# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=313

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

**Page:** 314

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## [Linux freezes completely when using 3D slicer gui](https://discourse.slicer.org/t/linux-freezes-completely-when-using-3d-slicer-gui/14237)

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**Author:** [@CST](https://discourse.slicer.org/u/CST)\
**Replies:** 7\
**Last updated:** [November 4, 2020, 9:42am UTC](https://discourse.slicer.org/t/linux-freezes-completely-when-using-3d-slicer-gui/14237 "2020-11-04T09:42:45Z")

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Operating system: Ubunutu 18.04 Slicer version: 4.10.2-linux-amd64 Expected behavior: run smoothly Actual behavior: Computer freezes completely and has to be forcefully rebooted Dear community, I use slicer for a co…

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## [Problem when adding second mrb file to scene](https://discourse.slicer.org/t/problem-when-adding-second-mrb-file-to-scene/14409)

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**Author:** [@alexjamesmajor](https://discourse.slicer.org/u/alexjamesmajor)\
**Replies:** 5\
**Last updated:** [November 3, 2020, 11:15pm UTC](https://discourse.slicer.org/t/problem-when-adding-second-mrb-file-to-scene/14409 "2020-11-03T23:15:41Z")

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Running on Windows 10 and a recent version of Slicer (shown in picture) When I add a second .mrb file (I’m aiming to compare two different scans) with File → Add Data, the scene goes blank. This doesn’t appear to be a R…

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## [How to get HU values at each fiducial points](https://discourse.slicer.org/t/how-to-get-hu-values-at-each-fiducial-points/14378)

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**Author:** [@MasatoshiOBA](https://discourse.slicer.org/u/MasatoshiOBA)\
**Replies:** 7\
**Last updated:** [November 3, 2020, 11:12pm UTC](https://discourse.slicer.org/t/how-to-get-hu-values-at-each-fiducial-points/14378 "2020-11-03T23:12:03Z")

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Operating system: windows 10 Slicer version: 4.11.20200930 How can I get the HU (CT) value at each fiducial placed on a model surface? I could convert vertices of an STL model to a group of fiducials as shown in the a…

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## [Blank display in standard views](https://discourse.slicer.org/t/blank-display-in-standard-views/14407)

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**Author:** [@Kalman](https://discourse.slicer.org/u/Kalman)\
**Replies:** 8\
**Last updated:** [November 3, 2020, 8:46pm UTC](https://discourse.slicer.org/t/blank-display-in-standard-views/14407 "2020-11-03T20:46:21Z")

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Hi All, I have a question regarding the display: My computer does not show the orthogonal views with the latest nightly build versions (in the past week). I’ve tried with the sample datasets too, but I can only visuali…

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## [Orientation Marker incorrect?](https://discourse.slicer.org/t/orientation-marker-incorrect/14399)

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**Author:** [@Tommaso\_Di\_Noto](https://discourse.slicer.org/u/Tommaso_Di_Noto)\
**Replies:** 2\
**Last updated:** [November 3, 2020, 8:17pm UTC](https://discourse.slicer.org/t/orientation-marker-incorrect/14399 "2020-11-03T20:17:23Z")

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Hi All! I have a dataset of MR angiography patients. Through sitk, I checked with GetDirections() the direction of every volume. It turns out they all have direction (1.0, 0.0, 0.0, 0.0, 1.0, 0.0, 0.0, 0.0, 1.0), excep…

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## [Latest Slicer showing black screen](https://discourse.slicer.org/t/latest-slicer-showing-black-screen/14303)

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**Author:** [@drvarunagarwal](https://discourse.slicer.org/u/drvarunagarwal)\
**Replies:** 5\
**Last updated:** [November 3, 2020, 6:19am UTC](https://discourse.slicer.org/t/latest-slicer-showing-black-screen/14303 "2020-11-03T06:19:54Z")

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Hi, I am using slicer version 4.11.20200930 on windows 10 Pro version 2004 - 64 bit with latest drivers running on macbook pro intel core i5-4288U @ 2.60GHz, 8.00 GB ram, Intel Iris graphics 5100 (driver date 15-05-2…

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## [Creating target points on a 3D model of a bone then exporting these out as a python script?](https://discourse.slicer.org/t/creating-target-points-on-a-3d-model-of-a-bone-then-exporting-these-out-as-a-python-script/14341)

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**Author:** [@tharisata\_c](https://discourse.slicer.org/u/tharisata_c)\
**Replies:** 5\
**Last updated:** [November 2, 2020, 8:31pm UTC](https://discourse.slicer.org/t/creating-target-points-on-a-3d-model-of-a-bone-then-exporting-these-out-as-a-python-script/14341 "2020-11-02T20:31:31Z")

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HI, I’m very new to Slicer 3D but I’m planning to use it for a surgical robot. Ideally, I want to be able to visualize a bone at position referenced to a frame (which I define). Then, I want to create target points on …

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## [Show Slicer Views in selected 3d windows](https://discourse.slicer.org/t/show-slicer-views-in-selected-3d-windows/14331)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [November 2, 2020, 8:18pm UTC](https://discourse.slicer.org/t/show-slicer-views-in-selected-3d-windows/14331 "2020-11-02T20:18:19Z")

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I have many 3d windows. And I want to show the slice view in only of the 3d view. How can I do that?

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## [Input files in Scattered Transform module](https://discourse.slicer.org/t/input-files-in-scattered-transform-module/13544)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 9\
**Last updated:** [November 2, 2020, 8:15pm UTC](https://discourse.slicer.org/t/input-files-in-scattered-transform-module/13544 "2020-11-02T20:15:53Z")

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Hi 3D Slicer experts and all I have 2 images (CT and MRI), which MRI image is with distortion. I want to calculate the B-Spline Transform, using Scattered Transform module. which one do I insert for “file with initial …

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## [How to get HU values at each fiducial points.](https://discourse.slicer.org/t/how-to-get-hu-values-at-each-fiducial-points/14383)

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**Author:** [@MasatoshiOBA](https://discourse.slicer.org/u/MasatoshiOBA)\
**Replies:** 0\
**Last updated:** [November 2, 2020, 12:52pm UTC](https://discourse.slicer.org/t/how-to-get-hu-values-at-each-fiducial-points/14383 "2020-11-02T12:52:52Z")

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I would like to know how I can get HU values at multiple fiducial points in the same group. Ultimately, I’d like to get the HU values of the pixels corresponding to the vertices of the STL model placed in the CT volume …

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## [Error in time stamp of multivolume data](https://discourse.slicer.org/t/error-in-time-stamp-of-multivolume-data/14357)

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**Author:** [@Selva](https://discourse.slicer.org/u/Selva)\
**Replies:** 3\
**Last updated:** [November 2, 2020, 7:00pm UTC](https://discourse.slicer.org/t/error-in-time-stamp-of-multivolume-data/14357 "2020-11-02T19:00:20Z")

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Hi all, I have a dynamic CT data set, saved as individual frames. when I load them in the order they appear , the order of the frames (the sequence) is wrong- Appear interlaced. How do I make the order according to co…

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## [MicroCT--Rescale, Resample](https://discourse.slicer.org/t/microct-rescale-resample/14388)

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**Author:** [@tsehrhardt](https://discourse.slicer.org/u/tsehrhardt)\
**Replies:** 4\
**Last updated:** [November 2, 2020, 5:24pm UTC](https://discourse.slicer.org/t/microct-rescale-resample/14388 "2020-11-02T17:24:45Z")

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I was recording dimension and resolution data for a set of microCT scans I’ve been working on and I noticed some issues between 16-bit and 8-bit nrrd volumes, resampled 8-bit (to larger slice thickness for modeling), and…

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## [Lung airway branching calculator](https://discourse.slicer.org/t/lung-airway-branching-calculator/1364)

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**Author:** [@jbassein](https://discourse.slicer.org/u/jbassein)\
**Replies:** 9\
**Last updated:** [November 2, 2020, 5:14pm UTC](https://discourse.slicer.org/t/lung-airway-branching-calculator/1364 "2020-11-02T17:14:16Z")

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Hey Guys, I am trying to calculate the number of airway branch points in the lungs of several patient CT scans. Does anyone know how to do this in a fairly automatic fashion? I am also looking to calculate the total di…

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## [Fuzzy Locally Adaptive Bayesian in 3D Slicer](https://discourse.slicer.org/t/fuzzy-locally-adaptive-bayesian-in-3d-slicer/14385)

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**Author:** [@Nora](https://discourse.slicer.org/u/Nora)\
**Replies:** 1\
**Last updated:** [November 2, 2020, 4:57pm UTC](https://discourse.slicer.org/t/fuzzy-locally-adaptive-bayesian-in-3d-slicer/14385 "2020-11-02T16:57:09Z")

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Hi all, I’ve been trying to use different segmentation methods to study the reproducibility of Radiomics in PET data. I was able to do the manual and the GrowCut algorithm for segmentation. Yet, I want to try to more m…

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## [Set center of rotation for transform in 3D view](https://discourse.slicer.org/t/set-center-of-rotation-for-transform-in-3d-view/14363)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 6\
**Last updated:** [November 2, 2020, 4:39pm UTC](https://discourse.slicer.org/t/set-center-of-rotation-for-transform-in-3d-view/14363 "2020-11-02T16:39:36Z")

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Even though it is possible to rotate the object in 3D view interactively whenever the rotation transformation is applied it is working as origin in the world origin ( I guess. ) 3D interactor is very difficult to precis…

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## [Sequence of PNGs, getting interlaced artifact](https://discourse.slicer.org/t/sequence-of-pngs-getting-interlaced-artifact/14374)

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**Author:** [@tomasb](https://discourse.slicer.org/u/tomasb)\
**Replies:** 3\
**Last updated:** [November 2, 2020, 2:54pm UTC](https://discourse.slicer.org/t/sequence-of-pngs-getting-interlaced-artifact/14374 "2020-11-02T14:54:23Z")

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Operating system: win10 Slicer version: 4.11.20200930 Expected behavior: I follow this one minute tutorial (Load sequence of PNG files as a 3D volume into 3D Slicer - YouTube) and expect the 3d model. Actual behavio…

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## [Smoothing Recursive Gaussian Image Filter](https://discourse.slicer.org/t/smoothing-recursive-gaussian-image-filter/14292)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 2\
**Last updated:** [November 1, 2020, 8:34pm UTC](https://discourse.slicer.org/t/smoothing-recursive-gaussian-image-filter/14292 "2020-11-01T20:34:03Z")

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Slicer version:4.10.1 Hi 3D Slicer experts and all I used Smoothing Recursive Gaussian Image Filter from simple filters module. My input volume is a CT image and I chose various sigma values, which in the below figure,…

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## [Help with flood filling segmentation](https://discourse.slicer.org/t/help-with-flood-filling-segmentation/14349)

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**Author:** [@carlos.rinaldi](https://discourse.slicer.org/u/carlos.rinaldi)\
**Replies:** 1\
**Last updated:** [November 1, 2020, 8:10pm UTC](https://discourse.slicer.org/t/help-with-flood-filling-segmentation/14349 "2020-11-01T20:10:54Z")

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I am new to slicer. Working on segmentation using the SegmentEditorExtraEffects on Slicer build 4.10.2 on a Mac running 10.13.6. I am trying to use flood filling to create a segmentation. I create a new segment, choose …

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## [How can I export 2 overlayed volumes to dicom files or save 2 overlayed volumes to a single nifty file?](https://discourse.slicer.org/t/how-can-i-export-2-overlayed-volumes-to-dicom-files-or-save-2-overlayed-volumes-to-a-single-nifty-file/14369)

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**Author:** [@AnnaZhuravleva](https://discourse.slicer.org/u/AnnaZhuravleva)\
**Replies:** 1\
**Last updated:** [November 1, 2020, 7:28pm UTC](https://discourse.slicer.org/t/how-can-i-export-2-overlayed-volumes-to-dicom-files-or-save-2-overlayed-volumes-to-a-single-nifty-file/14369 "2020-11-01T19:28:59Z")

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Operating system:Windows Slicer version: 4.11.20200930 Expected behavior: Save two overlayed modules into a single nifty file or dicom files Actual behavior:

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## [Collection of 2d images from a single 3d .stl object](https://discourse.slicer.org/t/collection-of-2d-images-from-a-single-3d-stl-object/14370)

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**Author:** [@puia](https://discourse.slicer.org/u/puia)\
**Replies:** 0\
**Last updated:** [November 1, 2020, 3:41pm UTC](https://discourse.slicer.org/t/collection-of-2d-images-from-a-single-3d-stl-object/14370 "2020-11-01T15:41:36Z")

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Hello I am researching to find a way to have a collection of 2d images from a single 3d .stl object in order to use that collection of 2d images for training a machine learning model. first : can i use the 3Dslicer as…

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## [Full installation for Qt, but compite Slicer met error: "Library not found: Qt5Cored"](https://discourse.slicer.org/t/full-installation-for-qt-but-compite-slicer-met-error-library-not-found-qt5cored/14329)

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**Author:** [@chenyx](https://discourse.slicer.org/u/chenyx)\
**Replies:** 7\
**Last updated:** [November 1, 2020, 10:12am UTC](https://discourse.slicer.org/t/full-installation-for-qt-but-compite-slicer-met-error-library-not-found-qt5cored/14329 "2020-11-01T10:12:05Z")

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I use Cmake Gui to compile Slicer Source code download. The develop tools are: 1.vs 2015 2.Qt 5.13.1 3. CMake \>3.15.1 4.Git \>1.7.10 I add Qt5\_DIR variable pointing to Qt5 folder : D:\\Qt\\Qt5.13.1\\5.13.1\\msvc2015\_64\\l…

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## [Black screen on Yellow, Red and Green views on Slicer Preview Release](https://discourse.slicer.org/t/black-screen-on-yellow-red-and-green-views-on-slicer-preview-release/14354)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 1\
**Last updated:** [November 1, 2020, 12:26am UTC](https://discourse.slicer.org/t/black-screen-on-yellow-red-and-green-views-on-slicer-preview-release/14354 "2020-11-01T00:26:08Z")

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This happens after you load a ScalarVolume (CTChest from SampleData), the slices are shown full of black and changing the slice has no effects This happens on the latest preview release. Slicer module to load models …

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## [Insert sequence Browser Toolbar in a python module](https://discourse.slicer.org/t/insert-sequence-browser-toolbar-in-a-python-module/14335)

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**Author:** [@marianaslicer](https://discourse.slicer.org/u/marianaslicer)\
**Replies:** 3\
**Last updated:** [October 30, 2020, 5:19pm UTC](https://discourse.slicer.org/t/insert-sequence-browser-toolbar-in-a-python-module/14335 "2020-10-30T17:19:38Z")

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Hello! I am trying to develop a python scripted module using Sequences extension. I already successfully create a sequence (although it appears as a vtkMRMLScalarVolumeNode) and I can display the sequence by using the S…

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## [Pedicle screw simulator extension - 3D rendering not functional](https://discourse.slicer.org/t/pedicle-screw-simulator-extension-3d-rendering-not-functional/14321)

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**Author:** [@drvarunagarwal](https://discourse.slicer.org/u/drvarunagarwal)\
**Replies:** 2\
**Last updated:** [October 30, 2020, 4:57pm UTC](https://discourse.slicer.org/t/pedicle-screw-simulator-extension-3d-rendering-not-functional/14321 "2020-10-30T16:57:51Z")

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hi I need some help with the pedicle screw simulator module. After loading CT DICOM, when I go to second step, automatic 3D rendering is not happening. it has a bug on the step 2 because volume rendering does not show…

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## [Transforms not appearing after modification of config file](https://discourse.slicer.org/t/transforms-not-appearing-after-modification-of-config-file/14328)

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**Author:** [@Ada\_123](https://discourse.slicer.org/u/Ada_123)\
**Replies:** 0\
**Last updated:** [October 30, 2020, 1:34pm UTC](https://discourse.slicer.org/t/transforms-not-appearing-after-modification-of-config-file/14328 "2020-10-30T13:34:46Z")

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Hello, I would be very grateful if someone could have a look at the config file. We wanted to add on one more tool (Biopsy Needle) after the modification of the config file. Previous tools transforms appear but Biopsy N…

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## [Convert .dcm images to DICOM case](https://discourse.slicer.org/t/convert-dcm-images-to-dicom-case/14314)

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**Author:** [@OLIVIA\_GENOVA](https://discourse.slicer.org/u/OLIVIA_GENOVA)\
**Replies:** 1\
**Last updated:** [October 30, 2020, 4:32am UTC](https://discourse.slicer.org/t/convert-dcm-images-to-dicom-case/14314 "2020-10-30T04:32:18Z")

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Operating system: iOS Slicer version: 4.10.2 Expected behavior: Open DICOM 3D image Actual behavior: 0 patients found… Hello, I’m a student and I need to do the segmentation and mesh of an aorta with a disease. We h…

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## [Interpolating points outside image](https://discourse.slicer.org/t/interpolating-points-outside-image/14319)

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**Author:** [@Nadun\_19](https://discourse.slicer.org/u/Nadun_19)\
**Replies:** 1\
**Last updated:** [October 30, 2020, 4:20am UTC](https://discourse.slicer.org/t/interpolating-points-outside-image/14319 "2020-10-30T04:20:53Z")

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Hi I was if there are any extensions on 3dslicer that fixes these flat edges due to images being cut off there: Thanks

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## [Errors occurred in the extraction of vascular centerlines from CT images](https://discourse.slicer.org/t/errors-occurred-in-the-extraction-of-vascular-centerlines-from-ct-images/14320)

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**Author:** [@Chefy21](https://discourse.slicer.org/u/Chefy21)\
**Replies:** 1\
**Last updated:** [October 30, 2020, 4:15am UTC](https://discourse.slicer.org/t/errors-occurred-in-the-extraction-of-vascular-centerlines-from-ct-images/14320 "2020-10-30T04:15:18Z")

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When using this software, I met two problems and asked for solutions… Cannot click Start while segmenting the blood vessel. An error was reported when using the model to calculate the centerline of the vessel.

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## [Some problems about elastix](https://discourse.slicer.org/t/some-problems-about-elastix/14316)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [October 30, 2020, 4:13am UTC](https://discourse.slicer.org/t/some-problems-about-elastix/14316 "2020-10-30T04:13:48Z")

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Hello, teacher, during the process of using Elastix registration, according to the default settings, after the configuration is completed, a part of the new CT image is automatically cropped. For example, I use CT to mat…

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## [Help with planning a path for biopsy using axial and saggital cuts (mark up a line or cylinder)](https://discourse.slicer.org/t/help-with-planning-a-path-for-biopsy-using-axial-and-saggital-cuts-mark-up-a-line-or-cylinder/14287)

<div class="topic-metadata">

**Author:** [@roger\_hightower](https://discourse.slicer.org/u/roger_hightower)\
**Replies:** 3\
**Last updated:** [October 29, 2020, 1:54pm UTC](https://discourse.slicer.org/t/help-with-planning-a-path-for-biopsy-using-axial-and-saggital-cuts-mark-up-a-line-or-cylinder/14287 "2020-10-29T13:54:59Z")

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Thank you so much for taking this question. I would like to plan a path for insertion of a biopsy probe on axial and sagittal images. I do not need anything in 3D rendering. Is there a simple way to do this? I would like…

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