually the continuation of elastix group discussion.. Currently I am trying to assess treatment success by registering pretreatment CT and post treatment CT. I want to keep the lesion region undeformed…

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## [Use of TransformRigidityPenalty Fails](https://discourse.itk.org/t/use-of-transformrigiditypenalty-fails/6273)

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**Author:** [@calici](https://discourse.itk.org/u/calici)\
**Replies:** 2\
**Last updated:** [November 17, 2023, 1:51pm UTC](https://discourse.itk.org/t/use-of-transformrigiditypenalty-fails/6273 "2023-11-17T13:51:34Z")

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Hi! I am using deformable intensity-based algorithm to register pretreatment and posttreatment CT pairs. I want a specific region defined by a segmentation not to be deformed much during nonlinear registration. For tha…

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## [registration of simple matrices of point](https://discourse.itk.org/t/registration-of-simple-matrices-of-point/6303)

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**Author:** [@Fabrizio\_B](https://discourse.itk.org/u/Fabrizio_B)\
**Replies:** 3\
**Last updated:** [November 16, 2023, 1:43pm UTC](https://discourse.itk.org/t/registration-of-simple-matrices-of-point/6303 "2023-11-16T13:43:33Z")

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Hello everybody, in my project we work with medical images of biopsies. Upstream, they analyze such images and convert the important features in CSV format. I find myself then with big data frames, containing the posi…

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## [Multi-resolution registration](https://discourse.itk.org/t/multi-resolution-registration/6300)

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**Author:** [@maxtj](https://discourse.itk.org/u/maxtj)\
**Replies:** 1\
**Last updated:** [November 15, 2023, 2:11pm UTC](https://discourse.itk.org/t/multi-resolution-registration/6300 "2023-11-15T14:11:44Z")

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I am very new to python and the use of SimpleITK. I have tried to construct python code to register 2 image modalities that have different spatial resolutions. I could not perform registration between 2 images if one of …

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## [IntensityWindowingImageFilter not working as expected with multiframe instances (JAVA)](https://discourse.itk.org/t/intensitywindowingimagefilter-not-working-as-expected-with-multiframe-instances-java/6289)

<div class="topic-metadata">

**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 7\
**Last updated:** [November 14, 2023, 9:27pm UTC](https://discourse.itk.org/t/intensitywindowingimagefilter-not-working-as-expected-with-multiframe-instances-java/6289 "2023-11-14T21:27:52Z")

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i have recorded my problem: As you can see, weasis is clearly displaying the image with \[128, 256\] and my software shows everything in white with same configuration. This is the function that applys the f…

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## [How to use a deformationField to deform a new volume?](https://discourse.itk.org/t/how-to-use-a-deformationfield-to-deform-a-new-volume/6294)

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**Author:** [@PolarBean](https://discourse.itk.org/u/PolarBean)\
**Replies:** 0\
**Last updated:** [November 8, 2023, 8:11pm UTC](https://discourse.itk.org/t/how-to-use-a-deformationfield-to-deform-a-new-volume/6294 "2023-11-08T20:11:02Z")

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Hi, Thank you for working on this package. I am using GitHub - SuperElastix/SimpleElastix: Multi-lingual medical image registration library which has now been integrated into SimpleITK. I have generated a deformation f…

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## [Reading and extracting images from a large DICOM file](https://discourse.itk.org/t/reading-and-extracting-images-from-a-large-dicom-file/6292)

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**Author:** [@Viktor\_Ustynov](https://discourse.itk.org/u/Viktor_Ustynov)\
**Replies:** 6\
**Last updated:** [November 8, 2023, 6:00pm UTC](https://discourse.itk.org/t/reading-and-extracting-images-from-a-large-dicom-file/6292 "2023-11-08T18:00:16Z")

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Hi everyone, I’m a beginner with ITK. I need to extract all the images from a very large (about 3 GB) .dcm file and save them as .bmp files. To do this, I’m trying to read the file as shown in the examples. However, t…

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## [Dice score and Hausdorff distance for inter-modal image registration](https://discourse.itk.org/t/dice-score-and-hausdorff-distance-for-inter-modal-image-registration/6268)

<div class="topic-metadata">

**Author:** [@debapriya](https://discourse.itk.org/u/debapriya)\
**Replies:** 9\
**Last updated:** [November 8, 2023, 12:03pm UTC](https://discourse.itk.org/t/dice-score-and-hausdorff-distance-for-inter-modal-image-registration/6268 "2023-11-08T12:03:42Z")

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I have 3D CT and MR images of the brain. I want to register these images and find out Dice score, Hausdorff distance, Jaccard index as measure of registration accuracy. I have segmented the whole brain (both CT and MR i…

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## [How to extract frame from Multiframe Image/FrameSet? (JAVA)](https://discourse.itk.org/t/how-to-extract-frame-from-multiframe-image-frameset-java/6288)

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**Author:** [@Salu\_Ramos](https://discourse.itk.org/u/Salu_Ramos)\
**Replies:** 4\
**Last updated:** [November 7, 2023, 7:34pm UTC](https://discourse.itk.org/t/how-to-extract-frame-from-multiframe-image-frameset-java/6288 "2023-11-07T19:34:23Z")

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I have a multiframe instance loaded with ImageSeriesReader, and i want to know how am i supposed to extract a frame from the result Image/frameSet. The below script was working fine for singleframe instances loaded as a…

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## [How to disable logging in python, jupyter notebook](https://discourse.itk.org/t/how-to-disable-logging-in-python-jupyter-notebook/6281)

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**Author:** [@hucang0](https://discourse.itk.org/u/hucang0)\
**Replies:** 4\
**Last updated:** [November 6, 2023, 3:52pm UTC](https://discourse.itk.org/t/how-to-disable-logging-in-python-jupyter-notebook/6281 "2023-11-06T15:52:44Z")

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I am executing parallel processes in VS Code on Ubuntu, with each process invoking SimpleITK. However, the console output from these processes is causing VS Code to crash. How can I disable the logging?

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## [Use BRAINSFit in a Python in-house software](https://discourse.itk.org/t/use-brainsfit-in-a-python-in-house-software/6283)

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**Author:** [@Icron1](https://discourse.itk.org/u/Icron1)\
**Replies:** 1\
**Last updated:** [November 6, 2023, 1:31pm UTC](https://discourse.itk.org/t/use-brainsfit-in-a-python-in-house-software/6283 "2023-11-06T13:31:33Z")

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Hello dear community, I am looking to use the BRAINSFit registration algorithm in a custom Python software to align cerebral MRIs. Is it possible to implement it in a Python-based software without using Slicer (which is…

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## [why can't itk read dicomdir files?](https://discourse.itk.org/t/why-cant-itk-read-dicomdir-files/6274)

<div class="topic-metadata">

**Author:** [@zx-lhb](https://discourse.itk.org/u/zx-lhb)\
**Replies:** 3\
**Last updated:** [November 6, 2023, 2:54am UTC](https://discourse.itk.org/t/why-cant-itk-read-dicomdir-files/6274 "2023-11-06T02:54:00Z")

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hi, I tried to read dicom files which are all stored in a directory using the following code void readDicomSeries(const std::string& dicom\_dir, itk::Image\<float, 3\>::Pointer& out\_image) { using ImageIOType = itk::GD…

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## [Evaluation of the registered image](https://discourse.itk.org/t/evaluation-of-the-registered-image/6275)

<div class="topic-metadata">

**Author:** [@pratibha](https://discourse.itk.org/u/pratibha)\
**Replies:** 4\
**Last updated:** [November 5, 2023, 7:48pm UTC](https://discourse.itk.org/t/evaluation-of-the-registered-image/6275 "2023-11-05T19:48:17Z")

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I want to evaluate whether the registration is done properly or not automatically or based on some metric. Normally I check it by manually aligning the registered image on the fixed image and for the TRE approach, I had …

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