# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=134

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

**Page:** 135

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## [Failed to fetch models from remote server. Make sure server address is correct and \<server\_uri\>/info/ is accessible in browser](https://discourse.slicer.org/t/failed-to-fetch-models-from-remote-server-make-sure-server-address-is-correct-and-server-uri-info-is-accessible-in-browser/32324)

<div class="topic-metadata">

**Author:** [@swin](https://discourse.slicer.org/u/swin)\
**Replies:** 0\
**Last updated:** [October 19, 2023, 10:33am UTC](https://discourse.slicer.org/t/failed-to-fetch-models-from-remote-server-make-sure-server-address-is-correct-and-server-uri-info-is-accessible-in-browser/32324 "2023-10-19T10:33:24Z")

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Hello, I’m getting the below warning when I try to use MONAILabel in 3D slicer. Could anyone advise how to fix Failed to fetch models from remote server. Make sure server address is correct and \<server\_uri\>/info/ is ac…

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## [Virtual Reality Oculus controller interaction behavior](https://discourse.slicer.org/t/virtual-reality-oculus-controller-interaction-behavior/32037)

<div class="topic-metadata">

**Author:** [@ally7113](https://discourse.slicer.org/u/ally7113)\
**Replies:** 7\
**Last updated:** [October 19, 2023, 5:27am UTC](https://discourse.slicer.org/t/virtual-reality-oculus-controller-interaction-behavior/32037 "2023-10-19T05:27:13Z")

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With the help of several posts, I was able to operate the Slicer virtual reality module on my Oculus Quest2 device. However, I would like to use rotation, zoom in/out, and two-handed gestures like the YouTube below. …

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## [Writing markups to FCSV in Slicer version 5+ adds additional columns](https://discourse.slicer.org/t/writing-markups-to-fcsv-in-slicer-version-5-adds-additional-columns/32318)

<div class="topic-metadata">

**Author:** [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Replies:** 5\
**Last updated:** [October 19, 2023, 4:32am UTC](https://discourse.slicer.org/t/writing-markups-to-fcsv-in-slicer-version-5-adds-additional-columns/32318 "2023-10-19T04:32:11Z")

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Hi all, I’ve noticed a bug when saving control points to FCSV in Slicer version 5.4. There is a trailing ,2,0 written at the end of each data line. These additional columns have not been in previous versions of Slicer a…

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## [Big image viewer extension not working on 5.4.0](https://discourse.slicer.org/t/big-image-viewer-extension-not-working-on-5-4-0/32307)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [October 19, 2023, 1:06am UTC](https://discourse.slicer.org/t/big-image-viewer-extension-not-working-on-5-4-0/32307 "2023-10-19T01:06:34Z")

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On linux I am getting an error regarding open-slide python package. Collecting openslide-python Using cached openslide-python-1.3.1.tar.gz (358 kB) Preparing metadata (setup.py): started Preparing metadata (setup.…

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## [Length measurement from 3 pts](https://discourse.slicer.org/t/length-measurement-from-3-pts/32308)

<div class="topic-metadata">

**Author:** [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Replies:** 1\
**Last updated:** [October 18, 2023, 9:00pm UTC](https://discourse.slicer.org/t/length-measurement-from-3-pts/32308 "2023-10-18T21:00:39Z")

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Is it possible to make a linear length measurement from 3 pts? First two points define the line and the third point defines the extent of the line. Length would be from the first to last point. Not sure if this is poss…

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## [DICOM to NRRD conversion in command line (for PyRadiomics)](https://discourse.slicer.org/t/dicom-to-nrrd-conversion-in-command-line-for-pyradiomics/32306)

<div class="topic-metadata">

**Author:** [@marcin.jakalski](https://discourse.slicer.org/u/marcin.jakalski)\
**Replies:** 1\
**Last updated:** [October 18, 2023, 5:50pm UTC](https://discourse.slicer.org/t/dicom-to-nrrd-conversion-in-command-line-for-pyradiomics/32306 "2023-10-18T17:50:25Z")

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Hello! I would like to recreate some of the functionality of 3D Slicer in command line for batch analysis of several hundred of patients’ images. I have a set of DICOM images along with their segmentations. For these I w…

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## [I am unable to appload my atlas file in 3D slicer5.4.0](https://discourse.slicer.org/t/i-am-unable-to-appload-my-atlas-file-in-3d-slicer5-4-0/32230)

<div class="topic-metadata">

**Author:** [@junaid](https://discourse.slicer.org/u/junaid)\
**Replies:** 2\
**Last updated:** [October 18, 2023, 3:39pm UTC](https://discourse.slicer.org/t/i-am-unable-to-appload-my-atlas-file-in-3d-slicer5-4-0/32230 "2023-10-18T15:39:56Z")

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

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## [Radiologist saved segmentations without references -\> annotations come out cropped when loading as numpy arrays](https://discourse.slicer.org/t/radiologist-saved-segmentations-without-references-annotations-come-out-cropped-when-loading-as-numpy-arrays/32277)

<div class="topic-metadata">

**Author:** [@neuronflow](https://discourse.slicer.org/u/neuronflow)\
**Replies:** 1\
**Last updated:** [October 18, 2023, 2:21pm UTC](https://discourse.slicer.org/t/radiologist-saved-segmentations-without-references-annotations-come-out-cropped-when-loading-as-numpy-arrays/32277 "2023-10-18T14:21:59Z")

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Dear forum, My dear radiologists saved all the segmentations they created without a reference as compressed niftis. Therefore, all the annotations appear cropped if I load them as numpy arrays using nibabel. My image d…

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## [Qt interface closes](https://discourse.slicer.org/t/qt-interface-closes/32158)

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**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 4\
**Last updated:** [October 18, 2023, 11:21am UTC](https://discourse.slicer.org/t/qt-interface-closes/32158 "2023-10-18T11:21:20Z")

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Hi all, I am implementing a very simple interface in Qt. The ui code is in a file called “myUI.py” and I want to call it from my “script.py” (call to run\_gui). It generates the window but closes it inmediately. How can …

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## [3dslicer v5.4.0, not able to download the slicerjupter-extension from developer tools](https://discourse.slicer.org/t/3dslicer-v5-4-0-not-able-to-download-the-slicerjupter-extension-from-developer-tools/32211)

<div class="topic-metadata">

**Author:** [@palak](https://discourse.slicer.org/u/palak)\
**Replies:** 1\
**Last updated:** [October 18, 2023, 10:40am UTC](https://discourse.slicer.org/t/3dslicer-v5-4-0-not-able-to-download-the-slicerjupter-extension-from-developer-tools/32211 "2023-10-18T10:40:58Z")

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not able to download the slicer jupyter extension, getting error: Failed downloading: https://slicer-packages.kitware.com/api/v1/file/64e0fcdb06a93d6cff366315/download

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## [Unclear branching and endpoint detection in vmtk-centerlines](https://discourse.slicer.org/t/unclear-branching-and-endpoint-detection-in-vmtk-centerlines/32256)

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**Author:** [@b\_gop](https://discourse.slicer.org/u/b_gop)\
**Replies:** 2\
**Last updated:** [October 18, 2023, 10:36am UTC](https://discourse.slicer.org/t/unclear-branching-and-endpoint-detection-in-vmtk-centerlines/32256 "2023-10-18T10:36:04Z")

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Hi all, I used the vmtk-centerlines module to auto-detect endpoints and then compute the centerline on my dataset. Using the centerline quantification data, I ran a script to add mark up points on each of the start and …

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## [RVesselX don't show current node placement help option](https://discourse.slicer.org/t/rvesselx-dont-show-current-node-placement-help-option/25454)

<div class="topic-metadata">

**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 1\
**Last updated:** [October 17, 2023, 10:37pm UTC](https://discourse.slicer.org/t/rvesselx-dont-show-current-node-placement-help-option/25454 "2023-10-17T22:37:18Z")

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Hi: I tried to use the “Show current node placement help” option in RVesselX, but appears a blank window. Why?. Sincerely, Gonzalo Rojas Costa

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## [How to run python based CLI modules?](https://discourse.slicer.org/t/how-to-run-python-based-cli-modules/4627)

<div class="topic-metadata">

**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 30\
**Last updated:** [October 17, 2023, 5:23am UTC](https://discourse.slicer.org/t/how-to-run-python-based-cli-modules/4627 "2023-10-17T05:23:40Z")

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I have gone through this https://www.slicer.org/wiki/Documentation/Nightly/Developers/SlicerExecutionModel/Python So, what I understand about python based CLI is: there is an xml file which will produce GUI for applic…

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## [Recommended file format for saving image and segmentations](https://discourse.slicer.org/t/recommended-file-format-for-saving-image-and-segmentations/32264)

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**Author:** [@S\_Arbabi](https://discourse.slicer.org/u/S_Arbabi)\
**Replies:** 1\
**Last updated:** [October 17, 2023, 5:12pm UTC](https://discourse.slicer.org/t/recommended-file-format-for-saving-image-and-segmentations/32264 "2023-10-17T17:12:41Z")

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I am working with CT images (DICOM) and the segmentation of bones. What file format you recommend to save the image and segmentations to follow standards, with going commercial in future in mind?

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## [OCT b-scan thickness is not being found on load](https://discourse.slicer.org/t/oct-b-scan-thickness-is-not-being-found-on-load/32273)

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**Author:** [@Mark\_Banghart](https://discourse.slicer.org/u/Mark_Banghart)\
**Replies:** 1\
**Last updated:** [October 17, 2023, 5:09pm UTC](https://discourse.slicer.org/t/oct-b-scan-thickness-is-not-being-found-on-load/32273 "2023-10-17T17:09:35Z")

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We have a number of legacy DICOM files that we would like to view in slicer. The files load with drag and drop. The user selects volume and the OCT is displayed. The pixel dimensions for the x and y dimensions are filled…

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## [Totalsegmentator error in first use, tried multiple times of uninstall and reinstall](https://discourse.slicer.org/t/totalsegmentator-error-in-first-use-tried-multiple-times-of-uninstall-and-reinstall/32263)

<div class="topic-metadata">

**Author:** [@pssi\_92](https://discourse.slicer.org/u/pssi_92)\
**Replies:** 4\
**Last updated:** [October 17, 2023, 3:55pm UTC](https://discourse.slicer.org/t/totalsegmentator-error-in-first-use-tried-multiple-times-of-uninstall-and-reinstall/32263 "2023-10-17T15:55:57Z")

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I just bought new desktop for my research, and installed Slicer 5.4.0 and Totalsegmentator extension. But an error showed up. I tried multiple times of deletion of the Slicer (Uninstall with Slicer.org folder deletion), …

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## [Filtering out shadows due to high dence material](https://discourse.slicer.org/t/filtering-out-shadows-due-to-high-dence-material/32271)

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**Author:** [@Fpuaw](https://discourse.slicer.org/u/Fpuaw)\
**Replies:** 0\
**Last updated:** [October 17, 2023, 2:42pm UTC](https://discourse.slicer.org/t/filtering-out-shadows-due-to-high-dence-material/32271 "2023-10-17T14:42:27Z")

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Is there a filter in 3D Slicer to reduce the shadows due to high and low dence material. Some programs combine a high voltage and a low voltage image to reduce this (like a HDR image). The picture is from a werth Th…

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## [scalar volume read as image sequence](https://discourse.slicer.org/t/scalar-volume-read-as-image-sequence/32270)

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**Author:** [@Giulio\_Vara](https://discourse.slicer.org/u/Giulio_Vara)\
**Replies:** 0\
**Last updated:** [October 17, 2023, 2:42pm UTC](https://discourse.slicer.org/t/scalar-volume-read-as-image-sequence/32270 "2023-10-17T14:42:20Z")

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I have a problem when trying to upload a sequence generated with “pMRI” to 3dslicer, as it loads the T1 map as an image sequence, displaying a single slice centered in space. I guess the problem is in the pmri dicom tag…

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## [Creating a Custom Slicer Module - which way to go?](https://discourse.slicer.org/t/creating-a-custom-slicer-module-which-way-to-go/32234)

<div class="topic-metadata">

**Author:** [@seanchoi0519](https://discourse.slicer.org/u/seanchoi0519)\
**Replies:** 5\
**Last updated:** [October 17, 2023, 2:42pm UTC](https://discourse.slicer.org/t/creating-a-custom-slicer-module-which-way-to-go/32234 "2023-10-17T14:42:07Z")

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Hello everyone I’m a long-time slicer lurker, who has received much help from everyone here and just want to extend my thanks. After a few years of using Slicer, I feel ready to start developing a few custom modules of …

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## [When I attempt local threshold extension, I cannot click with left mouse button.](https://discourse.slicer.org/t/when-i-attempt-local-threshold-extension-i-cannot-click-with-left-mouse-button/12850)

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**Author:** [@hsnam](https://discourse.slicer.org/u/hsnam)\
**Replies:** 4\
**Last updated:** [August 4, 2020, 1:59pm UTC](https://discourse.slicer.org/t/when-i-attempt-local-threshold-extension-i-cannot-click-with-left-mouse-button/12850 "2020-08-04T13:59:27Z")

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Operating system: Mac OS Mojave Slicer version: 4.10.2 Expected behavior: I want to get ROI using a local threshold extension. Actual behavior: When I attempt the local threshold, I cannot click with the left mouse …

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## [I broke my totalsegmentator](https://discourse.slicer.org/t/i-broke-my-totalsegmentator/32206)

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**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 6\
**Last updated:** [October 17, 2023, 11:58am UTC](https://discourse.slicer.org/t/i-broke-my-totalsegmentator/32206 "2023-10-17T11:58:51Z")

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Hello, I’ve been using total segmentator manually for some time and it was working well. I’ve recently tried too automatize the process and installed total segmentator directly by running pip install TotalSegmentato…

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## [Cross section analysis interpolates points](https://discourse.slicer.org/t/cross-section-analysis-interpolates-points/32266)

<div class="topic-metadata">

**Author:** [@bserrano](https://discourse.slicer.org/u/bserrano)\
**Replies:** 0\
**Last updated:** [October 17, 2023, 9:56am UTC](https://discourse.slicer.org/t/cross-section-analysis-interpolates-points/32266 "2023-10-17T09:56:14Z")

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Hi all, I’m attempting to automate the process of extracting the vessel area in a cross-sectional view. The plan is to utilize the cross-sectional analysis module. I initially expected that the number of points in the c…

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## [Finding centroid in the MRI scan](https://discourse.slicer.org/t/finding-centroid-in-the-mri-scan/32252)

<div class="topic-metadata">

**Author:** [@Michaela](https://discourse.slicer.org/u/Michaela)\
**Replies:** 2\
**Last updated:** [October 17, 2023, 2:20am UTC](https://discourse.slicer.org/t/finding-centroid-in-the-mri-scan/32252 "2023-10-17T02:20:46Z")

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Hello everybody, First of all, I am completely new to the 3D Slicer. My data consists of MRI scans of long bones. I need to measure cross sections of bones. I imagine something like this on the picture,but I did not fi…

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## [Reliability of extension stats](https://discourse.slicer.org/t/reliability-of-extension-stats/32236)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 7\
**Last updated:** [October 16, 2023, 11:18pm UTC](https://discourse.slicer.org/t/reliability-of-extension-stats/32236 "2023-10-16T23:18:02Z")

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@jcfr @Sam\_Horvath How reliable old download statistics? I just ran the extension download statistics, for all extensions, and why I sort them grand total, I am a little surprised with the some of the top results, such …

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## [Autocontouring the prostate ](https://discourse.slicer.org/t/autocontouring-the-prostate/32253)

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**Author:** [@swin](https://discourse.slicer.org/u/swin)\
**Replies:** 1\
**Last updated:** [October 16, 2023, 7:19pm UTC](https://discourse.slicer.org/t/autocontouring-the-prostate/32253 "2023-10-16T19:19:35Z")

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Hello, Could anyone recommend an extension to autocontour the prostate on either MRI or CT scan? Thanks

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## [Create gridlines in 3D view, similar to the effect in the figure](https://discourse.slicer.org/t/create-gridlines-in-3d-view-similar-to-the-effect-in-the-figure/29127)

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**Author:** [@q2577040659](https://discourse.slicer.org/u/q2577040659)\
**Replies:** 2\
**Last updated:** [October 16, 2023, 7:03pm UTC](https://discourse.slicer.org/t/create-gridlines-in-3d-view-similar-to-the-effect-in-the-figure/29127 "2023-10-16T19:03:55Z")

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## [Rendering images sequentially](https://discourse.slicer.org/t/rendering-images-sequentially/32231)

<div class="topic-metadata">

**Author:** [@ehdrmfdl3648](https://discourse.slicer.org/u/ehdrmfdl3648)\
**Replies:** 3\
**Last updated:** [October 16, 2023, 6:16pm UTC](https://discourse.slicer.org/t/rendering-images-sequentially/32231 "2023-10-16T18:16:56Z")

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Good to see you. Thank you very much for developing 3d slicer. I am currently working on a project using 3d slicer, but there is one problem. What I am trying to do is to display an ultrasound image in 3D space. I hav…

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## [Slicer for real-time visualisation from multiple data streams and sending control commands](https://discourse.slicer.org/t/slicer-for-real-time-visualisation-from-multiple-data-streams-and-sending-control-commands/32209)

<div class="topic-metadata">

**Author:** [@heiko](https://discourse.slicer.org/u/heiko)\
**Replies:** 6\
**Last updated:** [October 16, 2023, 2:21pm UTC](https://discourse.slicer.org/t/slicer-for-real-time-visualisation-from-multiple-data-streams-and-sending-control-commands/32209 "2023-10-16T14:21:33Z")

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Hi everybody, I am aware this question is quite broad, apology for that. I am planning to have a graphical user interface. The main purposes would be to pull data from multiple sources (X-Ray, some electric circuitry, ……

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## [How to perform the UKFTractography via command line on ubuntu 20.04?](https://discourse.slicer.org/t/how-to-perform-the-ukftractography-via-command-line-on-ubuntu-20-04/30657)

<div class="topic-metadata">

**Author:** [@dazhangge-666](https://discourse.slicer.org/u/dazhangge-666)\
**Replies:** 11\
**Last updated:** [October 16, 2023, 3:36am UTC](https://discourse.slicer.org/t/how-to-perform-the-ukftractography-via-command-line-on-ubuntu-20-04/30657 "2023-10-16T03:36:42Z")

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I want to use .sh to batch process my data via UKFTractography ,so maybe I must use the command line of it.How could I do?

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## [Create "heatmap" in slicer](https://discourse.slicer.org/t/create-heatmap-in-slicer/31976)

<div class="topic-metadata">

**Author:** [@umair04](https://discourse.slicer.org/u/umair04)\
**Replies:** 3\
**Last updated:** [October 15, 2023, 9:50pm UTC](https://discourse.slicer.org/t/create-heatmap-in-slicer/31976 "2023-10-15T21:50:48Z")

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Hi, Does anyone know how to create a “heatmap” on slicer? I am trying to overlay 5 different segmentations below and make areas where overlap occurs darker and highlight the areas where most overlap occurs. Thanks

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