# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=182

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

**Page:** 183

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## [Get the array of a transformed volume](https://discourse.slicer.org/t/get-the-array-of-a-transformed-volume/27495)

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**Author:** [@rodrigo.vargas](https://discourse.slicer.org/u/rodrigo.vargas)\
**Replies:** 6\
**Last updated:** [January 28, 2023, 5:57pm UTC](https://discourse.slicer.org/t/get-the-array-of-a-transformed-volume/27495 "2023-01-28T17:57:21Z")

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I’m trying to rotate a volume and then get the corresponding (rotated) array. I thought hardening and then using util.arrayFromVolume would do it, but it doesn’t (if I transform further, get again the array and compare, …

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## [MR Helium Pressure in DICOM TAGS](https://discourse.slicer.org/t/mr-helium-pressure-in-dicom-tags/27499)

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**Author:** [@Flavio\_Lemos](https://discourse.slicer.org/u/Flavio_Lemos)\
**Replies:** 1\
**Last updated:** [January 28, 2023, 5:54pm UTC](https://discourse.slicer.org/t/mr-helium-pressure-in-dicom-tags/27499 "2023-01-28T17:54:09Z")

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Hello everyone. Is there a DICOM tag in MR where the information about Helium pressure and Helium percent is stored? Thank You all.

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## [Red window object - Script Dev](https://discourse.slicer.org/t/red-window-object-script-dev/27477)

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**Author:** [@lucas\_sd](https://discourse.slicer.org/u/lucas_sd)\
**Replies:** 3\
**Last updated:** [January 28, 2023, 5:41pm UTC](https://discourse.slicer.org/t/red-window-object-script-dev/27477 "2023-01-28T17:41:49Z")

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Hi everybody, I would like to know if I can use/call the red window like an object to put it in a frame/container using it in another application. If its possible, what would the command be? Maybe with slicer.app.layou…

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## [Changed the format /resolution of volume, now I cant see my segmentations](https://discourse.slicer.org/t/changed-the-format-resolution-of-volume-now-i-cant-see-my-segmentations/27482)

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**Author:** [@Onur](https://discourse.slicer.org/u/Onur)\
**Replies:** 3\
**Last updated:** [January 28, 2023, 5:12pm UTC](https://discourse.slicer.org/t/changed-the-format-resolution-of-volume-now-i-cant-see-my-segmentations/27482 "2023-01-28T17:12:34Z")

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Hi there I tryed to apply some filters on my volume file with imageJ. then imported it to 3dslicer make a segment using threshold. saved it and call my old volume file. (because I cant see all details with filtered volu…

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## [Heart beat of my baby and error while opening files on 3D Slicer](https://discourse.slicer.org/t/heart-beat-of-my-baby-and-error-while-opening-files-on-3d-slicer/27516)

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**Author:** [@Marthm](https://discourse.slicer.org/u/Marthm)\
**Replies:** 0\
**Last updated:** [January 28, 2023, 3:37pm UTC](https://discourse.slicer.org/t/heart-beat-of-my-baby-and-error-while-opening-files-on-3d-slicer/27516 "2023-01-28T15:37:18Z")

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Hello, I just found this awesome community because I just got home from the 1st appointment where I heard my baby’s heartbeat. The doctor gave me some pictures and (she claims) the sound of baby’s heartbeat. I was not ab…

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## [Extension name vs repo name](https://discourse.slicer.org/t/extension-name-vs-repo-name/27507)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 1\
**Last updated:** [January 27, 2023, 10:30pm UTC](https://discourse.slicer.org/t/extension-name-vs-repo-name/27507 "2023-01-27T22:30:33Z")

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I am submitting a new extension: Add MEMOS extension by smrolfe · Pull Request #1908 · Slicer/ExtensionsIndex · GitHub and would like to understand how the extension names are set in the catalog. I would like the displ…

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## [Tracking of multiple objects to a reference](https://discourse.slicer.org/t/tracking-of-multiple-objects-to-a-reference/27450)

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**Author:** [@MPeiffer](https://discourse.slicer.org/u/MPeiffer)\
**Replies:** 6\
**Last updated:** [January 27, 2023, 6:28pm UTC](https://discourse.slicer.org/t/tracking-of-multiple-objects-to-a-reference/27450 "2023-01-27T18:28:47Z")

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Hi all, I’ve been working with slicerIGT to create a surgical navigation tool for the ankle. In this tool, we want to track the position of the Fibula (calf bone) with respect to the reference Tibia (shin bone). To tr…

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## [problem with files from new cbct scanner](https://discourse.slicer.org/t/problem-with-files-from-new-cbct-scanner/26167)

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**Author:** [@jeroen](https://discourse.slicer.org/u/jeroen)\
**Replies:** 4\
**Last updated:** [January 27, 2023, 4:11pm UTC](https://discourse.slicer.org/t/problem-with-files-from-new-cbct-scanner/26167 "2023-01-27T16:11:31Z")

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until now no problem, but when i recieve files from a new cbct scanner en load de filles the look like de picture below? what is wrong? please help!!! in the vierwer the scan is perfect, only in the 3dslicer it looks li…

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## [Quilt Displays on Laptop but not on Looking Glass](https://discourse.slicer.org/t/quilt-displays-on-laptop-but-not-on-looking-glass/27498)

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**Author:** [@mircat](https://discourse.slicer.org/u/mircat)\
**Replies:** 0\
**Last updated:** [January 27, 2023, 12:20pm UTC](https://discourse.slicer.org/t/quilt-displays-on-laptop-but-not-on-looking-glass/27498 "2023-01-27T12:20:21Z")

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Hello, I am trying to use the Looking Glass Extension on 3D Slicer 5.2.1. I have the Looking Glass Portrait. I cannot seem to connect to the hardware from Slicer. What happens is the quilt displays on my laptop screen …

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## [Buttons need color](https://discourse.slicer.org/t/buttons-need-color/27181)

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**Author:** [@Ulli\_Wagner](https://discourse.slicer.org/u/Ulli_Wagner)\
**Replies:** 11\
**Last updated:** [January 26, 2023, 6:39pm UTC](https://discourse.slicer.org/t/buttons-need-color/27181 "2023-01-26T18:39:51Z")

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Hi, I am a new Slicer user. I would like to suggest that buttons appear in color. It is hard to recognize that the Apply button needs to be clicked because it has the same color as the field labels and dropdown lists. S…

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## [How to collapse a folder by code?](https://discourse.slicer.org/t/how-to-collapse-a-folder-by-code/20082)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 16\
**Last updated:** [January 26, 2023, 6:12pm UTC](https://discourse.slicer.org/t/how-to-collapse-a-folder-by-code/20082 "2023-01-26T18:12:23Z")

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Hi everyone!! Order all new nodes maked by a process is wonderfull !!!.. Every thing in a human comprensive tree of elements… But I don´t find the way to collapse by code all made folders… Is it possible? Thanks in adv…

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## [SEEG Assistant for epileptosurgery](https://discourse.slicer.org/t/seeg-assistant-for-epileptosurgery/15663)

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**Author:** [@Barbora\_Cvickova](https://discourse.slicer.org/u/Barbora_Cvickova)\
**Replies:** 1\
**Last updated:** [January 26, 2023, 4:20pm UTC](https://discourse.slicer.org/t/seeg-assistant-for-epileptosurgery/15663 "2023-01-26T16:20:09Z")

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Hello. I have read there is SEEG Assistant (for planning of depth electrodes for epileptosurgery) as extension of 3D slicer. Do you know about it? It is possible to download it somewhere? And how can you install it? Tha…

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## [Unexpected behaviour with control point coordinates outside of Slicer](https://discourse.slicer.org/t/unexpected-behaviour-with-control-point-coordinates-outside-of-slicer/27460)

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**Author:** [@drobny](https://discourse.slicer.org/u/drobny)\
**Replies:** 3\
**Last updated:** [January 26, 2023, 4:08pm UTC](https://discourse.slicer.org/t/unexpected-behaviour-with-control-point-coordinates-outside-of-slicer/27460 "2023-01-26T16:08:45Z")

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I ran into a problem using a Slicer markup json file outside of Slicer. Either I am missing something or there might be a bug somewhere. Steps to reproduce: open CTchest sample image make point annotations and save th…

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## [How to export TotalSegmentator results as DICOM SEG?](https://discourse.slicer.org/t/how-to-export-totalsegmentator-results-as-dicom-seg/27229)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 7\
**Last updated:** [January 25, 2023, 8:31pm UTC](https://discourse.slicer.org/t/how-to-export-totalsegmentator-results-as-dicom-seg/27229 "2023-01-25T20:31:38Z")

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I would like to export results of TotalSegmentator into DICOM Segmentation format. I am using latest Slicer stable 5.2.1 on Mac. I loaded input CT series from DICOM Browser. I have QuantitativeReporting extension instal…

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## [Tag (0018,0050) Slice Thickness does not correspond to what I calculate in the image](https://discourse.slicer.org/t/tag-0018-0050-slice-thickness-does-not-correspond-to-what-i-calculate-in-the-image/27438)

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**Author:** [@francesca\_flore](https://discourse.slicer.org/u/francesca_flore)\
**Replies:** 4\
**Last updated:** [January 25, 2023, 8:26pm UTC](https://discourse.slicer.org/t/tag-0018-0050-slice-thickness-does-not-correspond-to-what-i-calculate-in-the-image/27438 "2023-01-25T20:26:11Z")

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In the two sagittal slices it can be seen that the difference between one slice and the other is 6.5mm, unlike 5mm as reported in the Tag (0018,0050) Slice Thickness. How is this possible? Which should I consider correct…

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## [object in subsurface](https://discourse.slicer.org/t/object-in-subsurface/27451)

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**Author:** [@THOD](https://discourse.slicer.org/u/THOD)\
**Replies:** 1\
**Last updated:** [January 24, 2023, 9:05pm UTC](https://discourse.slicer.org/t/object-in-subsurface/27451 "2023-01-24T21:05:59Z")

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Hello, i want help if anyone knows i’m looking a barried object (metal box) and i get some data from my gpr. i use raw image in the 3d slicer but i cant figure how can i see some structure in the image, is any other way…

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## [subarachnoid space geometry](https://discourse.slicer.org/t/subarachnoid-space-geometry/27452)

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**Author:** [@Hessam\_Mazaheri](https://discourse.slicer.org/u/Hessam_Mazaheri)\
**Replies:** 0\
**Last updated:** [January 24, 2023, 8:52pm UTC](https://discourse.slicer.org/t/subarachnoid-space-geometry/27452 "2023-01-24T20:52:31Z")

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Hello everyone I want to do a CFD model of CSF flow in the subarachnoid space region (in the spinal cord), is it possible to extract the geometry of the desired region from the 3D slicer? Thank you for your guidance.

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## [Multicenter MRI data for radiomics features extraction](https://discourse.slicer.org/t/multicenter-mri-data-for-radiomics-features-extraction/27448)

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**Author:** [@Amin](https://discourse.slicer.org/u/Amin)\
**Replies:** 0\
**Last updated:** [January 24, 2023, 8:52pm UTC](https://discourse.slicer.org/t/multicenter-mri-data-for-radiomics-features-extraction/27448 "2023-01-24T20:52:18Z")

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Hello I want to run pyradiomics on my MRI data with 3D slicer, Considering that my data was prepared with different devices (1.5 and 3 Tesla) and the resolution of the images is also different. Are the features extrac…

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## [How to import .json or .txt file markup file](https://discourse.slicer.org/t/how-to-import-json-or-txt-file-markup-file/27360)

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**Author:** [@Kae1](https://discourse.slicer.org/u/Kae1)\
**Replies:** 3\
**Last updated:** [January 24, 2023, 8:51pm UTC](https://discourse.slicer.org/t/how-to-import-json-or-txt-file-markup-file/27360 "2023-01-24T20:51:52Z")

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Hi there. How do you import a .json or .txt file to use as a markup file? I am quite new to Slicer, so a simple clear answer would be much appreciated. When I drag and drop the json or txt file into Slicer, or else go …

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## [Help with Local Threshold effect](https://discourse.slicer.org/t/help-with-local-threshold-effect/27426)

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**Author:** [@Ekaterina\_Savkina](https://discourse.slicer.org/u/Ekaterina_Savkina)\
**Replies:** 1\
**Last updated:** [January 24, 2023, 3:22pm UTC](https://discourse.slicer.org/t/help-with-local-threshold-effect/27426 "2023-01-24T15:22:48Z")

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As I understood, Local threshold selects the areas with definite threshold’s range, but then you can choose some region that could be connected to big area by some thin layer, or some region that is not connected and you…

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## [fill holes in segment](https://discourse.slicer.org/t/fill-holes-in-segment/27427)

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**Author:** [@ManiaFG](https://discourse.slicer.org/u/ManiaFG)\
**Replies:** 1\
**Last updated:** [January 24, 2023, 1:39pm UTC](https://discourse.slicer.org/t/fill-holes-in-segment/27427 "2023-01-24T13:39:03Z")

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Hello! Is there any way to fill holes in each slice? I’v downloaded some modules, but no result for me. Maybe there are few ways to do this? Would like to know all of them if possible : ) Operating system:win 10 S…

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## [ register and STL model into a dental Cbct scan ?](https://discourse.slicer.org/t/register-and-stl-model-into-a-dental-cbct-scan/27429)

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**Author:** [@zvifudim](https://discourse.slicer.org/u/zvifudim)\
**Replies:** 2\
**Last updated:** [January 24, 2023, 1:35pm UTC](https://discourse.slicer.org/t/register-and-stl-model-into-a-dental-cbct-scan/27429 "2023-01-24T13:35:49Z")

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Can anyone help me on how to register and STL model into a dental Cbct scan ?

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## [Including air as part of mesh](https://discourse.slicer.org/t/including-air-as-part-of-mesh/27439)

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**Author:** [@ascam](https://discourse.slicer.org/u/ascam)\
**Replies:** 1\
**Last updated:** [January 24, 2023, 12:26pm UTC](https://discourse.slicer.org/t/including-air-as-part-of-mesh/27439 "2023-01-24T12:26:57Z")

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Hi there. I’m looking to run a FEM model of light propagation across biological tissue (including free space / pockets of air), and am using Slicer to create a volumetric mesh. I need to include air as part of the mesh.…

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## [Problem with DICOM Dental files](https://discourse.slicer.org/t/problem-with-dicom-dental-files/1193)

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**Author:** [@Jonathan\_Dmello](https://discourse.slicer.org/u/Jonathan_Dmello)\
**Replies:** 5\
**Last updated:** [January 24, 2023, 12:21pm UTC](https://discourse.slicer.org/t/problem-with-dicom-dental-files/1193 "2023-01-24T12:21:51Z")

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Need some help with a dicom dental file. The 3D image loads in a elongated view. by which i mean the image is stretched vertically. Can anyone help with this. i am adding a link to the file. I think its a problem with t…

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## [Error in uploading DICOM Files ](https://discourse.slicer.org/t/error-in-uploading-dicom-files/27428)

<div class="topic-metadata">

**Author:** [@3DMedic](https://discourse.slicer.org/u/3DMedic)\
**Replies:** 3\
**Last updated:** [January 24, 2023, 10:16am UTC](https://discourse.slicer.org/t/error-in-uploading-dicom-files/27428 "2023-01-24T10:16:33Z")

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I have a compressed DICOM file (DICOMDIR) that I am trying to load into 3D Slicer and produce a 3D volume of a patient’s head. I have tried uploading the data into 3D Slicer, but I receive an error saying that the files …

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## [Regression associated with Slicer 5.3.0 2023-01-23 has been fixed](https://discourse.slicer.org/t/regression-associated-with-slicer-5-3-0-2023-01-23-has-been-fixed/27424)

<div class="topic-metadata">

**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 2\
**Last updated:** [January 24, 2023, 12:15am UTC](https://discourse.slicer.org/t/regression-associated-with-slicer-5-3-0-2023-01-23-has-been-fixed/27424 "2023-01-24T00:15:28Z")

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For future reference, the corresponding regression preventing from starting the application has been identified and fixed in PR-6793. :pray: @Connor-Bowley, @Sam\_Horvath and @lassoan

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## [How to visualize wall of trachea that is obstructed by tracheostomy tube lying alongside it](https://discourse.slicer.org/t/how-to-visualize-wall-of-trachea-that-is-obstructed-by-tracheostomy-tube-lying-alongside-it/27408)

<div class="topic-metadata">

**Author:** [@mdear](https://discourse.slicer.org/u/mdear)\
**Replies:** 1\
**Last updated:** [January 23, 2023, 8:22pm UTC](https://discourse.slicer.org/t/how-to-visualize-wall-of-trachea-that-is-obstructed-by-tracheostomy-tube-lying-alongside-it/27408 "2023-01-23T20:22:57Z")

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Hello again. My inability to visualize all aspects of the tracheal wall is handicapping my efforts to produce novel custom shaped tracheostomy tubes for my son by annealing off-the-shelf Shiley Medtronics tubes. In an …

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## [MonaiLabel vertebrae segmentation sample-app doesn't work for sample data](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243)

<div class="topic-metadata">

**Author:** [@mau\_igna\_06](https://discourse.slicer.org/u/mau_igna_06)\
**Replies:** 12\
**Last updated:** [January 23, 2023, 5:05pm UTC](https://discourse.slicer.org/t/monailabel-vertebrae-segmentation-sample-app-doesnt-work-for-sample-data/27243 "2023-01-23T17:05:58Z")

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After clicking Run Auto Segmentation, the segments of the segmentationNode are still empty. Another CT I tried only segmented half a vertebrae. If I try segmentation\_vertebrae model instead the monai-label server cr…

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## [Segmentation terminology to labelmap indices](https://discourse.slicer.org/t/segmentation-terminology-to-labelmap-indices/27405)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [January 23, 2023, 4:02pm UTC](https://discourse.slicer.org/t/segmentation-terminology-to-labelmap-indices/27405 "2023-01-23T16:02:23Z")

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In the SegmentationCategoryTypeModified-DICOM Master.json file, there are these fields called 3dSlicerIntergerLabel (like below). I thought these were the unique ID numbers that will be used when exporting a segmentatio…

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## [HU in Lung CT Analyzer](https://discourse.slicer.org/t/hu-in-lung-ct-analyzer/27418)

<div class="topic-metadata">

**Author:** [@Paula\_R](https://discourse.slicer.org/u/Paula_R)\
**Replies:** 1\
**Last updated:** [January 23, 2023, 3:51pm UTC](https://discourse.slicer.org/t/hu-in-lung-ct-analyzer/27418 "2023-01-23T15:51:49Z")

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Hello, I’m using the Lung CT Analyzer, and the thresholds range of HU for the lung parenchyma (bulla, vessels, etc) go from -1050 to 1000. Now, I’ve read in the literature that the whole range of HU goes from -1000 (for…

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