# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=235

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

**Page:** 236

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## [Saving segmentation as DICOM](https://discourse.slicer.org/t/saving-segmentation-as-dicom/21576)

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**Author:** [@WojtekL](https://discourse.slicer.org/u/WojtekL)\
**Replies:** 7\
**Last updated:** [March 2, 2022, 4:02pm UTC](https://discourse.slicer.org/t/saving-segmentation-as-dicom/21576 "2022-03-02T16:02:28Z")

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Hello Community, I’d like to save my segmentation shown on a picture below as a DICOM (.dcm) file instead of (.nrrd). Is there any way to do it?

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## [Error VTK Input port 0 of algorithm vtkTubeFilter has 0 connections but is not optional](https://discourse.slicer.org/t/error-vtk-input-port-0-of-algorithm-vtktubefilter-has-0-connections-but-is-not-optional/22153)

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**Author:** [@steffen-o](https://discourse.slicer.org/u/steffen-o)\
**Replies:** 3\
**Last updated:** [March 2, 2022, 10:22am UTC](https://discourse.slicer.org/t/error-vtk-input-port-0-of-algorithm-vtktubefilter-has-0-connections-but-is-not-optional/22153 "2022-03-02T10:22:14Z")

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Hi, Slicer version: 4.13.0 I’m using 3D Slicer for segmentation and landmarking of micro CT data for quite a while now and I like it very much! The new Markup functionality (Landmark templates,skipping Landmarks, edit…

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## [3D view control with Ctrl + mouse\_Left\_button](https://discourse.slicer.org/t/3d-view-control-with-ctrl-mouse-left-button/22253)

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**Author:** [@skyhsu](https://discourse.slicer.org/u/skyhsu)\
**Replies:** 0\
**Last updated:** [March 2, 2022, 4:00am UTC](https://discourse.slicer.org/t/3d-view-control-with-ctrl-mouse-left-button/22253 "2022-03-02T04:00:11Z")

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Hi , I am using the 3D view to verify CT 3D image. I use the Ctrl+mouse\_Left\_button to view the rotation in plane, it’s good. But is there any way to change the motion to rotation like spin the 3D view(Just YawLeft or…

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## [Trouble with thresholding](https://discourse.slicer.org/t/trouble-with-thresholding/21332)

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**Author:** [@Rosalee\_Elting](https://discourse.slicer.org/u/Rosalee_Elting)\
**Replies:** 10\
**Last updated:** [March 2, 2022, 1:44am UTC](https://discourse.slicer.org/t/trouble-with-thresholding/21332 "2022-03-02T01:44:06Z")

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Operating system: Slicer version: 4.11.20210226 Expected behavior: Segment of hummingbird bill/head Actual behavior: Fragmented segment Hoping for a little input on a set of .tiff files I’m working with. I have uploa…

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## [DICOM images out of order](https://discourse.slicer.org/t/dicom-images-out-of-order/22247)

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**Author:** [@carlosar](https://discourse.slicer.org/u/carlosar)\
**Replies:** 5\
**Last updated:** [March 1, 2022, 10:50pm UTC](https://discourse.slicer.org/t/dicom-images-out-of-order/22247 "2022-03-01T22:50:48Z")

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Operating system: Linux, Ubuntu 20.04 Slicer version: 4.11.20210226 Expected behavior: When loading a DICOM database from the root folder, the order of the images is not inferred from (0020, 0013) Instance Number tag,…

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## [3D slicer doesn't show masks on a NIfTI file](https://discourse.slicer.org/t/3d-slicer-doesnt-show-masks-on-a-nifti-file/22252)

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**Author:** [@Kamyar\_Ghabili](https://discourse.slicer.org/u/Kamyar_Ghabili)\
**Replies:** 1\
**Last updated:** [March 1, 2022, 10:37pm UTC](https://discourse.slicer.org/t/3d-slicer-doesnt-show-masks-on-a-nifti-file/22252 "2022-03-01T22:37:50Z")

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Hi. I want to see masked images as NIftI format using 3D slicer. I use “Add Data” option and upload the file. I can see the images on 3D slicer but not the masks (segmentations). Do you have any idea how to fix this? Tha…

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## [Markups Line discontinuities](https://discourse.slicer.org/t/markups-line-discontinuities/22189)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 4\
**Last updated:** [March 1, 2022, 9:51pm UTC](https://discourse.slicer.org/t/markups-line-discontinuities/22189 "2022-03-01T21:51:17Z")

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I have noticed for awhile these weird discontinuities in the markups line object. Specifically when the line is completely horizontal or vertical it can appear that the 2 control points that make up the line are not conn…

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## [SlicerRadiomics- 3D slicer not responding](https://discourse.slicer.org/t/slicerradiomics-3d-slicer-not-responding/21273)

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**Author:** [@MPhilip](https://discourse.slicer.org/u/MPhilip)\
**Replies:** 1\
**Last updated:** [March 1, 2022, 7:33pm UTC](https://discourse.slicer.org/t/slicerradiomics-3d-slicer-not-responding/21273 "2022-03-01T19:33:04Z")

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Operating system:Windows 11home Slicer version:3D Slicer 4.13.0-2021-12-28 3D slicer shows a greyed out screen/does not respond when I switch to Slicer radiomics module for feature extraction after performing segmentat…

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## [feature extraction is stuck on not responding. ](https://discourse.slicer.org/t/feature-extraction-is-stuck-on-not-responding/22246)

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**Author:** [@Alexandra1](https://discourse.slicer.org/u/Alexandra1)\
**Replies:** 0\
**Last updated:** [March 1, 2022, 7:25pm UTC](https://discourse.slicer.org/t/feature-extraction-is-stuck-on-not-responding/22246 "2022-03-01T19:25:40Z")

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The radiomic feature extraction is stuck on not responding and will take over 24 hours for one single study. Operating system: windows 10 Slicer version: 4.13.0

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## [Understanding the Behavior of the SegmentEditor with converted models](https://discourse.slicer.org/t/understanding-the-behavior-of-the-segmenteditor-with-converted-models/22245)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 0\
**Last updated:** [March 1, 2022, 7:05pm UTC](https://discourse.slicer.org/t/understanding-the-behavior-of-the-segmenteditor-with-converted-models/22245 "2022-03-01T19:05:42Z")

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Hello, When applying a segmentation effect on surface models (converted into segments), the effect needs to be applied twice to get the desired result. For instance, below I try to apply a Gaussian filter to a tube mode…

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## [Does anyone know how to visualize points in IJK coordinates in RAS coordinates?](https://discourse.slicer.org/t/does-anyone-know-how-to-visualize-points-in-ijk-coordinates-in-ras-coordinates/22229)

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**Author:** [@zhuyingxinxs](https://discourse.slicer.org/u/zhuyingxinxs)\
**Replies:** 3\
**Last updated:** [March 1, 2022, 11:12am UTC](https://discourse.slicer.org/t/does-anyone-know-how-to-visualize-points-in-ijk-coordinates-in-ras-coordinates/22229 "2022-03-01T11:12:46Z")

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Once you’ve determined the coordinates of a point in IJK coordinates, how do you visualize it in RAS coordinates? Do we have to do a coordinate transformation first?

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## [How do I clear all the nodes so that it looks like it just started to run?](https://discourse.slicer.org/t/how-do-i-clear-all-the-nodes-so-that-it-looks-like-it-just-started-to-run/22228)

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**Author:** [@yllgl](https://discourse.slicer.org/u/yllgl)\
**Replies:** 2\
**Last updated:** [March 1, 2022, 10:58am UTC](https://discourse.slicer.org/t/how-do-i-clear-all-the-nodes-so-that-it-looks-like-it-just-started-to-run/22228 "2022-03-01T10:58:05Z")

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I just want to use python to help me do some jobs on some patients’ data. Each patient data is independent, and to prevent interference between data while the code is running, I want to be able to clear all currently sav…

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## [Weird crash in 'Cross-section analysis' since VTK e0d1851e22](https://discourse.slicer.org/t/weird-crash-in-cross-section-analysis-since-vtk-e0d1851e22/22211)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 2\
**Last updated:** [March 1, 2022, 9:22am UTC](https://discourse.slicer.org/t/weird-crash-in-cross-section-analysis-since-vtk-e0d1851e22/22211 "2022-03-01T09:22:16Z")

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To reproduce this crash, click on the “show” MIS diameter button after processing a centerline curve generated by ‘Extract centerline’. The Python code does not seem to be in cause, it was working well not long ago. Th…

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## [What does R,A,S stands for?](https://discourse.slicer.org/t/what-does-r-a-s-stands-for/22104)

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**Author:** [@Kane\_Daizah](https://discourse.slicer.org/u/Kane_Daizah)\
**Replies:** 2\
**Last updated:** [March 1, 2022, 6:12am UTC](https://discourse.slicer.org/t/what-does-r-a-s-stands-for/22104 "2022-03-01T06:12:00Z")

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Hi, I’d like to export the Cartesian coordinates of the centerline which is extracted by extract centerline mode. What does R,A,S stands for? Is they correspond to x, y, z in Cartesian coordinate?

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## [An error was encountered while compiling from scratch2](https://discourse.slicer.org/t/an-error-was-encountered-while-compiling-from-scratch2/22223)

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**Author:** [@Tesla2678](https://discourse.slicer.org/u/Tesla2678)\
**Replies:** 0\
**Last updated:** [March 1, 2022, 3:16am UTC](https://discourse.slicer.org/t/an-error-was-encountered-while-compiling-from-scratch2/22223 "2022-03-01T03:16:27Z")

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Operating system: Win10, Visual Studio 2019. Slicer version: Compiling from GIT\_REPOSITORY git://github.com/Slicer/Slicer GIT\_TAG: master Expected behavior: Actual behavior: Severity Code Description Project Fil…

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## [Can you help me to segment the vertebral body of this lumbar spine?](https://discourse.slicer.org/t/can-you-help-me-to-segment-the-vertebral-body-of-this-lumbar-spine/22222)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 0\
**Last updated:** [February 28, 2022, 11:24pm UTC](https://discourse.slicer.org/t/can-you-help-me-to-segment-the-vertebral-body-of-this-lumbar-spine/22222 "2022-02-28T23:24:21Z")

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在segmentCT椎体时, 相邻椎体之间的小关节的连接总是分不开, 下面这个椎体的CTclip, 我做了好长时间做不出理想的model, 谁来帮帮忙呀? When segment CT vertebral bodies, the small joints between adjacent vertebral bodies are always inseparable. For this CT clip of the vertebr…

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## [Rotating an image to align with the 2D projection of the 3d model](https://discourse.slicer.org/t/rotating-an-image-to-align-with-the-2d-projection-of-the-3d-model/22219)

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**Author:** [@Hitesh\_Ganjoo](https://discourse.slicer.org/u/Hitesh_Ganjoo)\
**Replies:** 3\
**Last updated:** [February 28, 2022, 7:55pm UTC](https://discourse.slicer.org/t/rotating-an-image-to-align-with-the-2d-projection-of-the-3d-model/22219 "2022-02-28T19:55:58Z")

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Hi All, I want to rotate a slice view such that the projection of a model in the 2d views is always in the specific orientation(e.g. vertical US probe in the attached image). The 3d model is controlled by several transf…

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## [Gel dosimetry registration step fails](https://discourse.slicer.org/t/gel-dosimetry-registration-step-fails/22059)

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**Author:** [@Kawtar\_Lakrad](https://discourse.slicer.org/u/Kawtar_Lakrad)\
**Replies:** 6\
**Last updated:** [February 28, 2022, 5:10pm UTC](https://discourse.slicer.org/t/gel-dosimetry-registration-step-fails/22059 "2022-02-28T17:10:23Z")

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Thank you so much for your help, the slicelet window pops up again. but the problem now is that I can’t perform automatic registration, which used to take only few sec.

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## [The gamma bar showing pass/fail color](https://discourse.slicer.org/t/the-gamma-bar-showing-pass-fail-color/22218)

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**Author:** [@Kawtar\_Lakrad](https://discourse.slicer.org/u/Kawtar_Lakrad)\
**Replies:** 0\
**Last updated:** [February 28, 2022, 4:16pm UTC](https://discourse.slicer.org/t/the-gamma-bar-showing-pass-fail-color/22218 "2022-02-28T16:16:48Z")

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Operating system: windows 11 Slicer version: 4.13 Expected behavior: once we calculate gamma a bar should show the pass/fail color scale. Actual behavior: I can’t seem to find this scale

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## [Slicer does not recognize .h5 file](https://discourse.slicer.org/t/slicer-does-not-recognize-h5-file/22214)

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**Author:** [@sadaf\_hajiha](https://discourse.slicer.org/u/sadaf_hajiha)\
**Replies:** 0\
**Last updated:** [February 28, 2022, 2:11pm UTC](https://discourse.slicer.org/t/slicer-does-not-recognize-h5-file/22214 "2022-02-28T14:11:37Z")

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I am trying to upload a trained UNet model in .h5 format in 3D slicer, in order to perform segmentation on my ultrasound data. I am using the latest preview release (4.13.0) on my MacBook air. However, I face the error t…

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## [Issues of Extensions-Sandbox and VMTK](https://discourse.slicer.org/t/issues-of-extensions-sandbox-and-vmtk/22209)

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**Author:** [@xiaolin](https://discourse.slicer.org/u/xiaolin)\
**Replies:** 1\
**Last updated:** [February 28, 2022, 10:53am UTC](https://discourse.slicer.org/t/issues-of-extensions-sandbox-and-vmtk/22209 "2022-02-28T10:53:22Z")

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Hi, I am a doctoral student. I am working on the 4D reconstruction of animal cardiac CT now. I am having several issues when I installed the extensions. Windows 10 Professional version. VMTK extension is unavailable …

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## [Failed to fetch MONAI label server](https://discourse.slicer.org/t/failed-to-fetch-monai-label-server/19957)

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**Author:** [@ragwing\_mmh](https://discourse.slicer.org/u/ragwing_mmh)\
**Replies:** 5\
**Last updated:** [February 28, 2022, 10:29am UTC](https://discourse.slicer.org/t/failed-to-fetch-monai-label-server/19957 "2022-02-28T10:29:52Z")

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Operating system: Windows 7 Build 6.1.7601 Slicer version: 4.13.0 2021-08-16 The version of Python: Python 3.6.7 Expected behavior: Fetch MONAI label server and start Deepedit Actual behavior: failed I have setuped …

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## [\[Newbie\] Struggling with DICOM, MultiVolume and Sequences](https://discourse.slicer.org/t/newbie-struggling-with-dicom-multivolume-and-sequences/22134)

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**Author:** [@TiPunch](https://discourse.slicer.org/u/TiPunch)\
**Replies:** 7\
**Last updated:** [February 28, 2022, 10:00am UTC](https://discourse.slicer.org/t/newbie-struggling-with-dicom-multivolume-and-sequences/22134 "2022-02-28T10:00:12Z")

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Hi, I would like first to thank you for this great and powerful open-source software! In a world where every postprocessing tool can cost a kidney, it is a relief to see people who care about improving and sharing resea…

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## [Getting feret diameter value](https://discourse.slicer.org/t/getting-feret-diameter-value/22208)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 0\
**Last updated:** [February 28, 2022, 9:35am UTC](https://discourse.slicer.org/t/getting-feret-diameter-value/22208 "2022-02-28T09:35:13Z")

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Hello, I am trying to calculate the ‘Ellipsoidity’ of my sample using Segment Statistics. In according to do so, I would like to get the feret diameter of my sample. However, whenever I try to use the measurement, the…

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## [Increase slice thickness in only one plane (anisotropically)](https://discourse.slicer.org/t/increase-slice-thickness-in-only-one-plane-anisotropically/22201)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 2\
**Last updated:** [February 28, 2022, 3:51am UTC](https://discourse.slicer.org/t/increase-slice-thickness-in-only-one-plane-anisotropically/22201 "2022-02-28T03:51:37Z")

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Hello, I am trying to increase the slice thickness of a volume in one view/plane. The current volume features 0.3 mm slices in all three views/planes. I was hoping there was a way of creating a volume with 1 mm slices i…

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## [Save image with new window level](https://discourse.slicer.org/t/save-image-with-new-window-level/22186)

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**Author:** [@codeenthusiast](https://discourse.slicer.org/u/codeenthusiast)\
**Replies:** 2\
**Last updated:** [February 27, 2022, 4:20pm UTC](https://discourse.slicer.org/t/save-image-with-new-window-level/22186 "2022-02-27T16:20:12Z")

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Hi everyone, I’m working on a deep learning project to perform automated segmentation of a ROI for given tumors. I am finding that the tumor is not as visible with the pre-set window that is used upon opening the image.…

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## [3D Volume Reconstrucion](https://discourse.slicer.org/t/3d-volume-reconstrucion/22197)

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**Author:** [@mm\_mm](https://discourse.slicer.org/u/mm_mm)\
**Replies:** 0\
**Last updated:** [February 26, 2022, 3:29pm UTC](https://discourse.slicer.org/t/3d-volume-reconstrucion/22197 "2022-02-26T15:29:45Z")

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Hello，I have a problem.Now that I have ultrasound images and their corresponding position information, the position information is magnetic positioning, how to use 3dSlicer to combine the two for a 3D reconstruction?

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## [How to load Siemens 3D ultrasound data](https://discourse.slicer.org/t/how-to-load-siemens-3d-ultrasound-data/22070)

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**Author:** [@juanmaverde](https://discourse.slicer.org/u/juanmaverde)\
**Replies:** 4\
**Last updated:** [February 26, 2022, 8:31am UTC](https://discourse.slicer.org/t/how-to-load-siemens-3d-ultrasound-data/22070 "2022-02-26T08:31:33Z")

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hello Andras, and thanks for your support! I read this thread and many others because I’m having issues while trying to upload a 3D US volume acquired with a Siemens system. I will summarize, and I would like to know i…

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## [can one make transforms graphically rather than using Transforms Module?](https://discourse.slicer.org/t/can-one-make-transforms-graphically-rather-than-using-transforms-module/21944)

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**Author:** [@asdf](https://discourse.slicer.org/u/asdf)\
**Replies:** 4\
**Last updated:** [February 26, 2022, 5:25am UTC](https://discourse.slicer.org/t/can-one-make-transforms-graphically-rather-than-using-transforms-module/21944 "2022-02-26T05:25:36Z")

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Operating system: MacOS Catalina Slicer version: 4.13 Expected behavior: I know one can use the Transforms module to rotate, translate, and make other transforms on segmentations (ie, an object in .nrrd format). But th…

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## [Change resolution of JPG images](https://discourse.slicer.org/t/change-resolution-of-jpg-images/22177)

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**Author:** [@Nahuel\_Espinoza](https://discourse.slicer.org/u/Nahuel_Espinoza)\
**Replies:** 1\
**Last updated:** [February 25, 2022, 2:17pm UTC](https://discourse.slicer.org/t/change-resolution-of-jpg-images/22177 "2022-02-25T14:17:09Z")

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(auto-translated from Spanish) Good morning What I intend to do is generate slicer with a rectifier and photograph the sequence. The spacing of each image (Z) is known and I can modify it in 3D slicer. The problem is t…

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