# Uncategorized

**URL:** https://discourse.itk.org/c/uncategorized/1.md?no_subcategories=false&page=9

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

**Page:** 10

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

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**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")

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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.

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## [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)

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**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")

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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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## [How can I use ITK quickly reads DICOM file sequence and reconstructs it?](https://discourse.itk.org/t/how-can-i-use-itk-quickly-reads-dicom-file-sequence-and-reconstructs-it/3250)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 4\
**Last updated:** [July 3, 2020, 3:07am UTC](https://discourse.itk.org/t/how-can-i-use-itk-quickly-reads-dicom-file-sequence-and-reconstructs-it/3250 "2020-07-03T03:07:11Z")

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How can I use ITK quickly reads DICOM file sequence and reconstructs it? Can I use multi thread or Segmented reading? And now I just read dicom file sequence by ITK::ImageReader::SetDirectoryName and update()

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## [How to determine if the curve is closed?](https://discourse.itk.org/t/how-to-determine-if-the-curve-is-closed/3237)

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**Author:** [@guo7212](https://discourse.itk.org/u/guo7212)\
**Replies:** 3\
**Last updated:** [July 2, 2020, 11:06am UTC](https://discourse.itk.org/t/how-to-determine-if-the-curve-is-closed/3237 "2020-07-02T11:06:15Z")

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Hi all, I want to find the markers in CT scout. Is it possible to determine if the curve is closed?

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## [SimpleITK examples of registration whose transform with Shift, Rotation and Scale for 3D](https://discourse.itk.org/t/simpleitk-examples-of-registration-whose-transform-with-shift-rotation-and-scale-for-3d/3196)

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**Author:** [@Luis\_Carlos\_Carneiro](https://discourse.itk.org/u/Luis_Carlos_Carneiro)\
**Replies:** 1\
**Last updated:** [June 17, 2020, 12:42pm UTC](https://discourse.itk.org/t/simpleitk-examples-of-registration-whose-transform-with-shift-rotation-and-scale-for-3d/3196 "2020-06-17T12:42:32Z")

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Dear All, Can you please suggest SimpleITK examples for 3D (.mhd images) for registration whose transform supports Shift, Rotation and Scaling? I am using the example below which supports Shift and Rotation. Thanks, …

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## [Padding without extending image size to increase the field of view](https://discourse.itk.org/t/padding-without-extending-image-size-to-increase-the-field-of-view/3163)

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**Author:** [@isuruwi](https://discourse.itk.org/u/isuruwi)\
**Replies:** 4\
**Last updated:** [June 15, 2020, 4:25pm UTC](https://discourse.itk.org/t/padding-without-extending-image-size-to-increase-the-field-of-view/3163 "2020-06-15T16:25:13Z")

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I’m trying to add an uniform margin to a 3D CT volume using itk::ConstantPadImageFilter and then resize into original image size. My ultimate goal is ,for example, to transform the bottom image to the image at the top t…

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## [Is it possible to use GPU for image resample?](https://discourse.itk.org/t/is-it-possible-to-use-gpu-for-image-resample/2775)

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**Author:** [@qiang-zhang-neu](https://discourse.itk.org/u/qiang-zhang-neu)\
**Replies:** 13\
**Last updated:** [June 15, 2020, 2:37pm UTC](https://discourse.itk.org/t/is-it-possible-to-use-gpu-for-image-resample/2775 "2020-06-15T14:37:15Z")

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The image resample filter in ITK is slow, can we use GPU to accelerate it?

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## [what is denoted by sitk.GetDirection()](https://discourse.itk.org/t/what-is-denoted-by-sitk-getdirection/3162)

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**Author:** [@prms](https://discourse.itk.org/u/prms)\
**Replies:** 2\
**Last updated:** [June 13, 2020, 11:44am UTC](https://discourse.itk.org/t/what-is-denoted-by-sitk-getdirection/3162 "2020-06-13T11:44:06Z")

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I want to understand the interpretation of the array returned by GetDirection in case of MRI image. (-0.9998157207129488, 0.019196994953562158, 0.0, -0.019196994953562158, -0.9998157207129488, 0.0, 0.0, 0.0, 1.0…

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## [DICOM Print SCU and DICOM Print SCP](https://discourse.itk.org/t/dicom-print-scu-and-dicom-print-scp/3176)

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**Author:** [@gunaitk](https://discourse.itk.org/u/gunaitk)\
**Replies:** 3\
**Last updated:** [June 12, 2020, 2:15pm UTC](https://discourse.itk.org/t/dicom-print-scu-and-dicom-print-scp/3176 "2020-06-12T14:15:59Z")

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Hi Does DICOM print scp available in ITK or VTK ? Looking forward it. Thanks

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## [SimpleITK Bspline image representation](https://discourse.itk.org/t/simpleitk-bspline-image-representation/3170)

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**Author:** [@ibr](https://discourse.itk.org/u/ibr)\
**Replies:** 3\
**Last updated:** [June 11, 2020, 11:08pm UTC](https://discourse.itk.org/t/simpleitk-bspline-image-representation/3170 "2020-06-11T23:08:55Z")

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Dear all, I am trying to understand this paper \[1\] about B-spline. Is there a SimpleITK example to get a B-Spline representation of an image? Thanks in advance! \[1\] Splines - A perfect fit for signal and image process…

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## [Finally SimpleITK for python, .net c#, java, c++ working](https://discourse.itk.org/t/finally-simpleitk-for-python-net-c-java-c-working/3140)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 2\
**Last updated:** [June 5, 2020, 2:00am UTC](https://discourse.itk.org/t/finally-simpleitk-for-python-net-c-java-c-working/3140 "2020-06-05T02:00:26Z")

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Hi everyone, I just wanted to announce that another engineer in the forum is now very much set to work with SimpleITK, I finally could get the Fiji viewer to work with python! Thanks for the forum documentation … uhhhhh…

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## [Simpleitk python wrapper installation not working](https://discourse.itk.org/t/simpleitk-python-wrapper-installation-not-working/3114)

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**Author:** [@sag](https://discourse.itk.org/u/sag)\
**Replies:** 2\
**Last updated:** [June 2, 2020, 1:37pm UTC](https://discourse.itk.org/t/simpleitk-python-wrapper-installation-not-working/3114 "2020-06-02T13:37:38Z")

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I am struggling with getting right binary version of the SimpleITK python to work with Miniconda and still I can seem to make it work. python wrapper allows me to make things simpler to write with simpleitk. if some one…

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## [Filter used after LabelIntensityStatisticsImageFilter](https://discourse.itk.org/t/filter-used-after-labelintensitystatisticsimagefilter/3108)

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**Author:** [@flaviu2](https://discourse.itk.org/u/flaviu2)\
**Replies:** 10\
**Last updated:** [May 28, 2020, 4:19pm UTC](https://discourse.itk.org/t/filter-used-after-labelintensitystatisticsimagefilter/3108 "2020-05-28T16:19:45Z")

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I have used sitk::LabelIntensityStatisticsImageFilter like this: sitk::Image imgTemp(img); .... another filters sitk::Image cc = sitk::SLIC(imgTemp); sitk::LabelIntensityStatisticsImageFilter stat; stat.Exec…

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## [ITK.js: Mesh to polyData conversion](https://discourse.itk.org/t/itk-js-mesh-to-polydata-conversion/3065)

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**Author:** [@emmanuel\_madarassou](https://discourse.itk.org/u/emmanuel_madarassou)\
**Replies:** 3\
**Last updated:** [May 14, 2020, 2:15am UTC](https://discourse.itk.org/t/itk-js-mesh-to-polydata-conversion/3065 "2020-05-14T02:15:40Z")

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Hi everyone, I’m trying to manipulate itk.js and I’m stuck trying to understand the MeshToPolyData.js file in Pipelines. Does it really allow to do the Mesh/Polydata conversion ? if true, how can I use it ? Thanks.

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## [TransformIndexToPhysicalPoint. Shouldn't it take into account the starting index of the region?](https://discourse.itk.org/t/transformindextophysicalpoint-shouldnt-it-take-into-account-the-starting-index-of-the-region/3091)

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**Author:** [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Replies:** 2\
**Last updated:** [May 18, 2020, 3:41pm UTC](https://discourse.itk.org/t/transformindextophysicalpoint-shouldnt-it-take-into-account-the-starting-index-of-the-region/3091 "2020-05-18T15:41:40Z")

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This is the implementation of TransformToPhysicalPoint in itkImageBase: /\*\* Get a physical point (in the space which \* the origin and spacing information comes from) \* from a discrete index (in the index space) …

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## [how to pickle SimpleITK transforms?](https://discourse.itk.org/t/how-to-pickle-simpleitk-transforms/901)

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**Author:** [@Adi\_Zholkover](https://discourse.itk.org/u/Adi_Zholkover)\
**Replies:** 13\
**Last updated:** [May 18, 2020, 2:22pm UTC](https://discourse.itk.org/t/how-to-pickle-simpleitk-transforms/901 "2020-05-18T14:22:48Z")

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I’m trying to use python’s multiprocessing Pool.map\_async() with a function that returns a SimpleITK.Transform object, i.e.: res = \[\] for ref\_im in ref\_imgs: res.append(self.pool.apply\_async(register\_src…

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## [Error using RGBPixel with TileImageFilter](https://discourse.itk.org/t/error-using-rgbpixel-with-tileimagefilter/3082)

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**Author:** [@sarthakpati](https://discourse.itk.org/u/sarthakpati)\
**Replies:** 3\
**Last updated:** [May 18, 2020, 11:52am UTC](https://discourse.itk.org/t/error-using-rgbpixel-with-tileimagefilter/3082 "2020-05-18T11:52:06Z")

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Hi, I am getting a mutex error when using the following piece of code: using RGBPixelType = itk::RGBPixel\< unsigned char \>; using FinalOutputImageType = itk::Image\< RGBPixelType, 2 \>; using TileFilterType = itk::Til…

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## [Weird/Incorrect results from SimpleITK:ConnectedComponent()](https://discourse.itk.org/t/weird-incorrect-results-from-simpleitk-connectedcomponent/2923)

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**Author:** [@jbi35](https://discourse.itk.org/u/jbi35)\
**Replies:** 9\
**Last updated:** [May 3, 2020, 2:11pm UTC](https://discourse.itk.org/t/weird-incorrect-results-from-simpleitk-connectedcomponent/2923 "2020-05-03T14:11:16Z")

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Hi there, I’ve come across some unexpected behavior while using the procedural interface of the ConnectedComponentImageFilter in SimpleITK. When applying the filter in order to extract the largest connected components i…

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## [How to return PNG as an array instead of writing to file](https://discourse.itk.org/t/how-to-return-png-as-an-array-instead-of-writing-to-file/3013)

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**Author:** [@Henco](https://discourse.itk.org/u/Henco)\
**Replies:** 1\
**Last updated:** [April 28, 2020, 5:25pm UTC](https://discourse.itk.org/t/how-to-return-png-as-an-array-instead-of-writing-to-file/3013 "2020-04-28T17:25:25Z")

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Hi, I’m trying to use ITK in conjunction with Unity. Currently, when my program is called from Unity, it reads a .mha + .raw 3D image file, applies two filters, and outputs a 2D PNG, which is written to another folder w…

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## [OME TIFF pyramid format](https://discourse.itk.org/t/ome-tiff-pyramid-format/1610)

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**Author:** [@phcerdan](https://discourse.itk.org/u/phcerdan)\
**Replies:** 5\
**Last updated:** [April 27, 2020, 5:50pm UTC](https://discourse.itk.org/t/ome-tiff-pyramid-format/1610 "2020-04-27T17:50:35Z")

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It would be neat to add an IO module for this format!

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## [status of ITK+GPU ?](https://discourse.itk.org/t/status-of-itk-gpu/277)

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**Author:** [@nickmarch31](https://discourse.itk.org/u/nickmarch31)\
**Replies:** 10\
**Last updated:** [April 27, 2020, 5:38pm UTC](https://discourse.itk.org/t/status-of-itk-gpu/277 "2020-04-27T17:38:53Z")

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What is the status of ITK-GPU development? Is there anyone currently working on it? Seems like some OpenCL stuff… any CUDA updates besides the small Cuda ITK project released a few years ago?

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## [Connected component filter/ConnectedThresholdImageFilter](https://discourse.itk.org/t/connected-component-filter-connectedthresholdimagefilter/3001)

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**Author:** [@srbn.ghosh89](https://discourse.itk.org/u/srbn.ghosh89)\
**Replies:** 2\
**Last updated:** [April 26, 2020, 1:40pm UTC](https://discourse.itk.org/t/connected-component-filter-connectedthresholdimagefilter/3001 "2020-04-26T13:40:22Z")

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Hi, I have labeled 3D image with two different pixel values. I want to apply image connectivity filter to remove the other noises within the labeling which are creating problems to create a simple surface extraction in …

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## [How Segment the board in the red line of the picture?](https://discourse.itk.org/t/how-segment-the-board-in-the-red-line-of-the-picture/2973)

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**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 7\
**Last updated:** [April 22, 2020, 1:01pm UTC](https://discourse.itk.org/t/how-segment-the-board-in-the-red-line-of-the-picture/2973 "2020-04-22T13:01:07Z")

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image 1 This 3D image was constructed by a series of dicom file. Now I want to segment the content in the red closed line. how to DO!!! image 2 This is one of the series study of the dicom files.

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## [How to run examples from https://itk.org/Wiki/ITK/Examples where we need both ITK and VTK?](https://discourse.itk.org/t/how-to-run-examples-from-https-itk-org-wiki-itk-examples-where-we-need-both-itk-and-vtk/1674)

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**Author:** [@EE18D504\_SINDHURA\_C](https://discourse.itk.org/u/EE18D504_SINDHURA_C)\
**Replies:** 5\
**Last updated:** [April 20, 2020, 1:12pm UTC](https://discourse.itk.org/t/how-to-run-examples-from-https-itk-org-wiki-itk-examples-where-we-need-both-itk-and-vtk/1674 "2020-04-20T13:12:41Z")

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I wanted to try the examples from https://itk.org/Wiki/ITK/Examples. This needs "ITK-VTK glue " to be built. I am not understanding how to do this. I have installed ITK and tried executing a few examples. Do I need to…

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## [itk js readImageDICOMFileSeries Problem to read big series](https://discourse.itk.org/t/itk-js-readimagedicomfileseries-problem-to-read-big-series/2856)

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**Author:** [@Athius](https://discourse.itk.org/u/Athius)\
**Replies:** 18\
**Last updated:** [April 20, 2020, 7:33am UTC](https://discourse.itk.org/t/itk-js-readimagedicomfileseries-problem-to-read-big-series/2856 "2020-04-20T07:33:37Z")

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Hi everyone, I try itk.js using this example (ITK Read Dicom). So I have a NodeJS server and launch a simple webpage to open DICOM Series. When I try to load big Dicom Series (more than 700 images), then the loader do…

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## [How can i read a dicom file in "float pixel format", filtered and write it to an "unsigned char pixel format" dicom file?](https://discourse.itk.org/t/how-can-i-read-a-dicom-file-in-float-pixel-format-filtered-and-write-it-to-an-unsigned-char-pixel-format-dicom-file/2967)

<div class="topic-metadata">

**Author:** [@wulicheng](https://discourse.itk.org/u/wulicheng)\
**Replies:** 0\
**Last updated:** [April 18, 2020, 2:14am UTC](https://discourse.itk.org/t/how-can-i-read-a-dicom-file-in-float-pixel-format-filtered-and-write-it-to-an-unsigned-char-pixel-format-dicom-file/2967 "2020-04-18T02:14:42Z")

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ConnectedThresholdOutput3.dcm (513.0 KB) next is my code from web: typedef float InternalPixelType; const unsigned int Dimension = 2; typedef signed short InputPixelType; typedef signed short O…

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## [Decode Tiff Image Array Buffer to pixel data](https://discourse.itk.org/t/decode-tiff-image-array-buffer-to-pixel-data/2964)

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**Author:** [@Jayesh\_Borgaonkar](https://discourse.itk.org/u/Jayesh_Borgaonkar)\
**Replies:** 0\
**Last updated:** [April 17, 2020, 5:34pm UTC](https://discourse.itk.org/t/decode-tiff-image-array-buffer-to-pixel-data/2964 "2020-04-17T17:34:10Z")

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I want to decode a 16 bit Tiff Image Array Buffer shown below and extract the data in 16 bits, which is pixel intensities in Java script Any library or decoder that can extract 16 bit tiff image to 16 bit data, i know t…

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