# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=54

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

**Page:** 55

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## [Skull stripping/ Brain Extraction for canine brains with HDBrainExtraction a/o SwissSkullStripper](https://discourse.slicer.org/t/skull-stripping-brain-extraction-for-canine-brains-with-hdbrainextraction-a-o-swissskullstripper/41472)

<div class="topic-metadata">

**Author:** [@ma\_apan](https://discourse.slicer.org/u/ma_apan)\
**Replies:** 0\
**Last updated:** [February 3, 2025, 9:04pm UTC](https://discourse.slicer.org/t/skull-stripping-brain-extraction-for-canine-brains-with-hdbrainextraction-a-o-swissskullstripper/41472 "2025-02-03T21:04:47Z")

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I have to extract canine brains from around 60 patients in T1w 3D MRI-images. I tried both options SwissSkullstripper doesn’t extract all brain, but only a small part of the brain (image 1) HD Brain Extraction Tool wor…

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## [How to Integrate Threshold Effect from Segment Editor into a Custom Module](https://discourse.slicer.org/t/how-to-integrate-threshold-effect-from-segment-editor-into-a-custom-module/41334)

<div class="topic-metadata">

**Author:** [@igi133](https://discourse.slicer.org/u/igi133)\
**Replies:** 8\
**Last updated:** [February 3, 2025, 1:03pm UTC](https://discourse.slicer.org/t/how-to-integrate-threshold-effect-from-segment-editor-into-a-custom-module/41334 "2025-02-03T13:03:30Z")

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Hi everyone, I am currently working on a custom module in 3D Slicer and would like to incorporate the functionality of the “Threshold” effect from the Segment Editor module. My main goal is to allow users to: Set thr…

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## [Questions about Sandbox/Segment Cross-segment Area](https://discourse.slicer.org/t/questions-about-sandbox-segment-cross-segment-area/41035)

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**Author:** [@Magnus\_Wiman](https://discourse.slicer.org/u/Magnus_Wiman)\
**Replies:** 12\
**Last updated:** [February 3, 2025, 10:19am UTC](https://discourse.slicer.org/t/questions-about-sandbox-segment-cross-segment-area/41035 "2025-02-03T10:19:24Z")

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Hello. I´m an absolute newbie to Slicer so forgive me if my questions are a bit daft. I found 3D Slicer by chance searching for a solution to a problem I have. We have a lot of different cylindrical “connectors” that …

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## [Volume inside a mesh](https://discourse.slicer.org/t/volume-inside-a-mesh/41450)

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**Author:** [@Melodicpinpon](https://discourse.slicer.org/u/Melodicpinpon)\
**Replies:** 0\
**Last updated:** [February 2, 2025, 9:58am UTC](https://discourse.slicer.org/t/volume-inside-a-mesh/41450 "2025-02-02T09:58:48Z")

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Hi everyone! Is there a format that combines a mesh and a volume (the one contained in the mesh)? A developer can surely link each mesh to its corresponding volume but isn’t there already a format that gathers these inf…

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## [Error Loading Project Files with Missing .NRRD Files](https://discourse.slicer.org/t/error-loading-project-files-with-missing-nrrd-files/41448)

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**Author:** [@SLDT](https://discourse.slicer.org/u/SLDT)\
**Replies:** 0\
**Last updated:** [February 2, 2025, 4:00am UTC](https://discourse.slicer.org/t/error-loading-project-files-with-missing-nrrd-files/41448 "2025-02-02T04:00:55Z")

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Hello Slicer Community, I have recently encountered a problem loading a few sets of project files that I had a research assistant help me to prepare last year using Slicer 5.2.2. The problem is this: when I try to open …

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## [Total segmentator in 3d Slicer with python script](https://discourse.slicer.org/t/total-segmentator-in-3d-slicer-with-python-script/40251)

<div class="topic-metadata">

**Author:** [@Benutzer-0815](https://discourse.slicer.org/u/Benutzer-0815)\
**Replies:** 10\
**Last updated:** [February 1, 2025, 7:54pm UTC](https://discourse.slicer.org/t/total-segmentator-in-3d-slicer-with-python-script/40251 "2025-02-01T19:54:20Z")

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Hi there, I am trying to write a python script that uses Totalsegmentator in 3dSlicer, but so far I am not able to make good progress. The aim of using it in 3dslicer instead of standalone is to be able to exctract SUV v…

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## [Transforming a node back to original volume](https://discourse.slicer.org/t/transforming-a-node-back-to-original-volume/33266)

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**Author:** [@Yoyoman](https://discourse.slicer.org/u/Yoyoman)\
**Replies:** 6\
**Last updated:** [February 1, 2025, 10:06am UTC](https://discourse.slicer.org/t/transforming-a-node-back-to-original-volume/33266 "2025-02-01T10:06:42Z")

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Sorry if this question is rather basic. Please direct me to the thread if this topic has already been covered. I did look. This is my typical workflow…I import a DICOM file then centre the volume then rotate the volume,…

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## [Seeking paint bucket tool: Need to manually fill in segmented areas that are not fully enclosed](https://discourse.slicer.org/t/seeking-paint-bucket-tool-need-to-manually-fill-in-segmented-areas-that-are-not-fully-enclosed/41400)

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**Author:** [@connoryamsek](https://discourse.slicer.org/u/connoryamsek)\
**Replies:** 2\
**Last updated:** [January 31, 2025, 12:12pm UTC](https://discourse.slicer.org/t/seeking-paint-bucket-tool-need-to-manually-fill-in-segmented-areas-that-are-not-fully-enclosed/41400 "2025-01-31T12:12:07Z")

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I am 3D printing my friends skull. I did several hours of manual segmentation and have cleaned my model very well… however the thin bone/cartiledge/tissue is definitely trying. Is there a tool I can use that works a…

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## [Is SlicerMorph down?](https://discourse.slicer.org/t/is-slicermorph-down/41401)

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**Author:** [@Barons](https://discourse.slicer.org/u/Barons)\
**Replies:** 1\
**Last updated:** [January 31, 2025, 11:30am UTC](https://discourse.slicer.org/t/is-slicermorph-down/41401 "2025-01-31T11:30:34Z")

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Hi, I’m new to Slicer3D and would like to use SlicerMorph but the webpages don’t work and the extension won’t work - is it no longer available?

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## [ "no attribute 'SafeConfigParser'" during installation.](https://discourse.slicer.org/t/no-attribute-safeconfigparser-during-installation/41403)

<div class="topic-metadata">

**Author:** [@jxwang](https://discourse.slicer.org/u/jxwang)\
**Replies:** 0\
**Last updated:** [January 31, 2025, 11:28am UTC](https://discourse.slicer.org/t/no-attribute-safeconfigparser-during-installation/41403 "2025-01-31T11:28:42Z")

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File “C:\\Users\\User\\AppData\\Local\\Temp\\pip-install-98lxnlgs\\pyradiomics\_9d99062da3f5438592bc77f142141765\\versioneer.py”, line 342, in get\_config\_from\_root parser = configparser.SafeConfigParser() ^^^^^^^^^^^^^^^^^^^^^^…

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## [Unable to create a Docker container using a downloaded 3DSlicer version](https://discourse.slicer.org/t/unable-to-create-a-docker-container-using-a-downloaded-3dslicer-version/41384)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 1\
**Last updated:** [January 31, 2025, 2:16am UTC](https://discourse.slicer.org/t/unable-to-create-a-docker-container-using-a-downloaded-3dslicer-version/41384 "2025-01-31T02:16:10Z")

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Hi, I have been trying to build a Docker image to run a given 3DSlicer version (5.2.2) on an HPC system. Once I have the base installation working, I will be willing to instal SlicerDMRI, UKFTractography and SlicerWMA e…

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## [DICOM patient name not showing in database module](https://discourse.slicer.org/t/dicom-patient-name-not-showing-in-database-module/34368)

<div class="topic-metadata">

**Author:** [@Michael\_Allen](https://discourse.slicer.org/u/Michael_Allen)\
**Replies:** 15\
**Last updated:** [January 30, 2025, 9:19pm UTC](https://discourse.slicer.org/t/dicom-patient-name-not-showing-in-database-module/34368 "2025-01-30T21:19:14Z")

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Hello, at some point in recent updates the patient name field in the dicom browser has stopped displaying the name. If I right click and view metadata, the name is still there. If I search for the name in the browser, sl…

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## [Tumor Location in Image](https://discourse.slicer.org/t/tumor-location-in-image/41379)

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**Author:** [@sajad\_amiri](https://discourse.slicer.org/u/sajad_amiri)\
**Replies:** 0\
**Last updated:** [January 30, 2025, 5:55pm UTC](https://discourse.slicer.org/t/tumor-location-in-image/41379 "2025-01-30T17:55:02Z")

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I have a dataset of registered images, each with a segmentation, and I want to identify the location of the segmentation in the MRI intensity matrix: X, Y, Z. how it is possible ?

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## [Complete noob wants to 3d print his brain. Scans aren't perfect. Help?](https://discourse.slicer.org/t/complete-noob-wants-to-3d-print-his-brain-scans-arent-perfect-help/41278)

<div class="topic-metadata">

**Author:** [@Snoochers](https://discourse.slicer.org/u/Snoochers)\
**Replies:** 4\
**Last updated:** [January 30, 2025, 2:41pm UTC](https://discourse.slicer.org/t/complete-noob-wants-to-3d-print-his-brain-scans-arent-perfect-help/41278 "2025-01-30T14:41:24Z")

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Hi. I have DICOM files of my brain. There’s a lot of scans in there but many wouldn’t be suitable for a 3D model I think. The best scans seem to be 26 slices going ear to ear and 33 slices going top of head to bottom. I …

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## [I want to save : from dicom to VTK format for comparision T1, T2 Face image](https://discourse.slicer.org/t/i-want-to-save-from-dicom-to-vtk-format-for-comparision-t1-t2-face-image/41371)

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**Author:** [@Hyung\_Min\_Kim](https://discourse.slicer.org/u/Hyung_Min_Kim)\
**Replies:** 0\
**Last updated:** [January 30, 2025, 11:19am UTC](https://discourse.slicer.org/t/i-want-to-save-from-dicom-to-vtk-format-for-comparision-t1-t2-face-image/41371 "2025-01-30T11:19:59Z")

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Hello I’m a newbie user of 3d-slicer. I want to save a face image from a dicom file to a vtk file. I’m reaching out to you because I’ve been searching on my own and can’t seem to find the answer. I want to use the sh…

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## [Best Tools for Bone CT scan](https://discourse.slicer.org/t/best-tools-for-bone-ct-scan/41366)

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**Author:** [@Dimitri\_Gouvoussis](https://discourse.slicer.org/u/Dimitri_Gouvoussis)\
**Replies:** 0\
**Last updated:** [January 30, 2025, 3:08am UTC](https://discourse.slicer.org/t/best-tools-for-bone-ct-scan/41366 "2025-01-30T03:08:27Z")

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Hello, I am using segment editor tolls thresholding and cutting to outline bone structures in a CT scan. I’m wondering if anyone has a more accurate way of outlining these structures t. Thank you! Note: my 3D scan is …

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## [MOOSE dependencies can not be installed - extension does not work](https://discourse.slicer.org/t/moose-dependencies-can-not-be-installed-extension-does-not-work/41359)

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**Author:** [@MaxVs](https://discourse.slicer.org/u/MaxVs)\
**Replies:** 6\
**Last updated:** [January 29, 2025, 4:37pm UTC](https://discourse.slicer.org/t/moose-dependencies-can-not-be-installed-extension-does-not-work/41359 "2025-01-29T16:37:48Z")

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As the newest version 5.9.0 appeard, I found some new extensions. One of these is MOOSE extension, but unfortunatelly it doesnt work. Every time I click install dependencies, I wait even couple hours and nothing happen…

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## [Opening 5.6.2 recon with 5.8.0 version](https://discourse.slicer.org/t/opening-5-6-2-recon-with-5-8-0-version/41349)

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**Author:** [@BaptisteSVD](https://discourse.slicer.org/u/BaptisteSVD)\
**Replies:** 3\
**Last updated:** [January 29, 2025, 4:31pm UTC](https://discourse.slicer.org/t/opening-5-6-2-recon-with-5-8-0-version/41349 "2025-01-29T16:31:38Z")

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Hi, I produce 3D reconstructions using version 5.6.2 of 3D Slicer. Could this cause opening or reading errors if the reconstruction is opened with version 5.8.0 ?Thanks in advance !

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## ["Interaction in 3D Viewer" to align orthogonal planes missing in 5.8.0 update?](https://discourse.slicer.org/t/interaction-in-3d-viewer-to-align-orthogonal-planes-missing-in-5-8-0-update/41360)

<div class="topic-metadata">

**Author:** [@sck84](https://discourse.slicer.org/u/sck84)\
**Replies:** 1\
**Last updated:** [January 29, 2025, 4:03pm UTC](https://discourse.slicer.org/t/interaction-in-3d-viewer-to-align-orthogonal-planes-missing-in-5-8-0-update/41360 "2025-01-29T16:03:56Z")

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Hi everyone, I used to create a transform and use the “Interaction in 3D Viewer” tool to align structures to the orthogonal planes in Slicer. Following the most recent update, it appears this function has gone away.…

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## [Can't see my segment colors on the 2D CT scan images](https://discourse.slicer.org/t/cant-see-my-segment-colors-on-the-2d-ct-scan-images/41358)

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**Author:** [@Burhaan\_Toor](https://discourse.slicer.org/u/Burhaan_Toor)\
**Replies:** 0\
**Last updated:** [January 29, 2025, 3:09pm UTC](https://discourse.slicer.org/t/cant-see-my-segment-colors-on-the-2d-ct-scan-images/41358 "2025-01-29T15:09:39Z")

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Hello, I have created two segments- one for the femur and one for the right hip bone-which I have left unnamed in the photo. I am able to see the femur segment on my 2D images as the color I have chosen is showing in eac…

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## [Beam Hardening Detection and Correction - CT Head](https://discourse.slicer.org/t/beam-hardening-detection-and-correction-ct-head/41353)

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**Author:** [@JoshOnichino](https://discourse.slicer.org/u/JoshOnichino)\
**Replies:** 0\
**Last updated:** [January 29, 2025, 1:28pm UTC](https://discourse.slicer.org/t/beam-hardening-detection-and-correction-ct-head/41353 "2025-01-29T13:28:32Z")

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Hello everyone, I’m working on a project involving head CT imaging and need to identify and correct artifacts that may interfere with analysis. I’m particularly interested in open-source models or algorithms that can be…

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## [Closed surface area measurement going to 0](https://discourse.slicer.org/t/closed-surface-area-measurement-going-to-0/41299)

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**Author:** [@cgordon\_Slicer](https://discourse.slicer.org/u/cgordon_Slicer)\
**Replies:** 3\
**Last updated:** [January 29, 2025, 12:46pm UTC](https://discourse.slicer.org/t/closed-surface-area-measurement-going-to-0/41299 "2025-01-29T12:46:47Z")

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Hello! I’m trying to measure the surface areas of segmented muscle attachment sites using the Closed Curve (CC) Markups tool. However, whenever I trace too complex or too inwardly bending of a shape, its area automatica…

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## [Accessing information within ImageMetaList](https://discourse.slicer.org/t/accessing-information-within-imagemetalist/41350)

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**Author:** [@Arber\_Demi](https://discourse.slicer.org/u/Arber_Demi)\
**Replies:** 1\
**Last updated:** [January 29, 2025, 11:15am UTC](https://discourse.slicer.org/t/accessing-information-within-imagemetalist/41350 "2025-01-29T11:15:32Z")

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Hello! I am trying to automate a data extraction process from a medical device using python, however I’m having issue extracing the data from a ImageMetaList node after receiving it as a response. Is there a way I’m sup…

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## [How to integrate the dicom data from 3 series](https://discourse.slicer.org/t/how-to-integrate-the-dicom-data-from-3-series/41310)

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**Author:** [@cycycy](https://discourse.slicer.org/u/cycycy)\
**Replies:** 4\
**Last updated:** [January 29, 2025, 10:06am UTC](https://discourse.slicer.org/t/how-to-integrate-the-dicom-data-from-3-series/41310 "2025-01-29T10:06:39Z")

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Hello, I am trying to evaluate bone quality using the bone texture module of 3d slicer software (ver.5.6.2) from pre- and post-operative CT scans of a certain surgery. However, not just with 3d slicer, but I am having t…

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## [C/p segmentation](https://discourse.slicer.org/t/c-p-segmentation/41339)

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**Author:** [@BDhoth](https://discourse.slicer.org/u/BDhoth)\
**Replies:** 1\
**Last updated:** [January 29, 2025, 8:21am UTC](https://discourse.slicer.org/t/c-p-segmentation/41339 "2025-01-29T08:21:09Z")

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Is it possible to take a segmentation and c/p it? I segmented 5 pieces of anatomy; however, I needed them aligned to my CT not the MR. Trying to save time from re-segmenting all of them.

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## [Mirroring landmarks across midsagittal plane ](https://discourse.slicer.org/t/mirroring-landmarks-across-midsagittal-plane/41249)

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**Author:** [@sck84](https://discourse.slicer.org/u/sck84)\
**Replies:** 2\
**Last updated:** [January 28, 2025, 8:50pm UTC](https://discourse.slicer.org/t/mirroring-landmarks-across-midsagittal-plane/41249 "2025-01-28T20:50:52Z")

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Hello, I am trying to mirror landmarks applied to one half of a skull across the midsagittal plane. Really, my aim is to landmark half of the skull, and mirror any points that are not on the midsagittal line, so as to c…

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## [VMTK SlicerExtension Multiprocessing](https://discourse.slicer.org/t/vmtk-slicerextension-multiprocessing/41099)

<div class="topic-metadata">

**Author:** [@Tracy](https://discourse.slicer.org/u/Tracy)\
**Replies:** 7\
**Last updated:** [January 28, 2025, 8:40pm UTC](https://discourse.slicer.org/t/vmtk-slicerextension-multiprocessing/41099 "2025-01-28T20:40:27Z")

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Hi, I have a python pipeline that utilizes several functions, such as ExtractCenterline and ClipVessel, from the SlicerExtension-VMTK (GitHub - vmtk/SlicerExtension-VMTK) for analyzing vessel segmentation. Since I need …

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## [Endocranial volume in 3D Slicer](https://discourse.slicer.org/t/endocranial-volume-in-3d-slicer/41239)

<div class="topic-metadata">

**Author:** [@ThomasVanParys](https://discourse.slicer.org/u/ThomasVanParys)\
**Replies:** 5\
**Last updated:** [January 28, 2025, 3:34pm UTC](https://discourse.slicer.org/t/endocranial-volume-in-3d-slicer/41239 "2025-01-28T15:34:12Z")

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Hello, I am segmenting skulls from the NDMDID PM-CT dataset. I want to measure endocranial volume, or some measure of cranial capacity/brain size. What is best or easiest way to do this from the skull models? Here is …

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## [Placing Landmarks on 2D images](https://discourse.slicer.org/t/placing-landmarks-on-2d-images/41337)

<div class="topic-metadata">

**Author:** [@Kowsar\_Sheikhi](https://discourse.slicer.org/u/Kowsar_Sheikhi)\
**Replies:** 1\
**Last updated:** [January 28, 2025, 2:27pm UTC](https://discourse.slicer.org/t/placing-landmarks-on-2d-images/41337 "2025-01-28T14:27:17Z")

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How can I accurately place landmarks on 2D CT and MRI images of the knee? I have used the Markups tool before, but I’m not sure if I did it correctly. Could anyone guide me through the process of placing landmarks using…

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## [Threshold does not work when saved data loaded again](https://discourse.slicer.org/t/threshold-does-not-work-when-saved-data-loaded-again/37376)

<div class="topic-metadata">

**Author:** [@Figaya](https://discourse.slicer.org/u/Figaya)\
**Replies:** 3\
**Last updated:** [January 27, 2025, 9:18pm UTC](https://discourse.slicer.org/t/threshold-does-not-work-when-saved-data-loaded-again/37376 "2025-01-27T21:18:22Z")

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Hello, The threshold does not apply when I perform the following steps: Load MRHead sample data. Go to the Segment Editor module. Add a segment. Open the Threshold effect (DO NOT APPLY THE THRESHOLD NOW). Press CTRL+S…

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