# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=349

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

**Page:** 350

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## [Automate import-segmentation-export process for bronchial tree](https://discourse.slicer.org/t/automate-import-segmentation-export-process-for-bronchial-tree/10617)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 4\
**Last updated:** [March 12, 2020, 2:21pm UTC](https://discourse.slicer.org/t/automate-import-segmentation-export-process-for-bronchial-tree/10617 "2020-03-12T14:21:53Z")

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Hello, I have used 3DSlicer for a few years now, but have not attempted to automate any processes. My group is interested in segmenting air-filled structures and cavities, which ends-up becoming a very simple and consi…

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## [Creating masked nifti from ROI](https://discourse.slicer.org/t/creating-masked-nifti-from-roi/10539)

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**Author:** [@joelyss](https://discourse.slicer.org/u/joelyss)\
**Replies:** 2\
**Last updated:** [March 12, 2020, 1:53pm UTC](https://discourse.slicer.org/t/creating-masked-nifti-from-roi/10539 "2020-03-12T13:53:29Z")

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Software version: 3D Slicer 4.10.2 I would like to draw an ROI on a ACPC transformed dataset, then create a binary mask of that ROI whee everything inside has a value of 1 and zeroes outside, and to have the same dimens…

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## [Save nrrd as stl but only the outside](https://discourse.slicer.org/t/save-nrrd-as-stl-but-only-the-outside/10653)

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**Author:** [@guido\_galetto](https://discourse.slicer.org/u/guido_galetto)\
**Replies:** 1\
**Last updated:** [March 12, 2020, 4:08am UTC](https://discourse.slicer.org/t/save-nrrd-as-stl-but-only-the-outside/10653 "2020-03-12T04:08:09Z")

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Hi! I want to save a .nrrd file as a stl, but i want only the superficial mesh. I need the skin to make a 3d orthosis. THanks!

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## [Create Model from Scalar Volume with highest resolution](https://discourse.slicer.org/t/create-model-from-scalar-volume-with-highest-resolution/10644)

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**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 1\
**Last updated:** [March 11, 2020, 4:26pm UTC](https://discourse.slicer.org/t/create-model-from-scalar-volume-with-highest-resolution/10644 "2020-03-11T16:26:59Z")

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Hi, I have a ScalarVolume with only two intensities (0,1) and I would like to convert it into a vtkMRMLModelNode. The steps that I follow are the following: In Editor (I convert it into a Label Map) In Model Creator (…

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## [Need to change orientation marker (eg human figure) relative to volume](https://discourse.slicer.org/t/need-to-change-orientation-marker-eg-human-figure-relative-to-volume/10622)

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**Author:** [@Joshua\_Broder](https://discourse.slicer.org/u/Joshua_Broder)\
**Replies:** 3\
**Last updated:** [March 11, 2020, 7:57pm UTC](https://discourse.slicer.org/t/need-to-change-orientation-marker-eg-human-figure-relative-to-volume/10622 "2020-03-11T19:57:55Z")

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Operating system: Windows Slicer version: 4.11.0-2020-02-20 Expected behavior: I need to rotate the human figure orientation marker to match the orientation of my image volume. Actual behavior: Currently, the orienta…

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## [Piece of C++ programming in ITK examples](https://discourse.slicer.org/t/piece-of-c-programming-in-itk-examples/10648)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 5\
**Last updated:** [March 11, 2020, 7:47pm UTC](https://discourse.slicer.org/t/piece-of-c-programming-in-itk-examples/10648 "2020-03-11T19:47:38Z")

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Hey guys, very basic question here. What does the operator \<\< do in the following line of the example DeformableRegistration6.cxx? TransformType::MeshSizeType requiredMeshSize; for( unsigned int d = 0; d \< ImageDimensi…

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## [position and to move (x,y,z)  object in 3D Scene](https://discourse.slicer.org/t/position-and-to-move-x-y-z-object-in-3d-scene/10541)

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**Author:** [@kobidk](https://discourse.slicer.org/u/kobidk)\
**Replies:** 6\
**Last updated:** [March 11, 2020, 7:20pm UTC](https://discourse.slicer.org/t/position-and-to-move-x-y-z-object-in-3d-scene/10541 "2020-03-11T19:20:25Z")

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I would like to know whether the package 3D Slicer ( C++ Windows OS) provides APIs which allow to position and to move (x,y,z) object in 3D Scene ( build from DICOM CT scan files) and update the object position R.T (…

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## [Place fiducial button does not work after importing scene](https://discourse.slicer.org/t/place-fiducial-button-does-not-work-after-importing-scene/10643)

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**Author:** [@cpinter](https://discourse.slicer.org/u/cpinter)\
**Replies:** 3\
**Last updated:** [March 11, 2020, 2:53pm UTC](https://discourse.slicer.org/t/place-fiducial-button-does-not-work-after-importing-scene/10643 "2020-03-11T14:53:28Z")

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Hi all, I noticed with a very recent nightly that if I do the following: Load a scene Click the place fiducial button on the toolbar then the preview fiducial does not appear in the viewers under the cursor, and if I…

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## [Image Visualization](https://discourse.slicer.org/t/image-visualization/10639)

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**Author:** [@jaybabpeterson](https://discourse.slicer.org/u/jaybabpeterson)\
**Replies:** 1\
**Last updated:** [March 11, 2020, 2:18pm UTC](https://discourse.slicer.org/t/image-visualization/10639 "2020-03-11T14:18:58Z")

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Operating system: Slicer version: Expected behavior: Actual behavior: Please, i need you guys help on data visualization. I try loading MR-head.nrrd DICOM data into 3D Slicer but I could not visualise it. What can I…

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## [Orientation issue loading vtk mesh](https://discourse.slicer.org/t/orientation-issue-loading-vtk-mesh/10641)

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**Author:** [@alixchcl](https://discourse.slicer.org/u/alixchcl)\
**Replies:** 1\
**Last updated:** [March 11, 2020, 1:37pm UTC](https://discourse.slicer.org/t/orientation-issue-loading-vtk-mesh/10641 "2020-03-11T13:37:40Z")

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Operating system: Linux Slicer version: 4.11.0 (-2020-03-03) Expected behavior: Actual behavior: Hi, I am trying Slicer new version, and I encounter orientation problems while reading vtk meshes. The following segmen…

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## [Problems loading dicom file](https://discourse.slicer.org/t/problems-loading-dicom-file/10583)

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**Author:** [@hprint3d](https://discourse.slicer.org/u/hprint3d)\
**Replies:** 4\
**Last updated:** [March 11, 2020, 9:19am UTC](https://discourse.slicer.org/t/problems-loading-dicom-file/10583 "2020-03-11T09:19:08Z")

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Operating system: windows10 Slicer version: 4.10.2 Expected behavior: Actual behavior: Hello, first of all, sorry for my English, it is translated by google. I need help with some dicom files that I am unable to load…

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## [DICOM import can be attempted before creating database](https://discourse.slicer.org/t/dicom-import-can-be-attempted-before-creating-database/10459)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [February 28, 2020, 7:17pm UTC](https://discourse.slicer.org/t/dicom-import-can-be-attempted-before-creating-database/10459 "2020-02-28T19:17:38Z")

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Actually on this note I should mention that behavior of DICOMBrowser for the new users of Slicer is confusing. See the screenshot below. Even though there is an error message indicating that the DICOM DB needs to be crea…

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## [Show 3D crashing after threshold](https://discourse.slicer.org/t/show-3d-crashing-after-threshold/10593)

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**Author:** [@rfarman](https://discourse.slicer.org/u/rfarman)\
**Replies:** 15\
**Last updated:** [March 10, 2020, 5:46pm UTC](https://discourse.slicer.org/t/show-3d-crashing-after-threshold/10593 "2020-03-10T17:46:49Z")

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Hi, Was wondering if anyone could help me! I am trying to segment a frog skeleton. Once I have used threshold and want to view the 3d image it crashes. I have everything closed except for slicer and I suspect it might b…

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## [Warnings detected during DICOM load](https://discourse.slicer.org/t/warnings-detected-during-dicom-load/10614)

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**Author:** [@Taehyeong](https://discourse.slicer.org/u/Taehyeong)\
**Replies:** 2\
**Last updated:** [March 10, 2020, 3:13pm UTC](https://discourse.slicer.org/t/warnings-detected-during-dicom-load/10614 "2020-03-10T15:13:57Z")

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Import CT dicom image included structure~ . message find out!! Warnings detected during load. Examine data in Advanced mode for details. Load anyway? Could not load: 19: ARIA RadOnc Structure Sets as a Scalar Volume …

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## [DICOM structure set import](https://discourse.slicer.org/t/dicom-structure-set-import/10615)

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**Author:** [@Taehyeong](https://discourse.slicer.org/u/Taehyeong)\
**Replies:** 1\
**Last updated:** [March 10, 2020, 12:57pm UTC](https://discourse.slicer.org/t/dicom-structure-set-import/10615 "2020-03-10T12:57:30Z")

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Is there a method to import a contoured CT image (dicom file, Varian eclipse) with structures(Target, OAR) to 3D slider program? I want to bring back the structure that Eclipse drew.

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## [loading a huge amount of data](https://discourse.slicer.org/t/loading-a-huge-amount-of-data/10613)

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**Author:** [@mo\_es](https://discourse.slicer.org/u/mo_es)\
**Replies:** 0\
**Last updated:** [March 10, 2020, 12:41pm UTC](https://discourse.slicer.org/t/loading-a-huge-amount-of-data/10613 "2020-03-10T12:41:03Z")

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my images volume is about 6GB and i have a major problem for loading. please tell me how can i load this amount of data? Operating system: Slicer version:4.10.2 Expected behavior: Actual behavior:

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## [How to threshold only one slice in the DICOM Module](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602)

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**Author:** [@Vincent\_C](https://discourse.slicer.org/u/Vincent_C)\
**Replies:** 6\
**Last updated:** [March 10, 2020, 3:18am UTC](https://discourse.slicer.org/t/how-to-threshold-only-one-slice-in-the-dicom-module/10602 "2020-03-10T03:18:04Z")

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Hi all, I have loaded a 3D- CT scan into Slicer using the DICOM module. How can I apply thresholding to only one slice? Thanks

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## [Failed to run slicer codes in PyCharm, what's wrong with my settings?](https://discourse.slicer.org/t/failed-to-run-slicer-codes-in-pycharm-whats-wrong-with-my-settings/10015)

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**Author:** [@Illusion](https://discourse.slicer.org/u/Illusion)\
**Replies:** 11\
**Last updated:** [March 10, 2020, 1:26am UTC](https://discourse.slicer.org/t/failed-to-run-slicer-codes-in-pycharm-whats-wrong-with-my-settings/10015 "2020-03-10T01:26:50Z")

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Operating system: Tried both Windows10 and Linux Ubuntu Slicer version:4.10.2 Expected behavior:Run and debug slicer in PyCharm using codes from https://github.com/Slicer/SlicerNotebooks/blob/master/01\_Data\_Loading\_and…

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## [Convert 3d nfti data to 2d](https://discourse.slicer.org/t/convert-3d-nfti-data-to-2d/10605)

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**Author:** [@safa](https://discourse.slicer.org/u/safa)\
**Replies:** 2\
**Last updated:** [March 10, 2020, 12:05am UTC](https://discourse.slicer.org/t/convert-3d-nfti-data-to-2d/10605 "2020-03-10T00:05:03Z")

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Hi, I have 3D nifti data i want to convert it to 2d . Are there any tools in slicer you can recommend? Thanks a lot!

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## [Unable to show the result from filter - SimpleITK](https://discourse.slicer.org/t/unable-to-show-the-result-from-filter-simpleitk/10601)

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**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 1\
**Last updated:** [March 9, 2020, 6:51pm UTC](https://discourse.slicer.org/t/unable-to-show-the-result-from-filter-simpleitk/10601 "2020-03-09T18:51:55Z")

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Hello, What I am trying to achieve is to apply BinaryMorphologicalOpeningImageFilter to a vtkMRMLModelNode. These are the steps that I follow: Add the stl model as Segmentation into Slicer Convert Segmentation into v…

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## [Importing labeled image to segment directly](https://discourse.slicer.org/t/importing-labeled-image-to-segment-directly/10597)

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**Author:** [@muntahi398](https://discourse.slicer.org/u/muntahi398)\
**Replies:** 2\
**Last updated:** [March 9, 2020, 6:23pm UTC](https://discourse.slicer.org/t/importing-labeled-image-to-segment-directly/10597 "2020-03-09T18:23:32Z")

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Dear slicer experts, Recently I was working with some 3D image volume analysis in another software. Then I am trying to further analyze and visualize the volume in 3d slicer. work step Import volume of segemented and…

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## [Simulate user interactions](https://discourse.slicer.org/t/simulate-user-interactions/10598)

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**Author:** [@Yash\_Kumar\_Gumashta](https://discourse.slicer.org/u/Yash_Kumar_Gumashta)\
**Replies:** 1\
**Last updated:** [March 9, 2020, 1:24pm UTC](https://discourse.slicer.org/t/simulate-user-interactions/10598 "2020-03-09T13:24:24Z")

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Hello Experts, I am an IT professional who is trying to simulate a healthcare environment on a large scale and hence we are using software to simulate that workload on our systems, So I am basically trying to get 3D sli…

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## [CTKAPPLAUNCHER error with custom Slicer build in Visual Studio](https://discourse.slicer.org/t/ctkapplauncher-error-with-custom-slicer-build-in-visual-studio/10513)

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**Author:** [@aptirumalai](https://discourse.slicer.org/u/aptirumalai)\
**Replies:** 2\
**Last updated:** [March 7, 2020, 10:37pm UTC](https://discourse.slicer.org/t/ctkapplauncher-error-with-custom-slicer-build-in-visual-studio/10513 "2020-03-07T22:37:04Z")

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I am getting failures with a custom Slicer application that Kitware had helped us develop 3 years ago. Most of the projects build fine. The issue is with the CTKAPPLAUNCHER project. From what I can tell, it appears to h…

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## [Need a good source of animal CT scans](https://discourse.slicer.org/t/need-a-good-source-of-animal-ct-scans/10585)

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**Author:** [@dayanjan](https://discourse.slicer.org/u/dayanjan)\
**Replies:** 2\
**Last updated:** [March 7, 2020, 8:03pm UTC](https://discourse.slicer.org/t/need-a-good-source-of-animal-ct-scans/10585 "2020-03-07T20:03:39Z")

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Hi All, Been using Slicer for a long time but first time posting here. I am looking for a good source of CT scans obtained from animals such as cows, horses, dogs, pigs etc. Trying to see how well I can use slicer to ge…

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## [create color mask in dicom volumen and save this change.](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567)

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**Author:** [@Carlos\_Ferro](https://discourse.slicer.org/u/Carlos_Ferro)\
**Replies:** 13\
**Last updated:** [March 6, 2020, 3:23pm UTC](https://discourse.slicer.org/t/create-color-mask-in-dicom-volumen-and-save-this-change/10567 "2020-03-06T15:23:06Z")

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it´s posible to create color mask and add this color mask in dicom volume, without that this mask to see in binary. or is possible create color mask of fiducial an save this mask in dicom volume .

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## [Aligning Segmentations and images using python](https://discourse.slicer.org/t/aligning-segmentations-and-images-using-python/7446)

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**Author:** [@Andrea\_Barucci1](https://discourse.slicer.org/u/Andrea_Barucci1)\
**Replies:** 10\
**Last updated:** [March 6, 2020, 3:02pm UTC](https://discourse.slicer.org/t/aligning-segmentations-and-images-using-python/7446 "2020-03-06T15:02:22Z")

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Dear all I have a problem to understand how to use Segmentations nrrd file with image files in Python. My problem is: I’m able to open a stack of images and its segmentations using pynrrd. However I can’t understand …

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## [What is the simplest way to generate an IVUS 3D model from a set of pictures or an avi?](https://discourse.slicer.org/t/what-is-the-simplest-way-to-generate-an-ivus-3d-model-from-a-set-of-pictures-or-an-avi/10470)

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**Author:** [@gbolaga](https://discourse.slicer.org/u/gbolaga)\
**Replies:** 9\
**Last updated:** [March 6, 2020, 2:33pm UTC](https://discourse.slicer.org/t/what-is-the-simplest-way-to-generate-an-ivus-3d-model-from-a-set-of-pictures-or-an-avi/10470 "2020-03-06T14:33:35Z")

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## [Apply BSpline transformation in MATLAB](https://discourse.slicer.org/t/apply-bspline-transformation-in-matlab/10573)

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**Author:** [@Farah](https://discourse.slicer.org/u/Farah)\
**Replies:** 1\
**Last updated:** [March 6, 2020, 2:45am UTC](https://discourse.slicer.org/t/apply-bspline-transformation-in-matlab/10573 "2020-03-06T02:45:19Z")

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Hi, I have registered two CT scans using non-rigid registration and got a bspline transform as .h5 file. I applied this transform on my segmented geometry using 3Dslicer but I want to apply this transform on point set …

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## [DWIconvert error](https://discourse.slicer.org/t/dwiconvert-error/10561)

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**Author:** [@nabin](https://discourse.slicer.org/u/nabin)\
**Replies:** 1\
**Last updated:** [March 5, 2020, 8:26pm UTC](https://discourse.slicer.org/t/dwiconvert-error/10561 "2020-03-05T20:26:23Z")

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Operating system: macos 10.14.6 Slicer version: 4.10.2 Dear 3Dslicer team, I am trying to visualize a FSL output file in slicer. I am trying to convert the output nifti file to .nrrd format using DWIconvert but unfort…

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## [Color changing on selected area of DICOM volume](https://discourse.slicer.org/t/color-changing-on-selected-area-of-dicom-volume/4619)

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**Author:** [@M\_pavi](https://discourse.slicer.org/u/M_pavi)\
**Replies:** 1\
**Last updated:** [November 2, 2018, 1:27am UTC](https://discourse.slicer.org/t/color-changing-on-selected-area-of-dicom-volume/4619 "2018-11-02T01:27:25Z")

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Hi I want to change color/ brightness on selected area of my DICOM module. Not the full module but only selected area. For an example if I have a full body voume i want to change color or brigtness only head.

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