# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=90

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

**Page:** 91

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## [Deface MRI data](https://discourse.slicer.org/t/deface-mri-data/36729)

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**Author:** [@Basil\_Berinyuy](https://discourse.slicer.org/u/Basil_Berinyuy)\
**Replies:** 0\
**Last updated:** [June 12, 2024, 4:55pm UTC](https://discourse.slicer.org/t/deface-mri-data/36729 "2024-06-12T16:55:56Z")

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Hello, I would like to know if it is possible to use 3D slicer to deface an MRI for anonymisation. If yes how do I go about this? if no, would you recommend a software for such purposes? thank you in advance.

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## [Logging with a python script](https://discourse.slicer.org/t/logging-with-a-python-script/36726)

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**Author:** [@RomanStriker](https://discourse.slicer.org/u/RomanStriker)\
**Replies:** 0\
**Last updated:** [June 12, 2024, 2:59pm UTC](https://discourse.slicer.org/t/logging-with-a-python-script/36726 "2024-06-12T14:59:06Z")

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I am trying to log the output of a python script to a file and the console. The code works fine when run in a normal python env but with slicer it does not log anything. The code is as follows. import sys import argpars…

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## [Run a python script with command line arguments](https://discourse.slicer.org/t/run-a-python-script-with-command-line-arguments/36718)

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**Author:** [@RomanStriker](https://discourse.slicer.org/u/RomanStriker)\
**Replies:** 2\
**Last updated:** [June 12, 2024, 12:07pm UTC](https://discourse.slicer.org/t/run-a-python-script-with-command-line-arguments/36718 "2024-06-12T12:07:35Z")

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Hi, I am trying to run a python script that accepts command line arguments as follows. ./Slicer --python-script /home/user/extract\_centerlines\_vmtk.py --data\_dir /PATH/TO/DATA --end\_points --network --network\_curve --n…

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## [Avoid creating multiple module widget instances from a python script](https://discourse.slicer.org/t/avoid-creating-multiple-module-widget-instances-from-a-python-script/36717)

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**Author:** [@RomanStriker](https://discourse.slicer.org/u/RomanStriker)\
**Replies:** 1\
**Last updated:** [June 12, 2024, 10:55am UTC](https://discourse.slicer.org/t/avoid-creating-multiple-module-widget-instances-from-a-python-script/36717 "2024-06-12T10:55:08Z")

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Hi, I am trying to generate centerlines for a batch of segmentation masks. I use a python script that uses the VMTK Extract Centerline widget. The issue is that for every new segmentation, Slicer opens a new Extract Cen…

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## [Pop up said that the acquisition duration](https://discourse.slicer.org/t/pop-up-said-that-the-acquisition-duration/36716)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 0\
**Last updated:** [June 12, 2024, 8:26am UTC](https://discourse.slicer.org/t/pop-up-said-that-the-acquisition-duration/36716 "2024-06-12T08:26:55Z")

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Dear All, I was face problem once want to rescale data using OpenDose3D. The pop up said that the acquisition duration does not have. But I checked the Dicom it has. How to solve this problem?

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## [MTV and LTV Segmentation](https://discourse.slicer.org/t/mtv-and-ltv-segmentation/36714)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 0\
**Last updated:** [June 12, 2024, 7:44am UTC](https://discourse.slicer.org/t/mtv-and-ltv-segmentation/36714 "2024-06-12T07:44:46Z")

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Dear All, Any plug in can calculate the metabolic tumor volume (MTV) and tumor lesion glycolisis (TLG)?

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## [Create a voxel element per pixel in a segmentation/model](https://discourse.slicer.org/t/create-a-voxel-element-per-pixel-in-a-segmentation-model/36710)

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**Author:** [@William\_Kuo](https://discourse.slicer.org/u/William_Kuo)\
**Replies:** 0\
**Last updated:** [June 11, 2024, 11:35pm UTC](https://discourse.slicer.org/t/create-a-voxel-element-per-pixel-in-a-segmentation-model/36710 "2024-06-11T23:35:32Z")

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I would like to generate a voxel element that is the size of each pixel (voxel in 3D) and get the densities of each element. However, I am not quite sure how to do that in SegmentMesher. I played around with the setting…

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## [How to exclude area through thresholding?](https://discourse.slicer.org/t/how-to-exclude-area-through-thresholding/36703)

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**Author:** [@kev1n](https://discourse.slicer.org/u/kev1n)\
**Replies:** 3\
**Last updated:** [June 11, 2024, 6:38pm UTC](https://discourse.slicer.org/t/how-to-exclude-area-through-thresholding/36703 "2024-06-11T18:38:46Z")

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Hi there, I’m trying to segment out a CT w/ contrast of the L hip. I’m trying to use a threshold to segment just the bone but the contrast has the same intensity as the bone and I’m unable to effectively separate out th…

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## [3D Slicer Error](https://discourse.slicer.org/t/3d-slicer-error/36623)

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**Author:** [@Hala\_Madi](https://discourse.slicer.org/u/Hala_Madi)\
**Replies:** 3\
**Last updated:** [June 11, 2024, 9:22am UTC](https://discourse.slicer.org/t/3d-slicer-error/36623 "2024-06-11T09:22:13Z")

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Good afternoon, As i’m trying to view some of the sample data from the bone reconstruction planar extension, I come across a reoccurring error. it states the following: TypeError: method requires a VTK object. I have tr…

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## [Orbital calculation](https://discourse.slicer.org/t/orbital-calculation/36694)

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**Author:** [@YLX](https://discourse.slicer.org/u/YLX)\
**Replies:** 0\
**Last updated:** [June 11, 2024, 7:14am UTC](https://discourse.slicer.org/t/orbital-calculation/36694 "2024-06-11T07:14:20Z")

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I would like to ask whether 3D Slicer can calculate the orbital volume and surface area of CT images, as well as the orbital depth? And if so, how do you calculate it Operating system: Slicer version:5.7.0 Expected …

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## [How to load .3ddose file with SlicerRT extensions](https://discourse.slicer.org/t/how-to-load-3ddose-file-with-slicerrt-extensions/36621)

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**Author:** [@JamsNeroc](https://discourse.slicer.org/u/JamsNeroc)\
**Replies:** 4\
**Last updated:** [June 11, 2024, 12:34am UTC](https://discourse.slicer.org/t/how-to-load-3ddose-file-with-slicerrt-extensions/36621 "2024-06-11T00:34:16Z")

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Hello everyone.  It could be found that many topics had successfully load 3ddose file with SlicerRT extensions, and @cpinter had also mentioned that “after you install the SlicerRT extension from the Extension Manager…

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## [When did the Slicer switch to LPS for fcsv?](https://discourse.slicer.org/t/when-did-the-slicer-switch-to-lps-for-fcsv/36677)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [June 10, 2024, 2:42pm UTC](https://discourse.slicer.org/t/when-did-the-slicer-switch-to-lps-for-fcsv/36677 "2024-06-10T14:42:02Z")

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As per Markups — 3D Slicer documentation There was a time coordinates was written in RAS. Is it possible to get the specific date LPS became the “standard” for markup files?

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## [UnicodeDecodeError when running DentalSegmentator](https://discourse.slicer.org/t/unicodedecodeerror-when-running-dentalsegmentator/36684)

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**Author:** [@viet\_duc\_Vu](https://discourse.slicer.org/u/viet_duc_Vu)\
**Replies:** 0\
**Last updated:** [June 9, 2024, 8:30am UTC](https://discourse.slicer.org/t/unicodedecodeerror-when-running-dentalsegmentator/36684 "2024-06-09T08:30:47Z")

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Thank you. Recently I use this extension in other computer. But when running it I have a problem when the error was informed that Check the inference folder content C:\\Temp\\Slicer-igReWK\\output .This below is my python …

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## [DentalSegmentator inaccuracies separating cortical bone and teeth](https://discourse.slicer.org/t/dentalsegmentator-inaccuracies-separating-cortical-bone-and-teeth/36683)

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**Author:** [@viet\_duc\_Vu](https://discourse.slicer.org/u/viet_duc_Vu)\
**Replies:** 1\
**Last updated:** [June 7, 2024, 8:01am UTC](https://discourse.slicer.org/t/dentalsegmentator-inaccuracies-separating-cortical-bone-and-teeth/36683 "2024-06-07T08:01:40Z")

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Hi. I really appreciate what you have done so far. The software is amazing. I have compared to between conventional segmentation ( with commercial software) and your segmentation extension. this extension helps reduce…

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## [DentalSegmentator version of 2024-04-22 fails to load segmentation result](https://discourse.slicer.org/t/dentalsegmentator-version-of-2024-04-22-fails-to-load-segmentation-result/36682)

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**Author:** [@Muaiyed](https://discourse.slicer.org/u/Muaiyed)\
**Replies:** 2\
**Last updated:** [May 16, 2024, 5:57pm UTC](https://discourse.slicer.org/t/dentalsegmentator-version-of-2024-04-22-fails-to-load-segmentation-result/36682 "2024-05-16T17:57:22Z")

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hi dears when i click apply it stuck and no progress how i can solve it

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## ["Constrain points to surface" feature ](https://discourse.slicer.org/t/constrain-points-to-surface-feature/36632)

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**Author:** [@taylorfisher](https://discourse.slicer.org/u/taylorfisher)\
**Replies:** 2\
**Last updated:** [June 9, 2024, 11:14pm UTC](https://discourse.slicer.org/t/constrain-points-to-surface-feature/36632 "2024-06-09T23:14:36Z")

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Operating system: 3D Slicer Slicer version: 5.6.1 Expected behavior: My colleague has an older version of 3D slicer. In Markups → Resample section he has an option of “constrain points to surface” Actual behavior: I c…

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## [Reconstruction of synchrotron-based X-ray tomographic microscopy (SRXTM) images](https://discourse.slicer.org/t/reconstruction-of-synchrotron-based-x-ray-tomographic-microscopy-srxtm-images/36653)

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**Author:** [@Trung\_L\_i\_Quang](https://discourse.slicer.org/u/Trung_L_i_Quang)\
**Replies:** 3\
**Last updated:** [June 9, 2024, 5:58pm UTC](https://discourse.slicer.org/t/reconstruction-of-synchrotron-based-x-ray-tomographic-microscopy-srxtm-images/36653 "2024-06-09T17:58:17Z")

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Dear community, I am a newbie to 3D Slicer and I’m hoping to get some advice. I have a set of Synchrotron-based X-ray tomographic microscopy (SRXTM) images including 1700 slices (2D). I would like to visualize its 3D vo…

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## [How to be able to edit a 3D Model (.stl) keeping high resolution of the output](https://discourse.slicer.org/t/how-to-be-able-to-edit-a-3d-model-stl-keeping-high-resolution-of-the-output/36656)

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**Author:** [@MAXFAXSURGEON](https://discourse.slicer.org/u/MAXFAXSURGEON)\
**Replies:** 1\
**Last updated:** [June 9, 2024, 3:57am UTC](https://discourse.slicer.org/t/how-to-be-able-to-edit-a-3d-model-stl-keeping-high-resolution-of-the-output/36656 "2024-06-09T03:57:16Z")

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Hi everyone in this great forum, I need to modify an .stl file in form of 3D model to be used in another software for orthognathic virtual planning. When I loaded the 3D model to generate a master volume to be then open…

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## [How can I load a default segment color config from customized file,like export from itk-snap](https://discourse.slicer.org/t/how-can-i-load-a-default-segment-color-config-from-customized-file-like-export-from-itk-snap/24988)

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**Author:** [@SlicerIsGood](https://discourse.slicer.org/u/SlicerIsGood)\
**Replies:** 5\
**Last updated:** [June 9, 2024, 3:51am UTC](https://discourse.slicer.org/t/how-can-i-load-a-default-segment-color-config-from-customized-file-like-export-from-itk-snap/24988 "2024-06-09T03:51:33Z")

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like this, itk-snap has a eport label description file funciton, so I want load this file to slicer to perform segmentation with color described in file, how can I do this?

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## [3D object color map creation](https://discourse.slicer.org/t/3d-object-color-map-creation/36664)

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**Author:** [@capucinelab](https://discourse.slicer.org/u/capucinelab)\
**Replies:** 0\
**Last updated:** [June 8, 2024, 11:37pm UTC](https://discourse.slicer.org/t/3d-object-color-map-creation/36664 "2024-06-08T23:37:22Z")

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Hello everyone! Do you know if it is possible to create a deformation map of an object (in my case a human skull) on this software, without going through a segmentation phase? In fact, I’d like to compare the different…

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## [Measure length and width in 2D MRI slice](https://discourse.slicer.org/t/measure-length-and-width-in-2d-mri-slice/36421)

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**Author:** [@therapistlee](https://discourse.slicer.org/u/therapistlee)\
**Replies:** 3\
**Last updated:** [June 8, 2024, 11:18pm UTC](https://discourse.slicer.org/t/measure-length-and-width-in-2d-mri-slice/36421 "2024-06-08T23:18:00Z")

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Hello, I am a new user of the 3D slicer community who is currently engaged in speech studies using MRI and seeking advice on using the 3D slicer program. The aim of my study is to measure the length and width of the 2D…

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## [Problems saving MRB file, seems to be related to having two image sets at different time points](https://discourse.slicer.org/t/problems-saving-mrb-file-seems-to-be-related-to-having-two-image-sets-at-different-time-points/36630)

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**Author:** [@kkwst2](https://discourse.slicer.org/u/kkwst2)\
**Replies:** 3\
**Last updated:** [June 7, 2024, 3:31pm UTC](https://discourse.slicer.org/t/problems-saving-mrb-file-seems-to-be-related-to-having-two-image-sets-at-different-time-points/36630 "2024-06-07T15:31:33Z")

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Problem report for Slicer 5.7.0-2024-06-05 win-amd64: \[Imported two different MRA sequences with same volume but gated to two different time points in the cardiac cycle. It seemed to automatically bundes them into a time…

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## [Any good way to Cut at the pickPoint on 1 branch, while keep all the other branches not cut?](https://discourse.slicer.org/t/any-good-way-to-cut-at-the-pickpoint-on-1-branch-while-keep-all-the-other-branches-not-cut/36640)

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**Author:** [@gpu](https://discourse.slicer.org/u/gpu)\
**Replies:** 0\
**Last updated:** [June 7, 2024, 9:59am UTC](https://discourse.slicer.org/t/any-good-way-to-cut-at-the-pickpoint-on-1-branch-while-keep-all-the-other-branches-not-cut/36640 "2024-06-07T09:59:57Z")

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any good way to Cut at the pickPoint on 1 branch, while keep all the other branches not cut? Thanks!

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## [Any tutorial about using VMTK in C++ project?and organize the result of BranchClipper as multi-branch tree?](https://discourse.slicer.org/t/any-tutorial-about-using-vmtk-in-c-project-and-organize-the-result-of-branchclipper-as-multi-branch-tree/36639)

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**Author:** [@gpu](https://discourse.slicer.org/u/gpu)\
**Replies:** 0\
**Last updated:** [June 7, 2024, 9:57am UTC](https://discourse.slicer.org/t/any-tutorial-about-using-vmtk-in-c-project-and-organize-the-result-of-branchclipper-as-multi-branch-tree/36639 "2024-06-07T09:57:45Z")

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any tutorial about using VMTK in C++ project? and organize the result of BranchClipper as multi-branch tree? Thanks!

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## [Offline 3D reconstruction from .mhd file using SlicerIGSIO extension](https://discourse.slicer.org/t/offline-3d-reconstruction-from-mhd-file-using-slicerigsio-extension/36602)

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**Author:** [@Viktor\_Sokolov](https://discourse.slicer.org/u/Viktor_Sokolov)\
**Replies:** 3\
**Last updated:** [June 7, 2024, 7:55am UTC](https://discourse.slicer.org/t/offline-3d-reconstruction-from-mhd-file-using-slicerigsio-extension/36602 "2024-06-07T07:55:46Z")

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Hello everyone! I have a few questions about how to use the SlicerIGSIO tool for offline 3D reconstruction. The available tutorial only shows reconstruction in the Plus App. Should I load the .mhd/.mha file as a Volum…

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## ["Markups to model" did not strictly go through all control points of the markups, resulting in the surface not being what I expected. Unable to create complex surfaces](https://discourse.slicer.org/t/markups-to-model-did-not-strictly-go-through-all-control-points-of-the-markups-resulting-in-the-surface-not-being-what-i-expected-unable-to-create-complex-surfaces/36633)

<div class="topic-metadata">

**Author:** [@linhuanfeng](https://discourse.slicer.org/u/linhuanfeng)\
**Replies:** 4\
**Last updated:** [June 7, 2024, 6:04am UTC](https://discourse.slicer.org/t/markups-to-model-did-not-strictly-go-through-all-control-points-of-the-markups-resulting-in-the-surface-not-being-what-i-expected-unable-to-create-complex-surfaces/36633 "2024-06-07T06:04:46Z")

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“Markups to model” did not strictly go through all control points of the markups, resulting in the surface not being what I expected. Unable to create complex surfaces.

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## [How to Export Reconstructed Volume and Position Data](https://discourse.slicer.org/t/how-to-export-reconstructed-volume-and-position-data/36626)

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**Author:** [@valerie](https://discourse.slicer.org/u/valerie)\
**Replies:** 1\
**Last updated:** [June 6, 2024, 11:04pm UTC](https://discourse.slicer.org/t/how-to-export-reconstructed-volume-and-position-data/36626 "2024-06-06T23:04:17Z")

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Hi, I made a previous post about live reconstruction of the kidney using Telemed and NDI Aurora, which was somewhat successful (I still have to troubleshoot some things). My next question is how I can export the recon…

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## [MONAI Project Resources for Mandible Image Segmentation](https://discourse.slicer.org/t/monai-project-resources-for-mandible-image-segmentation/36127)

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**Author:** [@Havay](https://discourse.slicer.org/u/Havay)\
**Replies:** 6\
**Last updated:** [June 6, 2024, 7:58pm UTC](https://discourse.slicer.org/t/monai-project-resources-for-mandible-image-segmentation/36127 "2024-06-06T19:58:42Z")

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Hello, we are a medical research team from Duke & JHU, currently working on image segmentation tasks for damaged mandibles. I have reviewed your MONAI project, and I am impressed by the results. I would like to inquire i…

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## [ALPACA "import itk" error](https://discourse.slicer.org/t/alpaca-import-itk-error/36625)

<div class="topic-metadata">

**Author:** [@EllaNicklin](https://discourse.slicer.org/u/EllaNicklin)\
**Replies:** 3\
**Last updated:** [June 6, 2024, 6:06pm UTC](https://discourse.slicer.org/t/alpaca-import-itk-error/36625 "2024-06-06T18:06:36Z")

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Hello 3D Slicer community, I have just tried to use ALPACA module for the first time on a new lab laptop (Windows 11) running 3D Slicer 5.7.0 (preview release). Slicer ran into an issue loading in the python script then…

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## [Slicer crashed after run this script](https://discourse.slicer.org/t/slicer-crashed-after-run-this-script/36605)

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**Author:** [@Xiaojie\_Guo](https://discourse.slicer.org/u/Xiaojie_Guo)\
**Replies:** 5\
**Last updated:** [June 6, 2024, 5:28pm UTC](https://discourse.slicer.org/t/slicer-crashed-after-run-this-script/36605 "2024-06-06T17:28:19Z")

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Hi, all After running MaskVolumeHistogramPlot.py, delete the segmentation, which includes Tumor, Reference, and Background, from Data module, Slicer crashed. How to fix this?

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