# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=173

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

**Page:** 174

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## [Total Segmentator can not adjust labels](https://discourse.slicer.org/t/total-segmentator-can-not-adjust-labels/28300)

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**Author:** [@coffee.ewa](https://discourse.slicer.org/u/coffee.ewa)\
**Replies:** 2\
**Last updated:** [March 16, 2023, 3:20pm UTC](https://discourse.slicer.org/t/total-segmentator-can-not-adjust-labels/28300 "2023-03-16T15:20:40Z")

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I use totalSegmentator to get the label of ROI. I want to adjust the label. But, the buttons on Segment Editor seem unfunctional. I want to shrink 3.0mm from edge of the label. It will be appreciate if someone can tea…

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## [New feature: Soft edge option in volume masking](https://discourse.slicer.org/t/new-feature-soft-edge-option-in-volume-masking/28310)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 4\
**Last updated:** [March 16, 2023, 1:28pm UTC](https://discourse.slicer.org/t/new-feature-soft-edge-option-in-volume-masking/28310 "2023-03-16T13:28:14Z")

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“Mask Volume” is a Segment Editor effect that can paint a a segment’s shape inside an image volume. It can be used for removing anything from the image (e.g., remove the patient table from a CT by blanking out the area) …

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## [Can OCT scans (of file format .E2E) be uploaded into 3D slicer](https://discourse.slicer.org/t/can-oct-scans-of-file-format-e2e-be-uploaded-into-3d-slicer/3831)

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**Author:** [@Ingie\_Baho](https://discourse.slicer.org/u/Ingie_Baho)\
**Replies:** 5\
**Last updated:** [March 16, 2023, 10:23am UTC](https://discourse.slicer.org/t/can-oct-scans-of-file-format-e2e-be-uploaded-into-3d-slicer/3831 "2023-03-16T10:23:17Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [Error during segmentation in TotalSegmentator](https://discourse.slicer.org/t/error-during-segmentation-in-totalsegmentator/27812)

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**Author:** [@Luo\_Dr](https://discourse.slicer.org/u/Luo_Dr)\
**Replies:** 13\
**Last updated:** [March 4, 2023, 3:25am UTC](https://discourse.slicer.org/t/error-during-segmentation-in-totalsegmentator/27812 "2023-03-04T03:25:31Z")

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raceback (most recent call last): File “/home/ubuntu/Slicer-5.3.0-2023-02-08-linux-amd64/bin/Python/slicer/util.py”, line 2973, in tryWithErrorDisplay yield File “/home/ubuntu/Slicer-5.3.0-2023-02-08-linux-amd64/NA-MI…

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## [There are no extensions in the extension manager-5.3.0 build](https://discourse.slicer.org/t/there-are-no-extensions-in-the-extension-manager-5-3-0-build/28394)

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**Author:** [@MikhayEeer](https://discourse.slicer.org/u/MikhayEeer)\
**Replies:** 3\
**Last updated:** [March 16, 2023, 7:48am UTC](https://discourse.slicer.org/t/there-are-no-extensions-in-the-extension-manager-5-3-0-build/28394 "2023-03-16T07:48:56Z")

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Hi, I built slicer from source, but I can’t find the extension in the extension manager, nor can I install it from the file. I click to open the webpage, and the expanded webpage doesn’t have any extensions either. In t…

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## [Axes of a markup plane](https://discourse.slicer.org/t/axes-of-a-markup-plane/28404)

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**Author:** [@yshi](https://discourse.slicer.org/u/yshi)\
**Replies:** 4\
**Last updated:** [March 16, 2023, 4:45am UTC](https://discourse.slicer.org/t/axes-of-a-markup-plane/28404 "2023-03-16T04:45:21Z")

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Hi Slicer Community, I created a plane with 3 markup points and would like to know how x, y, and z axes are defined. The document describes how x-axis is defined: “… the x-axis will be defined by the second (control poi…

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## [Attribute error when trying to get transform between two coords](https://discourse.slicer.org/t/attribute-error-when-trying-to-get-transform-between-two-coords/28290)

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**Author:** [@yshi](https://discourse.slicer.org/u/yshi)\
**Replies:** 2\
**Last updated:** [March 16, 2023, 12:24am UTC](https://discourse.slicer.org/t/attribute-error-when-trying-to-get-transform-between-two-coords/28290 "2023-03-16T00:24:20Z")

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Hello Slicer Community, I created a simple plane P with 3 points and am hoping to get the transform between its coordinate system and the system default coord. I tried this script: planeToWorld = vtk.vtkMatrix4x4() …

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## [Buffering issue while optically tracking a stylus](https://discourse.slicer.org/t/buffering-issue-while-optically-tracking-a-stylus/28401)

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**Author:** [@askaderd](https://discourse.slicer.org/u/askaderd)\
**Replies:** 0\
**Last updated:** [March 15, 2023, 10:07pm UTC](https://discourse.slicer.org/t/buffering-issue-while-optically-tracking-a-stylus/28401 "2023-03-15T22:07:43Z")

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Hi there, I’m currently trying to optically track a stylus as it moves through space using an NDI Vega optical tracker. At times this works perfectly fine, but a lot of times I end up running into buffering issues with …

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## [Extract values at voxels within a segment](https://discourse.slicer.org/t/extract-values-at-voxels-within-a-segment/28077)

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**Author:** [@ZSoltani](https://discourse.slicer.org/u/ZSoltani)\
**Replies:** 6\
**Last updated:** [March 15, 2023, 5:32pm UTC](https://discourse.slicer.org/t/extract-values-at-voxels-within-a-segment/28077 "2023-03-15T17:32:35Z")

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Hello everyone, I want to extract HU values at each voxel from my CT scan files, which for I use the following command: HU\_Array = slicer.util.array(‘myfile.nrrd’) However, using “nrrd” file I get the values at all vo…

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## [How to extract waveform from DCM?](https://discourse.slicer.org/t/how-to-extract-waveform-from-dcm/28398)

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**Author:** [@LukasKnybel](https://discourse.slicer.org/u/LukasKnybel)\
**Replies:** 2\
**Last updated:** [March 15, 2023, 4:42pm UTC](https://discourse.slicer.org/t/how-to-extract-waveform-from-dcm/28398 "2023-03-15T16:42:10Z")

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Dear Slicer Users, we have waveforms from 4DCT stored as DICOM files. I am wondering if there is any option in Slicer how to visualize them. I have never work with “non-image” DICOM till now and I am little bit lost …

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## [Coordinates of pixels in a mesh file](https://discourse.slicer.org/t/coordinates-of-pixels-in-a-mesh-file/28389)

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**Author:** [@ZSoltani](https://discourse.slicer.org/u/ZSoltani)\
**Replies:** 5\
**Last updated:** [March 15, 2023, 4:26pm UTC](https://discourse.slicer.org/t/coordinates-of-pixels-in-a-mesh-file/28389 "2023-03-15T16:26:38Z")

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Hello everyone, I’m trying to get the coordinates of each voxel in my model through the following code: volumeNode=slicer.util.getNode(“myfile.nrrd”) ijkToRas = vtk.vtkMatrix4x4() imageData=volumeNode.GetImageData() …

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## [Texture analysis from MRI in python and question](https://discourse.slicer.org/t/texture-analysis-from-mri-in-python-and-question/28384)

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**Author:** [@peterwsnow](https://discourse.slicer.org/u/peterwsnow)\
**Replies:** 2\
**Last updated:** [March 15, 2023, 10:36am UTC](https://discourse.slicer.org/t/texture-analysis-from-mri-in-python-and-question/28384 "2023-03-15T10:36:15Z")

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Dear Slicer community, Apologies if this is the wrong category. Long time slicer user! I’m interested in texture analysis from a DICOM file. Is there a slicer add on that would do this? Also I’ve looked at papers to tr…

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## [Should I resample on z-axis if forcing 2D feature extraction?](https://discourse.slicer.org/t/should-i-resample-on-z-axis-if-forcing-2d-feature-extraction/28295)

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**Author:** [@fabio.b](https://discourse.slicer.org/u/fabio.b)\
**Replies:** 1\
**Last updated:** [March 15, 2023, 9:50am UTC](https://discourse.slicer.org/t/should-i-resample-on-z-axis-if-forcing-2d-feature-extraction/28295 "2023-03-15T09:50:32Z")

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Dear all, I have a question about a problem I am facing. I am currently working on MRI images with a slice thickness which is either 2 mm (in some patients) or 3 mm (in some other patients). And I would like to extract…

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## [Lost an ffmpeg utility in Screen Capture after an update](https://discourse.slicer.org/t/lost-an-ffmpeg-utility-in-screen-capture-after-an-update/28382)

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**Author:** [@Beth\_Bearce](https://discourse.slicer.org/u/Beth_Bearce)\
**Replies:** 4\
**Last updated:** [March 14, 2023, 8:30pm UTC](https://discourse.slicer.org/t/lost-an-ffmpeg-utility-in-screen-capture-after-an-update/28382 "2023-03-14T20:30:44Z")

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Hi all, Up until recently, I was using the Screen Capture module & ffmpeg to generate GIFs of my rotating scans with transparent backgrounds. (I use strange colored slides, and I like having my fish movies just float on…

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## [Total Segmentor Lung Basic BUG report on Version 5.2.2 while working perfectly on 5.2.1](https://discourse.slicer.org/t/total-segmentor-lung-basic-bug-report-on-version-5-2-2-while-working-perfectly-on-5-2-1/28238)

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**Author:** [@Khaldoun](https://discourse.slicer.org/u/Khaldoun)\
**Replies:** 10\
**Last updated:** [March 14, 2023, 7:45pm UTC](https://discourse.slicer.org/t/total-segmentor-lung-basic-bug-report-on-version-5-2-2-while-working-perfectly-on-5-2-1/28238 "2023-03-14T19:45:48Z")

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Operating system:: Windows 10 Professionnel Intel(R) Core™ i5-10505 CPU @ 3.20GHz 3.19 GHz 16Go RAM Slicer version:5.2.2 Expected behavior:Should be working as well as on version 5.2.1 installed on the same compute…

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## [Uniform spacing for prediction task](https://discourse.slicer.org/t/uniform-spacing-for-prediction-task/28374)

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**Author:** [@Nima\_Yousefi](https://discourse.slicer.org/u/Nima_Yousefi)\
**Replies:** 3\
**Last updated:** [March 14, 2023, 6:57pm UTC](https://discourse.slicer.org/t/uniform-spacing-for-prediction-task/28374 "2023-03-14T18:57:54Z")

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Hi, In case of prediction and feature extraction, is it necessary to have uniform spacing for ct images by doing resampling? @lassoan I would appreciate if you share your opinions with me. Best regard

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## [External GPU to speed up slicer running on an Imac](https://discourse.slicer.org/t/external-gpu-to-speed-up-slicer-running-on-an-imac/28381)

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**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 3\
**Last updated:** [March 14, 2023, 6:14pm UTC](https://discourse.slicer.org/t/external-gpu-to-speed-up-slicer-running-on-an-imac/28381 "2023-03-14T18:14:09Z")

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I wonder whether I can use an external GPU to speed up my Imac when running Slicer. If so, is there some setting to do in Slicer or in my IMac?

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## [Giving my 3d model a dark grey color (instead of almost white)?](https://discourse.slicer.org/t/giving-my-3d-model-a-dark-grey-color-instead-of-almost-white/28360)

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**Author:** [@PixelTreason](https://discourse.slicer.org/u/PixelTreason)\
**Replies:** 4\
**Last updated:** [March 14, 2023, 3:51pm UTC](https://discourse.slicer.org/t/giving-my-3d-model-a-dark-grey-color-instead-of-almost-white/28360 "2023-03-14T15:51:38Z")

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Hi all! I just downloaded this very helpful application today and have been learning how to make a 3d model of a skull. When I see it in the viewer, it has a nice, gunmetal grey kind of color, but when I segment it and…

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## [acquisitionNumber](https://discourse.slicer.org/t/acquisitionnumber/28361)

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**Author:** [@analubonaldo](https://discourse.slicer.org/u/analubonaldo)\
**Replies:** 1\
**Last updated:** [March 14, 2023, 3:06pm UTC](https://discourse.slicer.org/t/acquisitionnumber/28361 "2023-03-14T15:06:37Z")

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Hi! I’m trying to import a CT scan using the DICOM browser in Slicer 5.3.0. For some patients, instead of opening all slices, they only open a few with the additional name “acquisitionNumber”. Consequently, I lose most …

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## [CT images has dark lines after being normalized](https://discourse.slicer.org/t/ct-images-has-dark-lines-after-being-normalized/28366)

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**Author:** [@anusree\_sunilkumar](https://discourse.slicer.org/u/anusree_sunilkumar)\
**Replies:** 1\
**Last updated:** [March 14, 2023, 2:02pm UTC](https://discourse.slicer.org/t/ct-images-has-dark-lines-after-being-normalized/28366 "2023-03-14T14:02:52Z")

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I am trying to train a model for reconstruction. My CBCT dataset is of DICOM format with datatype uint16. When I normalize the volume to uint8 based on the maximum intensity of the volume, my model doesn’t give expected …

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## [Dicom PACS retrieve fail](https://discourse.slicer.org/t/dicom-pacs-retrieve-fail/28270)

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**Author:** [@skyhsu](https://discourse.slicer.org/u/skyhsu)\
**Replies:** 2\
**Last updated:** [March 14, 2023, 3:04am UTC](https://discourse.slicer.org/t/dicom-pacs-retrieve-fail/28270 "2023-03-14T03:04:03Z")

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Hi, We are using 3D Slicer to obtain dicom dataset via PACS system in Our Hospital, We are using version:5.2.1 Windows 10 pro and we get some error message as below it will cause some dicom file loss, maybe the…

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## [Disable middle-mouse drag for markups](https://discourse.slicer.org/t/disable-middle-mouse-drag-for-markups/28356)

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**Author:** [@JASON](https://discourse.slicer.org/u/JASON)\
**Replies:** 10\
**Last updated:** [March 14, 2023, 12:03am UTC](https://discourse.slicer.org/t/disable-middle-mouse-drag-for-markups/28356 "2023-03-14T00:03:53Z")

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Hello, I am placing many markup points on a surface in the 3D view. Occasionally I middle-mouse drag to pan the 3D view and I accidentally end up dragging all the control points for the node. This operation is not undo-a…

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## [Would Slicer Volume Rendering improve by using other interpolation functions?](https://discourse.slicer.org/t/would-slicer-volume-rendering-improve-by-using-other-interpolation-functions/28328)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 2\
**Last updated:** [March 13, 2023, 9:16pm UTC](https://discourse.slicer.org/t/would-slicer-volume-rendering-improve-by-using-other-interpolation-functions/28328 "2023-03-13T21:16:55Z")

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Here is a short video that showcases different interpolation functions: Could this be used for transfer functions of opacity or colormapping? Thanks

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## [Quick Q for RemoveObserver](https://discourse.slicer.org/t/quick-q-for-removeobserver/28354)

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**Author:** [@aiden.zhu](https://discourse.slicer.org/u/aiden.zhu)\
**Replies:** 2\
**Last updated:** [March 13, 2023, 8:08pm UTC](https://discourse.slicer.org/t/quick-q-for-removeobserver/28354 "2023-03-13T20:08:39Z")

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Hi all, quick question about “RemoveObserver”==\> After I did the following to add one observer “”" crosshairNode=slicer.util.getNode(“Crosshair”) crosshairNode.AddObserver(slicer.vtkMRMLCrosshairNode.CursorPositionM…

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## [3D render resolution comparison](https://discourse.slicer.org/t/3d-render-resolution-comparison/28160)

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**Author:** [@Cervantes](https://discourse.slicer.org/u/Cervantes)\
**Replies:** 2\
**Last updated:** [March 13, 2023, 6:07pm UTC](https://discourse.slicer.org/t/3d-render-resolution-comparison/28160 "2023-03-13T18:07:57Z")

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Hi Everyone, I understand this may be less of a 3D slicer specific question, and more of a general resolution question. I’m working on something that includes using both 3D renders from DICOM images, and models created…

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## [Install extensions is not working on latest preview release](https://discourse.slicer.org/t/install-extensions-is-not-working-on-latest-preview-release/28316)

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**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 7\
**Last updated:** [March 13, 2023, 6:01pm UTC](https://discourse.slicer.org/t/install-extensions-is-not-working-on-latest-preview-release/28316 "2023-03-13T18:01:33Z")

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I’m on ubuntu Thanks for the help

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## [Volume masking "soft edge" option requires non-empty output volume](https://discourse.slicer.org/t/volume-masking-soft-edge-option-requires-non-empty-output-volume/28349)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 4\
**Last updated:** [March 13, 2023, 8:54am UTC](https://discourse.slicer.org/t/volume-masking-soft-edge-option-requires-non-empty-output-volume/28349 "2023-03-13T08:54:49Z")

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This backtrace is obtained with ‘Mask volume’ effect while setting ‘Soft edge’ : Traceback (most recent call last): File "/home/user/programs/Slicer/lib/Slicer-5.3/qt-scripted-modules/SegmentEditorEffects/SegmentEdito…

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## [Volume generation in a different plane/coordinates](https://discourse.slicer.org/t/volume-generation-in-a-different-plane-coordinates/28348)

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**Author:** [@ConstanzaMor](https://discourse.slicer.org/u/ConstanzaMor)\
**Replies:** 0\
**Last updated:** [March 13, 2023, 2:05pm UTC](https://discourse.slicer.org/t/volume-generation-in-a-different-plane-coordinates/28348 "2023-03-13T14:05:07Z")

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Hello, I’m currently trying to image intervertebral discs in the ultrasound machine. I have acquired a video as either DICOM or mp4 file by rotating the probe around the disc and obtaining a 360 representation. However…

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## [Parameters file: If the default normalisation (z-score) narrows the pixel intensity range to -3/+3 this should mean that binWidth cannot be lower than 6? And that is for only one bin?](https://discourse.slicer.org/t/parameters-file-if-the-default-normalisation-z-score-narrows-the-pixel-intensity-range-to-3-3-this-should-mean-that-binwidth-cannot-be-lower-than-6-and-that-is-for-only-one-bin/28346)

<div class="topic-metadata">

**Author:** [@harad](https://discourse.slicer.org/u/harad)\
**Replies:** 0\
**Last updated:** [March 13, 2023, 1:33pm UTC](https://discourse.slicer.org/t/parameters-file-if-the-default-normalisation-z-score-narrows-the-pixel-intensity-range-to-3-3-this-should-mean-that-binwidth-cannot-be-lower-than-6-and-that-is-for-only-one-bin/28346 "2023-03-13T13:33:16Z")

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This parameter file (below) works fine and calculates about 2200 features but I am still concerned that any of the settings may contradict each other, or be in the wrong order and therefore deliver incorrect values. If …

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## [About the colormapping](https://discourse.slicer.org/t/about-the-colormapping/28344)

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**Author:** [@miao1](https://discourse.slicer.org/u/miao1)\
**Replies:** 0\
**Last updated:** [March 13, 2023, 12:59pm UTC](https://discourse.slicer.org/t/about-the-colormapping/28344 "2023-03-13T12:59:28Z")

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Hello everyone, I was working on some PET images recently, and I found that the PET-DICOM display in the Volume module in the 3D slicer is exactly what I want. Where can I find the source code to implement this feature? …

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