# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=339

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

**Page:** 340

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## [Set and observe transform node to markups curve node: bug or feature?](https://discourse.slicer.org/t/set-and-observe-transform-node-to-markups-curve-node-bug-or-feature/11599)

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**Author:** [@Mik](https://discourse.slicer.org/u/Mik)\
**Replies:** 14\
**Last updated:** [May 26, 2020, 4:09pm UTC](https://discourse.slicer.org/t/set-and-observe-transform-node-to-markups-curve-node-bug-or-feature/11599 "2020-05-26T16:09:20Z")

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Greeting, Transformation of vtkMRMLMarkupsClosedCurveNode looks like a little bit buggy. Points of the curve are transformed correctly, but not the curve itself. There is no such problem with markups line node, where …

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## [PT Beam Data not loading](https://discourse.slicer.org/t/pt-beam-data-not-loading/11710)

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**Author:** [@mdsainth](https://discourse.slicer.org/u/mdsainth)\
**Replies:** 0\
**Last updated:** [May 26, 2020, 2:26pm UTC](https://discourse.slicer.org/t/pt-beam-data-not-loading/11710 "2020-05-26T14:26:22Z")

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I am loading a DICOM dataset from a proton therapy treatment plan from a RaySearch TPS. This inclused the DICOM-CT, DICOM-RTDOSE, DICOM-RTPLAN and DICOM-STRUCT files, However I have problems with the beam data and receiv…

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## [Running Slicer on headless server (Installing Extensions and more...)](https://discourse.slicer.org/t/running-slicer-on-headless-server-installing-extensions-and-more/11689)

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**Author:** [@Davide\_Cester](https://discourse.slicer.org/u/Davide_Cester)\
**Replies:** 11\
**Last updated:** [May 26, 2020, 1:52pm UTC](https://discourse.slicer.org/t/running-slicer-on-headless-server-installing-extensions-and-more/11689 "2020-05-26T13:52:11Z")

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Dear all, I am setting up a shared server for the research in our group, it’s a headless Ubuntu 20.04. People are supposed to log in to web services and share the computing power. JupyterHub is already up & running, wit…

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## [Robust statistic segmentation crash](https://discourse.slicer.org/t/robust-statistic-segmentation-crash/11697)

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**Author:** [@fsangalli](https://discourse.slicer.org/u/fsangalli)\
**Replies:** 0\
**Last updated:** [May 25, 2020, 4:58pm UTC](https://discourse.slicer.org/t/robust-statistic-segmentation-crash/11697 "2020-05-25T16:58:34Z")

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Hi! I have a problem with the plugin Robust Statistic Segmentation. It crashes when i launch it with a previously saved segmentation, it works quite well if I use a segmentation it is done in a single session. I am us…

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## [Markups - highlight selected markup clicked in 3D view?](https://discourse.slicer.org/t/markups-highlight-selected-markup-clicked-in-3d-view/11670)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 28\
**Last updated:** [May 25, 2020, 3:48pm UTC](https://discourse.slicer.org/t/markups-highlight-selected-markup-clicked-in-3d-view/11670 "2020-05-25T15:48:52Z")

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Hi all, I looked through the topics and docs and this seems like a pretty obvious thing, but I didn’t find it anywhere. Is there a way to click on a markup in the 3D view and have it highlighted in the markups list in …

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## [Trouble with data from Philips Qlab](https://discourse.slicer.org/t/trouble-with-data-from-philips-qlab/11695)

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**Author:** [@MarekJedrzejek](https://discourse.slicer.org/u/MarekJedrzejek)\
**Replies:** 2\
**Last updated:** [May 25, 2020, 2:43pm UTC](https://discourse.slicer.org/t/trouble-with-data-from-philips-qlab/11695 "2020-05-25T14:43:48Z")

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Hello, I’m working on Mac. I have slicer 4.10.2. I’ve installed SlicerHeart, Sequences module. I’ve changed directory to be without any special characters. And I want to use Philips4dUsDicomPatcher I choose directory an…

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## [How to see the 3D rendering of my .tiff?](https://discourse.slicer.org/t/how-to-see-the-3d-rendering-of-my-tiff/11691)

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**Author:** [@Ezzmazz](https://discourse.slicer.org/u/Ezzmazz)\
**Replies:** 1\
**Last updated:** [May 25, 2020, 1:29pm UTC](https://discourse.slicer.org/t/how-to-see-the-3d-rendering-of-my-tiff/11691 "2020-05-25T13:29:51Z")

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Hello, I’m new here and in the 3D field. For my university project, I’ve scanned some bone ( I study archeology and paleonthology ) with the software avizo. Before the lockdown, I’ve been enable to recover all my .tiff…

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## [User setting for coordinate system in v4.11?](https://discourse.slicer.org/t/user-setting-for-coordinate-system-in-v4-11/11567)

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**Author:** [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Replies:** 3\
**Last updated:** [May 25, 2020, 4:16am UTC](https://discourse.slicer.org/t/user-setting-for-coordinate-system-in-v4-11/11567 "2020-05-25T04:16:31Z")

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Hi, I am working with v4.11 and recently became aware that v4.11 has changed the default coordinate system (RAS -\> LPS). Wondering if there will be an option in settings for the user to select their preferred coordinate…

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## [Question About Loading Data in 3D Slicer](https://discourse.slicer.org/t/question-about-loading-data-in-3d-slicer/11686)

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**Author:** [@eKwas](https://discourse.slicer.org/u/eKwas)\
**Replies:** 1\
**Last updated:** [May 25, 2020, 2:02am UTC](https://discourse.slicer.org/t/question-about-loading-data-in-3d-slicer/11686 "2020-05-25T02:02:53Z")

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Hello: When loading data (not DICOM) into 3D Slicer (using Windows 10 Slicer version 4.11.0, but I have had this same issue with 4.10.2), is there a way to change the presets (what appears when you click “Show Options”)…

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## [Register uCT scans with conventional CT scan](https://discourse.slicer.org/t/register-uct-scans-with-conventional-ct-scan/11424)

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**Author:** [@sfglio](https://discourse.slicer.org/u/sfglio)\
**Replies:** 4\
**Last updated:** [May 24, 2020, 6:29pm UTC](https://discourse.slicer.org/t/register-uct-scans-with-conventional-ct-scan/11424 "2020-05-24T18:29:33Z")

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I am trying to register a microCT scan of an implant with a conv. CT of the same implant within the jaw. I transformed the microCT scan to the correct position however the final 3d-3d registration fails. Even when I res…

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## [Editor module and pixel radius](https://discourse.slicer.org/t/editor-module-and-pixel-radius/11679)

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**Author:** [@aileeno](https://discourse.slicer.org/u/aileeno)\
**Replies:** 3\
**Last updated:** [May 24, 2020, 3:41pm UTC](https://discourse.slicer.org/t/editor-module-and-pixel-radius/11679 "2020-05-24T15:41:42Z")

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Hi everyone, A colleague and I are working on a project where we want to do repeated measurements on images acquired by different scanners. In an effort to hold as many variables constant as is possible, we have noted t…

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## [Post-crop return to original volume and re-crop](https://discourse.slicer.org/t/post-crop-return-to-original-volume-and-re-crop/11677)

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**Author:** [@Hannnonk](https://discourse.slicer.org/u/Hannnonk)\
**Replies:** 1\
**Last updated:** [May 23, 2020, 6:29pm UTC](https://discourse.slicer.org/t/post-crop-return-to-original-volume-and-re-crop/11677 "2020-05-23T18:29:34Z")

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Operating system:windows 10 Slicer version: enter dicom successfully crop and segment is there any way to return to the original volume to do another crop? thx

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## [Registration of consecutive CT volumes](https://discourse.slicer.org/t/registration-of-consecutive-ct-volumes/11649)

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**Author:** [@Farah](https://discourse.slicer.org/u/Farah)\
**Replies:** 5\
**Last updated:** [May 23, 2020, 6:27pm UTC](https://discourse.slicer.org/t/registration-of-consecutive-ct-volumes/11649 "2020-05-23T18:27:39Z")

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Hi community, I am trying to register consecutive CT volumes of the abdominal aortic aneurysm, I have 10 volumes during the cardiac cycle of the patient. I tried BSpline with different grid sizes but the algorithm is ge…

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## [Slicer crashes when attempting to retrieve camera node for non-existent 3D view](https://discourse.slicer.org/t/slicer-crashes-when-attempting-to-retrieve-camera-node-for-non-existent-3d-view/11672)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 3\
**Last updated:** [May 23, 2020, 5:31am UTC](https://discourse.slicer.org/t/slicer-crashes-when-attempting-to-retrieve-camera-node-for-non-existent-3d-view/11672 "2020-05-23T05:31:35Z")

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The following command entered at the Python interactor of a newly opened Slicer crashes the program and the window closes: camNode = slicer.modules.cameras.logic().GetViewActiveCameraNode(slicer.app.layoutManager.th…

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## [Volume measurement = 0](https://discourse.slicer.org/t/volume-measurement-0/11490)

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**Author:** [@Gaborri](https://discourse.slicer.org/u/Gaborri)\
**Replies:** 9\
**Last updated:** [May 23, 2020, 5:10am UTC](https://discourse.slicer.org/t/volume-measurement-0/11490 "2020-05-23T05:10:04Z")

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Hello there, I am a new user. Windows 10 and Slicer 4.10.1 version. I have a problem in measuring a volume. I have the segmentation done and it is displayed correctly in the 3d views. Unfortunately when I go for Quan…

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## [Text annotations](https://discourse.slicer.org/t/text-annotations/11558)

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**Author:** [@joachim](https://discourse.slicer.org/u/joachim)\
**Replies:** 19\
**Last updated:** [May 22, 2020, 9:35pm UTC](https://discourse.slicer.org/t/text-annotations/11558 "2020-05-22T21:35:52Z")

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I would like to add notes to my project. I thought this feature could be found in the Annotation module, but I haven’t found anything in Slicer, so I guess this is a feature request. Plain text will work, but it would a…

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## [Q3DC Quantification Tool](https://discourse.slicer.org/t/q3dc-quantification-tool/11372)

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**Author:** [@Joao\_L](https://discourse.slicer.org/u/Joao_L)\
**Replies:** 7\
**Last updated:** [May 5, 2020, 9:16pm UTC](https://discourse.slicer.org/t/q3dc-quantification-tool/11372 "2020-05-05T21:16:15Z")

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Operating system: Slicer version: 5.0 Expected behavior: Calculating angle between two lines using Q3DC Quantificatio tool. Actual behavior: When choosing landmarks of two different stl. archives and selecting the opt…

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## [Error when saving labelmap to jpg](https://discourse.slicer.org/t/error-when-saving-labelmap-to-jpg/11630)

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**Author:** [@Emmanuel\_Salinas\_Mir](https://discourse.slicer.org/u/Emmanuel_Salinas_Mir)\
**Replies:** 1\
**Last updated:** [May 22, 2020, 3:16pm UTC](https://discourse.slicer.org/t/error-when-saving-labelmap-to-jpg/11630 "2020-05-22T15:16:29Z")

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Hi. I am working with JPG images: When I try to save a labelmap to any of the JPG or PNG formats I get this error: “Cannot write data file: /Users/xx/Documents/Segmentation-labe.jpg. Do you want to continue saving?” …

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## [Question on using Mask volume](https://discourse.slicer.org/t/question-on-using-mask-volume/11662)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 1\
**Last updated:** [May 22, 2020, 3:15am UTC](https://discourse.slicer.org/t/question-on-using-mask-volume/11662 "2020-05-22T03:15:20Z")

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Continuing the discussion from Extracting a subnetwork from 3D volume: To retain only green and exclude red from a volume like below I’m using the Mask volume option. I’ve selected the segment (e.g. segment\_3, se…

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## [Registration time with CPU speed](https://discourse.slicer.org/t/registration-time-with-cpu-speed/11652)

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**Author:** [@mmtg](https://discourse.slicer.org/u/mmtg)\
**Replies:** 4\
**Last updated:** [May 21, 2020, 5:30pm UTC](https://discourse.slicer.org/t/registration-time-with-cpu-speed/11652 "2020-05-21T17:30:36Z")

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Hello, I have a rather random question. I am using BRAINSFit to do some registrations. I am adjusting some parameters, one of them being the “sampling percentage.” Lets say i was to record the registration time when usi…

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## [How can I do multiple segmentations of the same bodypart without automatically transferring the setup from one to the other?](https://discourse.slicer.org/t/how-can-i-do-multiple-segmentations-of-the-same-bodypart-without-automatically-transferring-the-setup-from-one-to-the-other/11654)

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**Author:** [@Jeff\_S](https://discourse.slicer.org/u/Jeff_S)\
**Replies:** 0\
**Last updated:** [May 21, 2020, 5:04pm UTC](https://discourse.slicer.org/t/how-can-i-do-multiple-segmentations-of-the-same-bodypart-without-automatically-transferring-the-setup-from-one-to-the-other/11654 "2020-05-21T17:04:05Z")

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Dear 3DSlicer-Community, I am facing a Problem right now and could not find a solution for that here yet. I want to create different Segmentations of the same part (here a vertebra) but one, showing the whole vertebra,…

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## [Convert binary mask from MATLAB to segmentation in 3DSlicer](https://discourse.slicer.org/t/convert-binary-mask-from-matlab-to-segmentation-in-3dslicer/11607)

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**Author:** [@go-lauren](https://discourse.slicer.org/u/go-lauren)\
**Replies:** 12\
**Last updated:** [May 21, 2020, 1:19am UTC](https://discourse.slicer.org/t/convert-binary-mask-from-matlab-to-segmentation-in-3dslicer/11607 "2020-05-21T01:19:12Z")

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I have created binary masks for hrd/img scans in MATLAB, but I want to export them as segmentations in 3DSlicer. I have tried saving the masks as a .nii file and adding data as labelmap, but nothing shows up.

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## [Using crop volume module](https://discourse.slicer.org/t/using-crop-volume-module/11595)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 4\
**Last updated:** [May 20, 2020, 3:48pm UTC](https://discourse.slicer.org/t/using-crop-volume-module/11595 "2020-05-20T15:48:59Z")

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This is a follow up to my previous post here After loading the data, I try to use the crop volume module to downsample the data and the error that is displayed in the snapshot occurs. Any suggestions on how to resolve…

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## [Compute thickness of branches in a 2D image](https://discourse.slicer.org/t/compute-thickness-of-branches-in-a-2d-image/11389)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 2\
**Last updated:** [May 20, 2020, 3:30pm UTC](https://discourse.slicer.org/t/compute-thickness-of-branches-in-a-2d-image/11389 "2020-05-20T15:30:16Z")

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I would like to ask for suggestions on how to obtain the thickness of the edges in a given input image Sample image: Suggestions on how to proceed will be really helpful. In the end, I would like to obtain the cente…

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## [Issue with coordinate system mismatch](https://discourse.slicer.org/t/issue-with-coordinate-system-mismatch/11622)

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**Author:** [@KatS](https://discourse.slicer.org/u/KatS)\
**Replies:** 1\
**Last updated:** [May 19, 2020, 11:47pm UTC](https://discourse.slicer.org/t/issue-with-coordinate-system-mismatch/11622 "2020-05-19T23:47:45Z")

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Dear Slicer community, I’m having issues when trying to register small animal brains (scanned on a 9.4T Bruker system, exported as DICOM using ParaVision) to each other which are likely due to a coordinate system mismat…

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## [Steps to convert a STL file to DICOM](https://discourse.slicer.org/t/steps-to-convert-a-stl-file-to-dicom/11638)

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**Author:** [@Zehra](https://discourse.slicer.org/u/Zehra)\
**Replies:** 0\
**Last updated:** [May 20, 2020, 1:57pm UTC](https://discourse.slicer.org/t/steps-to-convert-a-stl-file-to-dicom/11638 "2020-05-20T13:57:20Z")

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Hi, I am very new in with this software. I would like to have a 3D model of an implant converted into dicom CT series. As I understood, it cannot be converted directly to dicom since it is not a solid object it is a surf…

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## [Landmark Registration in different version](https://discourse.slicer.org/t/landmark-registration-in-different-version/11628)

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**Author:** [@syh91006](https://discourse.slicer.org/u/syh91006)\
**Replies:** 1\
**Last updated:** [May 20, 2020, 4:19am UTC](https://discourse.slicer.org/t/landmark-registration-in-different-version/11628 "2020-05-20T04:19:09Z")

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Operating system: win10 Slicer version: 4.10.2 and 4.11.0 Expected behavior: try to use Landmark Registration and “create and place” in the same version Actual behavior: I would like to use Landmark Registration and …

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## [Access widget class from the test class in a Slicer plugin](https://discourse.slicer.org/t/access-widget-class-from-the-test-class-in-a-slicer-plugin/11585)

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**Author:** [@brhoom](https://discourse.slicer.org/u/brhoom)\
**Replies:** 4\
**Last updated:** [May 19, 2020, 11:41pm UTC](https://discourse.slicer.org/t/access-widget-class-from-the-test-class-in-a-slicer-plugin/11585 "2020-05-19T23:41:11Z")

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Dear all, Is it possible to access a widget class element from the test class in a slicer plugin? I know this is not how the test class works but I am controlling the logic functions with an extra variable taht indicate…

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## [Prepare labelmap for parenchyma analysis](https://discourse.slicer.org/t/prepare-labelmap-for-parenchyma-analysis/411)

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**Author:** [@broccoli](https://discourse.slicer.org/u/broccoli)\
**Replies:** 8\
**Last updated:** [May 20, 2020, 12:07am UTC](https://discourse.slicer.org/t/prepare-labelmap-for-parenchyma-analysis/411 "2020-05-20T00:07:42Z")

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I want to use the Parenchyma Analysis module, but want to use a segmentation that was done by different software. What I tried: - Convert the surface mesh to a label map using the Model to Label Map module. - Use this …

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## [Shape mismatch after exporting segmented labels](https://discourse.slicer.org/t/shape-mismatch-after-exporting-segmented-labels/11502)

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**Author:** [@Flash](https://discourse.slicer.org/u/Flash)\
**Replies:** 5\
**Last updated:** [May 19, 2020, 10:16am UTC](https://discourse.slicer.org/t/shape-mismatch-after-exporting-segmented-labels/11502 "2020-05-19T10:16:54Z")

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Hello, I have generated mask labels for brain tumor with nvidia clara…I am overlaying these mask labels on the original brain tumor image.I have edited the generated the mask lables with segment editor and later tried t…

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