# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=111

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

**Page:** 112

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## [Directly interacting with python console](https://discourse.slicer.org/t/directly-interacting-with-python-console/34455)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 11\
**Last updated:** [February 24, 2024, 12:41am UTC](https://discourse.slicer.org/t/directly-interacting-with-python-console/34455 "2024-02-24T00:41:37Z")

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Is there a way to send python scripts from a text editor or an IDE directly to Slicer’s python? Copy and paste occasionally fails or creates weird issues (I am on remote connection). I am not a big fan of jupyter noteboo…

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## [Problem in render a volume on import](https://discourse.slicer.org/t/problem-in-render-a-volume-on-import/34428)

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**Author:** [@calvinsuzuki](https://discourse.slicer.org/u/calvinsuzuki)\
**Replies:** 2\
**Last updated:** [February 23, 2024, 4:00pm UTC](https://discourse.slicer.org/t/problem-in-render-a-volume-on-import/34428 "2024-02-23T16:00:47Z")

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Hey guys, I’ve been trying to do a very simple task on Slicer. Just to display the rendered model on drag n drop import. It rarely works, but in most cases I got the error: Warning: In /work/Stable/Slicer-0/Modules/Lo…

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## [Sorting data by type and name in Scene](https://discourse.slicer.org/t/sorting-data-by-type-and-name-in-scene/34499)

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**Author:** [@S\_Motch\_Perrine](https://discourse.slicer.org/u/S_Motch_Perrine)\
**Replies:** 7\
**Last updated:** [February 23, 2024, 5:15pm UTC](https://discourse.slicer.org/t/sorting-data-by-type-and-name-in-scene/34499 "2024-02-23T17:15:31Z")

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I have a large number of files in my Scene, and would like to have them ordered by name. I’m sure there’s got to be a way to do this quickly, but I either can’t remember or find it quickly. Example… my files are all name…

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## [Data sorting in scene by type and file name](https://discourse.slicer.org/t/data-sorting-in-scene-by-type-and-file-name/34500)

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**Author:** [@S\_Motch\_Perrine](https://discourse.slicer.org/u/S_Motch_Perrine)\
**Replies:** 0\
**Last updated:** [February 23, 2024, 3:37pm UTC](https://discourse.slicer.org/t/data-sorting-in-scene-by-type-and-file-name/34500 "2024-02-23T15:37:43Z")

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As noted in this support thread: Sorting data by type and name in Scene I had asked about sorting data in a scene by file type and name. This is not currently supported, but I think it would be a really useful feature …

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## [How to load one specific series of a DICOM scanning in Python](https://discourse.slicer.org/t/how-to-load-one-specific-series-of-a-dicom-scanning-in-python/34448)

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**Author:** [@paleomariomm](https://discourse.slicer.org/u/paleomariomm)\
**Replies:** 2\
**Last updated:** [February 23, 2024, 3:24pm UTC](https://discourse.slicer.org/t/how-to-load-one-specific-series-of-a-dicom-scanning-in-python/34448 "2024-02-23T15:24:18Z")

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Hi everyone. I have an issue when loading DICOM files. I have this code, which iteratively opens different scannings of baboon skulls placed in different folders: import os from DICOMLib import DICOMUtils yourpath = …

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## [Trouble reading NRRD file](https://discourse.slicer.org/t/trouble-reading-nrrd-file/34494)

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**Author:** [@Ben\_Fong](https://discourse.slicer.org/u/Ben_Fong)\
**Replies:** 1\
**Last updated:** [February 23, 2024, 2:19pm UTC](https://discourse.slicer.org/t/trouble-reading-nrrd-file/34494 "2024-02-23T14:19:01Z")

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I am working on CT and MRI DICOMs with version 5.4.0 in Windows 10 and MacBook Pro Sonoma with no problem. I added on DICOM series and segmentations in MacBook and saved. Then I upgraded to 5.6.1 in both Windows 10 and S…

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## [Add an observer to the SliceNode's scrollbar](https://discourse.slicer.org/t/add-an-observer-to-the-slicenodes-scrollbar/34399)

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**Author:** [@waromero](https://discourse.slicer.org/u/waromero)\
**Replies:** 2\
**Last updated:** [February 23, 2024, 2:17pm UTC](https://discourse.slicer.org/t/add-an-observer-to-the-slicenodes-scrollbar/34399 "2024-02-23T14:17:35Z")

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Hello! I would like to add an observer to the scrollbar events of a given view. I cannot find the right event to add the callback function. viewerNode = slicer.util.getNode("vtkMRMLSliceDisplayNode1") # Or should that …

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## [Vessel centerline extraction and metrics](https://discourse.slicer.org/t/vessel-centerline-extraction-and-metrics/34488)

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**Author:** [@sampadsengupta](https://discourse.slicer.org/u/sampadsengupta)\
**Replies:** 2\
**Last updated:** [February 23, 2024, 12:26pm UTC](https://discourse.slicer.org/t/vessel-centerline-extraction-and-metrics/34488 "2024-02-23T12:26:10Z")

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Hi, I have CFD results for vascular flow which I am processing and want to correlate geometric factors with haemodynamic metrics. Is it possible to: a) automate the computation of a centerline through a vessel for a l…

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## [Problem running TotalSegmentator in Slicer-5.4](https://discourse.slicer.org/t/problem-running-totalsegmentator-in-slicer-5-4/32491)

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**Author:** [@Investigacion\_y\_des1](https://discourse.slicer.org/u/Investigacion_y_des1)\
**Replies:** 11\
**Last updated:** [February 23, 2024, 8:43am UTC](https://discourse.slicer.org/t/problem-running-totalsegmentator-in-slicer-5-4/32491 "2024-02-23T08:43:06Z")

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Hi ! I have a question, do the previous version works with Slicer 5.4? because I’m not been able to run it on my pc. I will appreciate an answer, best regards.

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## [I create lung vessels in 3d slicer now i want to save this 3d lung vessels because after i will change this 3d lung vessels into stl file for 3d printing](https://discourse.slicer.org/t/i-create-lung-vessels-in-3d-slicer-now-i-want-to-save-this-3d-lung-vessels-because-after-i-will-change-this-3d-lung-vessels-into-stl-file-for-3d-printing/34490)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 0\
**Last updated:** [February 23, 2024, 7:13am UTC](https://discourse.slicer.org/t/i-create-lung-vessels-in-3d-slicer-now-i-want-to-save-this-3d-lung-vessels-because-after-i-will-change-this-3d-lung-vessels-into-stl-file-for-3d-printing/34490 "2024-02-23T07:13:19Z")

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i create lung vessels in 3d slicer now i want to save this 3d lung vessels because after i will change this 3d lung vessels into stl file for 3d printing. any body help me

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## [Virtual Reality installation](https://discourse.slicer.org/t/virtual-reality-installation/34452)

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**Author:** [@LukasKnybel](https://discourse.slicer.org/u/LukasKnybel)\
**Replies:** 2\
**Last updated:** [February 23, 2024, 4:37am UTC](https://discourse.slicer.org/t/virtual-reality-installation/34452 "2024-02-23T04:37:53Z")

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Dear Slicer Users, I am not able to install Slicer VR extension for some reason (V 5.6.0) I add the correct path in App settings but the VR module is not present and visible. I am affraid that problem is on my side bu…

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## [How to make a transparent brain model?](https://discourse.slicer.org/t/how-to-make-a-transparent-brain-model/34486)

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**Author:** [@Salil\_Bhole](https://discourse.slicer.org/u/Salil_Bhole)\
**Replies:** 0\
**Last updated:** [February 23, 2024, 2:50am UTC](https://discourse.slicer.org/t/how-to-make-a-transparent-brain-model/34486 "2024-02-23T02:50:49Z")

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Hi, I’ve recently been having some trouble making a transparent 3D model of the brain to visualize the position of my segmentation of an ablation cavity in the medial temporal area. Any ideas on how to do this? I’ve tri…

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## [Saving mesh as ASCII with Segment Mesher](https://discourse.slicer.org/t/saving-mesh-as-ascii-with-segment-mesher/34480)

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**Author:** [@Vasko](https://discourse.slicer.org/u/Vasko)\
**Replies:** 0\
**Last updated:** [February 22, 2024, 8:08pm UTC](https://discourse.slicer.org/t/saving-mesh-as-ascii-with-segment-mesher/34480 "2024-02-22T20:08:14Z")

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Hello, I’ve been using Segment Mesher for creating volumetric mesh of a tooth. The default option for saving the vtk file is binary. I saw that there is way to save it as ASCII, by deactivating option “Compress”. Unfort…

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## [Data save error: failed to save scene](https://discourse.slicer.org/t/data-save-error-failed-to-save-scene/34409)

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**Author:** [@Gonzo009](https://discourse.slicer.org/u/Gonzo009)\
**Replies:** 8\
**Last updated:** [February 22, 2024, 4:05pm UTC](https://discourse.slicer.org/t/data-save-error-failed-to-save-scene/34409 "2024-02-22T16:05:43Z")

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hi, i am new to 3dslicer, but i have a very basic error all the time. after loading a .nrrd file, data are accepted and shown in all planes and 3d. Any saving of these data, with or without a scene, causes all the time…

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## [Error giving inputs from console](https://discourse.slicer.org/t/error-giving-inputs-from-console/34423)

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**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 5\
**Last updated:** [February 22, 2024, 4:02pm UTC](https://discourse.slicer.org/t/error-giving-inputs-from-console/34423 "2024-02-22T16:02:34Z")

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Hi to everyone. the question today is the following one: · I’m trying to read some specific inputs from user in python console in Slicer. For this purpose I use: def entryLetterReader(prompt): while True: t…

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## [Camera calibration](https://discourse.slicer.org/t/camera-calibration/1874)

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**Author:** [@adamrankin](https://discourse.slicer.org/u/adamrankin)\
**Replies:** 12\
**Last updated:** [February 22, 2024, 3:41pm UTC](https://discourse.slicer.org/t/camera-calibration/1874 "2024-02-22T15:41:14Z")

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Hello, Are there any current extensions for camera calibration and registration? Adam

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## [Markups tools not measuring Slicer 5.4.0](https://discourse.slicer.org/t/markups-tools-not-measuring-slicer-5-4-0/31609)

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**Author:** [@jmhuie](https://discourse.slicer.org/u/jmhuie)\
**Replies:** 12\
**Last updated:** [February 22, 2024, 3:33pm UTC](https://discourse.slicer.org/t/markups-tools-not-measuring-slicer-5-4-0/31609 "2024-02-22T15:33:04Z")

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With Slicer 5.4.0, it seems that the MarkupsLineNode and other Markups Nodes are not showing their measurements, nor does it appear to be registering an actual measurement. When I try to get the measured length using pyt…

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## [Segmentation issue - "invisible" labels](https://discourse.slicer.org/t/segmentation-issue-invisible-labels/34460)

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**Author:** [@Dhartez](https://discourse.slicer.org/u/Dhartez)\
**Replies:** 3\
**Last updated:** [February 22, 2024, 2:44pm UTC](https://discourse.slicer.org/t/segmentation-issue-invisible-labels/34460 "2024-02-22T14:44:59Z")

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Hi all, sorry for semi-reposting (I initially thought this was a pyradiomics issue and therefore posted there, but now figured that it is a segmentation issue): I am having a problem with importing CNN generated segmen…

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## [How to rebuild the skull](https://discourse.slicer.org/t/how-to-rebuild-the-skull/15591)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 2\
**Last updated:** [February 22, 2024, 9:18am UTC](https://discourse.slicer.org/t/how-to-rebuild-the-skull/15591 "2024-02-22T09:18:08Z")

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It is hard for me，this is the data ，I hope get some help ! I tried to do it, but failed. nrrd data

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## [Show a video sequence in Slicer](https://discourse.slicer.org/t/show-a-video-sequence-in-slicer/34464)

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**Author:** [@schcat](https://discourse.slicer.org/u/schcat)\
**Replies:** 1\
**Last updated:** [February 22, 2024, 6:33am UTC](https://discourse.slicer.org/t/show-a-video-sequence-in-slicer/34464 "2024-02-22T06:33:08Z")

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I connect video data to Slicer using OpenIGTLinkIF, and the video appeared as an vtkMRMLVectorVolumeNode in my scene, When I click it’s “Visible” buttom, it shows in my first slice view. But I want it to show in a new vi…

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## [Trying to make 3d model of brain from MRI](https://discourse.slicer.org/t/trying-to-make-3d-model-of-brain-from-mri/6113)

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**Author:** [@tjop92](https://discourse.slicer.org/u/tjop92)\
**Replies:** 12\
**Last updated:** [February 22, 2024, 6:31am UTC](https://discourse.slicer.org/t/trying-to-make-3d-model-of-brain-from-mri/6113 "2024-02-22T06:31:51Z")

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Hello. I am trying to create a 3d model of my brain so that I can 3d print it. I have MRI scans that were done last year. I have no experience with this software or anything like this. I have tried a few tutorials an…

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## [For 3d lung vessels model](https://discourse.slicer.org/t/for-3d-lung-vessels-model/34465)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 0\
**Last updated:** [February 22, 2024, 5:42am UTC](https://discourse.slicer.org/t/for-3d-lung-vessels-model/34465 "2024-02-22T05:42:31Z")

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there is any tutorial for create 3d lung vessels model for 3d printing

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## [Totalsegmentator failing with error 120](https://discourse.slicer.org/t/totalsegmentator-failing-with-error-120/34434)

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**Author:** [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)\
**Replies:** 13\
**Last updated:** [February 22, 2024, 5:06am UTC](https://discourse.slicer.org/t/totalsegmentator-failing-with-error-120/34434 "2024-02-22T05:06:07Z")

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Hi all, I am having issues with the Totalsegmentator module. I have tried the steps that I have seen here:TotalSegmentator fails with error 120 - #4 by lassoan and here:TotalSegmentator error at first run: Command ...Py…

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## [3D Ultrasound Reconstruction with openIGTL (Verasonics & Polhemus)](https://discourse.slicer.org/t/3d-ultrasound-reconstruction-with-openigtl-verasonics-polhemus/32240)

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**Author:** [@ehdrmfdl3648](https://discourse.slicer.org/u/ehdrmfdl3648)\
**Replies:** 8\
**Last updated:** [February 22, 2024, 12:59am UTC](https://discourse.slicer.org/t/3d-ultrasound-reconstruction-with-openigtl-verasonics-polhemus/32240 "2024-02-22T00:59:34Z")

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US img: Verasonics 64 LE Position Sensor: Polhemus EMT Sensor Here’s what’s going on made Verasonics’ images available for import in Python. the values of the EMT sensor were imported into Python and a transform …

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## [There is no total segmentation in 3d slicer](https://discourse.slicer.org/t/there-is-no-total-segmentation-in-3d-slicer/34446)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 1\
**Last updated:** [February 21, 2024, 8:34pm UTC](https://discourse.slicer.org/t/there-is-no-total-segmentation-in-3d-slicer/34446 "2024-02-21T20:34:41Z")

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there is no total segmentation in 3d slicer ,which i download any one can help me

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## [Track images using Polhemus Fastrak electromagnetic tracker](https://discourse.slicer.org/t/track-images-using-polhemus-fastrak-electromagnetic-tracker/7056)

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**Author:** [@Satvika](https://discourse.slicer.org/u/Satvika)\
**Replies:** 5\
**Last updated:** [September 15, 2023, 2:44am UTC](https://discourse.slicer.org/t/track-images-using-polhemus-fastrak-electromagnetic-tracker/7056 "2023-09-15T02:44:29Z")

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Hi, We are working on tracking images with Electromagnetic Tracker (Polhemus Fastrak) using PLUS/Slicer. We have position data from the emt and images from ultrasound system: Q How do we obtain real-time transform matr…

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## [Comparing 2 MRI volumes to measure muscle atrophy](https://discourse.slicer.org/t/comparing-2-mri-volumes-to-measure-muscle-atrophy/28678)

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**Author:** [@feynmansum1](https://discourse.slicer.org/u/feynmansum1)\
**Replies:** 5\
**Last updated:** [March 31, 2023, 5:08pm UTC](https://discourse.slicer.org/t/comparing-2-mri-volumes-to-measure-muscle-atrophy/28678 "2023-03-31T17:08:09Z")

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Hello, I am new to Slicer and was hoping for some advice. I have 2 MRI’s of my right leg, 1 newer from a 3T instrument and 1 older study with a 1.5T. The study areas are slightly different but mostly overlap. I have m…

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## [How i can adjust slice](https://discourse.slicer.org/t/how-i-can-adjust-slice/34445)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 1\
**Last updated:** [February 21, 2024, 3:44pm UTC](https://discourse.slicer.org/t/how-i-can-adjust-slice/34445 "2024-02-21T15:44:01Z")

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WHEN I OPEN HRCT IMGAE IN 3D SLICE THERE IS ERROR IN SAGGITAL AND CORONAL PALE , THESE BOTH SLICE SHOW WRONGLY FROM DOWN I DONT KNOW WHY I ALSO ATTACH SS OF THIS IMAGE

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## [Unable to open vff file](https://discourse.slicer.org/t/unable-to-open-vff-file/34265)

<div class="topic-metadata">

**Author:** [@sieunmiin96](https://discourse.slicer.org/u/sieunmiin96)\
**Replies:** 6\
**Last updated:** [February 21, 2024, 12:44pm UTC](https://discourse.slicer.org/t/unable-to-open-vff-file/34265 "2024-02-21T12:44:45Z")

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I have Slicer 5.6.1, but I’m unable to open the vff file despite having the SlicerRT extension installed. The following is the error log: LoadVffFile: The values for the origin must each be greater than or equal to 0. …

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## [I can't use the lung lesion analyzer module of CIP](https://discourse.slicer.org/t/i-cant-use-the-lung-lesion-analyzer-module-of-cip/34398)

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**Author:** [@gokcetaniyan](https://discourse.slicer.org/u/gokcetaniyan)\
**Replies:** 3\
**Last updated:** [February 21, 2024, 12:30pm UTC](https://discourse.slicer.org/t/i-cant-use-the-lung-lesion-analyzer-module-of-cip/34398 "2024-02-21T12:30:43Z")

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I want to use the lung lesion analyzer module for lung nodule segmentation and analysis of nodule characteristics. I loaded my lung CT data. Then switched to the lung analyzer module, and put the fiducial on the nodule t…

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