# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=188

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

**Page:** 189

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## [Markups "save to defaults" colors misremembered](https://discourse.slicer.org/t/markups-save-to-defaults-colors-misremembered/26732)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 4\
**Last updated:** [December 23, 2022, 10:50pm UTC](https://discourse.slicer.org/t/markups-save-to-defaults-colors-misremembered/26732 "2022-12-23T22:50:15Z")

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In stable 5.2.1 in Linux, I change the colors of markups states and hit save to defaults. After slicer restart, this is what it comes back as: Same on windows. saved to defaults after restart Looks like ac…

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## [Model point count changing after transformation](https://discourse.slicer.org/t/model-point-count-changing-after-transformation/26736)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 33\
**Last updated:** [December 23, 2022, 7:21pm UTC](https://discourse.slicer.org/t/model-point-count-changing-after-transformation/26736 "2022-12-23T19:21:02Z")

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We have a visualization tool in SlicerMorph that applies a TPS transformation derived from PCA to a reference model. I have exported transformed models. I am trying to use the model to model distance to visualize a heatm…

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## [Save data without blocking the main thread](https://discourse.slicer.org/t/save-data-without-blocking-the-main-thread/26886)

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**Author:** [@Osspoor](https://discourse.slicer.org/u/Osspoor)\
**Replies:** 2\
**Last updated:** [December 22, 2022, 10:45pm UTC](https://discourse.slicer.org/t/save-data-without-blocking-the-main-thread/26886 "2022-12-22T22:45:50Z")

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Hello! How can I save a certain data in the scene or the whole scene without blocking the main thread (I can do anything else during the save)

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## [Mac Os Monterey](https://discourse.slicer.org/t/mac-os-monterey/26892)

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**Author:** [@Prof\_Aurel\_Messas](https://discourse.slicer.org/u/Prof_Aurel_Messas)\
**Replies:** 1\
**Last updated:** [December 22, 2022, 10:34pm UTC](https://discourse.slicer.org/t/mac-os-monterey/26892 "2022-12-22T22:34:33Z")

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Slicer 3D does not work on Monterey Do you have a solution I am going to buy a PC on Windows 10 will it work better ? Could you give me some help on this PC configuration to be able to use Slicer 3D easally ?

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## [Markup subject/folder disappears after toggling visibility in data module](https://discourse.slicer.org/t/markup-subject-folder-disappears-after-toggling-visibility-in-data-module/26890)

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**Author:** [@Karl\_Hahn](https://discourse.slicer.org/u/Karl_Hahn)\
**Replies:** 2\
**Last updated:** [December 22, 2022, 9:59pm UTC](https://discourse.slicer.org/t/markup-subject-folder-disappears-after-toggling-visibility-in-data-module/26890 "2022-12-22T21:59:12Z")

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The following steps seem to produce unexpected behavior. In Markups module “Node” table, right click and choose either “Create new subject” or “Create new folder”. In Data module, locate newly created subject/folder an…

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## [Accuracy measurement between two STL model T1 - immediate after surgery T2 one year after surgery](https://discourse.slicer.org/t/accuracy-measurement-between-two-stl-model-t1-immediate-after-surgery-t2-one-year-after-surgery/26880)

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**Author:** [@wael\_telha](https://discourse.slicer.org/u/wael_telha)\
**Replies:** 1\
**Last updated:** [December 22, 2022, 7:05pm UTC](https://discourse.slicer.org/t/accuracy-measurement-between-two-stl-model-t1-immediate-after-surgery-t2-one-year-after-surgery/26880 "2022-12-22T19:05:35Z")

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Dear 3D- Slicer Community I am conducting a research regarding the accuracy between two STL model following orthognathic surgery to check the accuracy between model immediate surgery and one following surgery. the steps…

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## [3D Rotation without mouse press after Popup "Operate on invisible segment?"](https://discourse.slicer.org/t/3d-rotation-without-mouse-press-after-popup-operate-on-invisible-segment/26889)

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**Author:** [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Replies:** 2\
**Last updated:** [December 22, 2022, 7:04pm UTC](https://discourse.slicer.org/t/3d-rotation-without-mouse-press-after-popup-operate-on-invisible-segment/26889 "2022-12-22T19:04:52Z")

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I am assuming that this is a small bug. Have had this problem with many versions of Slicer including 5.3.0. Here is a reproducible example. Download Sample Data CTChest. Run TotalSegmentator. Select All Segmentation…

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## [Measure (part of) model volume along centerline](https://discourse.slicer.org/t/measure-part-of-model-volume-along-centerline/26853)

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**Author:** [@SvElst](https://discourse.slicer.org/u/SvElst)\
**Replies:** 7\
**Last updated:** [December 22, 2022, 6:35pm UTC](https://discourse.slicer.org/t/measure-part-of-model-volume-along-centerline/26853 "2022-12-22T18:35:05Z")

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Hi, I have a tubular model (segmentation of a nerve). I used the ExtracCenterline module to extract the centerline of this model and the Cross-Section Analysis module to determine the diameter and cross-sectional area a…

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## [Distance (height) between two landmarks](https://discourse.slicer.org/t/distance-height-between-two-landmarks/26805)

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**Author:** [@EinatKe](https://discourse.slicer.org/u/EinatKe)\
**Replies:** 7\
**Last updated:** [December 22, 2022, 5:39pm UTC](https://discourse.slicer.org/t/distance-height-between-two-landmarks/26805 "2022-12-22T17:39:46Z")

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Hello, I am new to 3D Slicer. sorry if this question was asked before. I have transform the volume (inside the original ORI) to align with the Frankfurt plane. I want to calculate distances between landmarks, and I can…

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## [What's wrong with my DWI? Failed to convert from DWI to tensors](https://discourse.slicer.org/t/whats-wrong-with-my-dwi-failed-to-convert-from-dwi-to-tensors/26864)

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**Author:** [@peter\_adidharma](https://discourse.slicer.org/u/peter_adidharma)\
**Replies:** 3\
**Last updated:** [December 22, 2022, 1:40pm UTC](https://discourse.slicer.org/t/whats-wrong-with-my-dwi-failed-to-convert-from-dwi-to-tensors/26864 "2022-12-22T13:40:38Z")

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Hi all, I’ve been working to do some tractography using slicerDMRI, but seems to encounter the same problem with all DWI files that i have as i failed to convert it to tensors. Here, I attached the .nrrd file of our DWI…

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## [3D reconstruction from coronary angiogram](https://discourse.slicer.org/t/3d-reconstruction-from-coronary-angiogram/19931)

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**Author:** [@navidvd](https://discourse.slicer.org/u/navidvd)\
**Replies:** 4\
**Last updated:** [December 22, 2022, 12:38pm UTC](https://discourse.slicer.org/t/3d-reconstruction-from-coronary-angiogram/19931 "2022-12-22T12:38:55Z")

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Hi all, I was wondering if I can use coronary angiogram images as an input for 3D Slicer in order to create models of the arteries. What I’ve seen so far in the tutorials, mainly CT and MRI images were used. but no coro…

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## [Orienting views with respect to a selected markup](https://discourse.slicer.org/t/orienting-views-with-respect-to-a-selected-markup/26780)

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**Author:** [@Karl\_Hahn](https://discourse.slicer.org/u/Karl_Hahn)\
**Replies:** 3\
**Last updated:** [December 21, 2022, 10:21pm UTC](https://discourse.slicer.org/t/orienting-views-with-respect-to-a-selected-markup/26780 "2022-12-21T22:21:30Z")

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Hello, For sake of reference, are there any particular Slicer modules that implement functionality to orient views with respect to a markup selected in the Markups module? For example, selecting a Plane reformats the vi…

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## [Error opening Extensions Manager and loading previous developed Modules](https://discourse.slicer.org/t/error-opening-extensions-manager-and-loading-previous-developed-modules/26871)

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**Author:** [@LuisaDantas](https://discourse.slicer.org/u/LuisaDantas)\
**Replies:** 3\
**Last updated:** [December 21, 2022, 4:49pm UTC](https://discourse.slicer.org/t/error-opening-extensions-manager-and-loading-previous-developed-modules/26871 "2022-12-21T16:49:03Z")

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Hey all, I’ve been using 3D Slicer for a while but I had to install it on a different machine and it’s giving some errors right after the installation. When I open Extensions Manager this error is printed: \[Qt\] An Ope…

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## [Totalsegmentator - volume information and slicing through volumes?](https://discourse.slicer.org/t/totalsegmentator-volume-information-and-slicing-through-volumes/26825)

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**Author:** [@a.mohseni](https://discourse.slicer.org/u/a.mohseni)\
**Replies:** 14\
**Last updated:** [December 21, 2022, 1:01pm UTC](https://discourse.slicer.org/t/totalsegmentator-volume-information-and-slicing-through-volumes/26825 "2022-12-21T13:01:19Z")

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Operating system: Windows 11 Pro Slicer version: 5.2.1 Hello, So I have been using the 3DSlicer and Totalsegmentator extension recently for the segmentation of the abdominal organs in a CT-abdomen scan, but I have the…

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## [5 mm slices with segmentation reload out of place](https://discourse.slicer.org/t/5-mm-slices-with-segmentation-reload-out-of-place/26861)

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**Author:** [@bcahill24](https://discourse.slicer.org/u/bcahill24)\
**Replies:** 2\
**Last updated:** [December 21, 2022, 12:05am UTC](https://discourse.slicer.org/t/5-mm-slices-with-segmentation-reload-out-of-place/26861 "2022-12-21T00:05:35Z")

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Hello! I have been working in 3D slicer a lot lately, but don’t know much of the technical aspect of things so maybe this has been answered before. I will create segmentations on a scan with thicker slices, save it, and …

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## [After MRI Dicom file registration ... How to export this registration file in DICOM format](https://discourse.slicer.org/t/after-mri-dicom-file-registration-how-to-export-this-registration-file-in-dicom-format/26855)

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**Author:** [@mahmoud](https://discourse.slicer.org/u/mahmoud)\
**Replies:** 1\
**Last updated:** [December 20, 2022, 6:40pm UTC](https://discourse.slicer.org/t/after-mri-dicom-file-registration-how-to-export-this-registration-file-in-dicom-format/26855 "2022-12-20T18:40:53Z")

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Hello :wave::wave: Please, can help me to how export DICOM format after the two mri sequence Images registration. I mean in my question I want to get Dicom new registration images separately from move and fix image …t…

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## [Saving interaction slice planes and/or reformat values](https://discourse.slicer.org/t/saving-interaction-slice-planes-and-or-reformat-values/26852)

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**Author:** [@Thijs](https://discourse.slicer.org/u/Thijs)\
**Replies:** 1\
**Last updated:** [December 20, 2022, 6:03pm UTC](https://discourse.slicer.org/t/saving-interaction-slice-planes-and-or-reformat-values/26852 "2022-12-20T18:03:48Z")

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Hi! I am struggling a bit with creating markups in resliced planes. I hope that someone here might have some insight if what I want to achieve is possible? Using the interactive slice planes is great, I can use it to f…

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## [PETDICOMExtension](https://discourse.slicer.org/t/petdicomextension/26854)

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**Author:** [@Mahdieh\_Jajroudi](https://discourse.slicer.org/u/Mahdieh_Jajroudi)\
**Replies:** 0\
**Last updated:** [December 20, 2022, 4:41pm UTC](https://discourse.slicer.org/t/petdicomextension/26854 "2022-12-20T16:41:36Z")

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When I loaded PET DICOM, I found this error what is meaning and what should i do? Traceback (most recent call last): File “G:\\3d slicer\\Slicer 5.1.0-2022-07-26\\lib\\Slicer-5.1\\qt-scripted-modules\\DICOMLib\\DICOMUtils.py”…

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## [Heart reconstruction based on 2d Echo](https://discourse.slicer.org/t/heart-reconstruction-based-on-2d-echo/26847)

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**Author:** [@Jonathan](https://discourse.slicer.org/u/Jonathan)\
**Replies:** 0\
**Last updated:** [December 20, 2022, 1:13pm UTC](https://discourse.slicer.org/t/heart-reconstruction-based-on-2d-echo/26847 "2022-12-20T13:13:35Z")

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Hi all, Can one reconstruct a 3D heart model (myocardium and endocardium) from 2D echo images? Is there any recommended module? A gross estimation of cardiac dimensions will do. Much appreciated

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## [Problems when segmenting blood vessels using VMTK (threshold)](https://discourse.slicer.org/t/problems-when-segmenting-blood-vessels-using-vmtk-threshold/8536)

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**Author:** [@Deyline](https://discourse.slicer.org/u/Deyline)\
**Replies:** 11\
**Last updated:** [December 20, 2022, 1:00pm UTC](https://discourse.slicer.org/t/problems-when-segmenting-blood-vessels-using-vmtk-threshold/8536 "2022-12-20T13:00:24Z")

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Hello Slicer wizards, I’ve been trying for the past weeks to segement brain arteries using Slicer. I’ve already seen a few topics on the discussin forum about this topic, but I still haven’t been successful reconstructi…

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## [Can customized layouts, such as 5 by 4, be possible?](https://discourse.slicer.org/t/can-customized-layouts-such-as-5-by-4-be-possible/26816)

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**Author:** [@Jinhee\_Jang](https://discourse.slicer.org/u/Jinhee_Jang)\
**Replies:** 5\
**Last updated:** [December 20, 2022, 5:50am UTC](https://discourse.slicer.org/t/can-customized-layouts-such-as-5-by-4-be-possible/26816 "2022-12-20T05:50:48Z")

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Hi!, I am using slicer as an end-user for a while and I like it. The reason why I am using slicer is that I could see many nifti files at once, and I could save the entire working environment. By the way, as increasing…

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## [My DICOM file isn't loaded with proper view](https://discourse.slicer.org/t/my-dicom-file-isnt-loaded-with-proper-view/26826)

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**Author:** [@fluidko](https://discourse.slicer.org/u/fluidko)\
**Replies:** 4\
**Last updated:** [December 20, 2022, 5:46am UTC](https://discourse.slicer.org/t/my-dicom-file-isnt-loaded-with-proper-view/26826 "2022-12-20T05:46:37Z")

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When I open tutorial file, all of file is placed properly. As you can see from uploaded picture, bottom to Top view is placed to 2nd quadrant and front view is placed to 3rd quadrant and side view is placed to 4th qu…

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## [Change spacing and thickness](https://discourse.slicer.org/t/change-spacing-and-thickness/26818)

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**Author:** [@dszimatore](https://discourse.slicer.org/u/dszimatore)\
**Replies:** 2\
**Last updated:** [December 20, 2022, 5:39am UTC](https://discourse.slicer.org/t/change-spacing-and-thickness/26818 "2022-12-20T05:39:49Z")

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Can Anybody tell me how to modiphy spacing and thickness of a DICOM file. I think it’s a function of the Crop Module, but I can’t find how to use it. Thank you very much

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## [TotalSegmentator problem - Macbook M1 Max](https://discourse.slicer.org/t/totalsegmentator-problem-macbook-m1-max/26802)

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**Author:** [@miklontzas](https://discourse.slicer.org/u/miklontzas)\
**Replies:** 4\
**Last updated:** [December 19, 2022, 4:08pm UTC](https://discourse.slicer.org/t/totalsegmentator-problem-macbook-m1-max/26802 "2022-12-19T16:08:59Z")

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Hi there, I have been trying to use the Totalsegmentator extension in a MacBook M1 Max. The extension gets installed properly but when trying to run a segmentation for the first time, it starts installing some python pa…

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## [Export scene as dicom](https://discourse.slicer.org/t/export-scene-as-dicom/23645)

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**Author:** [@Pheasant](https://discourse.slicer.org/u/Pheasant)\
**Replies:** 18\
**Last updated:** [December 19, 2022, 11:51am UTC](https://discourse.slicer.org/t/export-scene-as-dicom/23645 "2022-12-19T11:51:54Z")

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Hi, I am a bit new at using the Dicom export function and currently it gives the error: Traceback (most recent call last): File “”, line 2, in TypeError: init() missing 1 required positional argument: ‘referenceFile…

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## [Volume of 3D model](https://discourse.slicer.org/t/volume-of-3d-model/26798)

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**Author:** [@damiazlkflee](https://discourse.slicer.org/u/damiazlkflee)\
**Replies:** 4\
**Last updated:** [December 19, 2022, 5:32am UTC](https://discourse.slicer.org/t/volume-of-3d-model/26798 "2022-12-19T05:32:54Z")

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Windows 10, slicer 4.11. This is a common question I think. My apologies for asking this simple question but after reading all the manuals, definitions, and answers in the support, I still cannot understand. Issue: I h…

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## [Analyzing myelography images](https://discourse.slicer.org/t/analyzing-myelography-images/26806)

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**Author:** [@Lohi](https://discourse.slicer.org/u/Lohi)\
**Replies:** 2\
**Last updated:** [December 18, 2022, 7:20pm UTC](https://discourse.slicer.org/t/analyzing-myelography-images/26806 "2022-12-18T19:20:42Z")

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Hi; Well, new challenges for me…I have some GB of imaging from 3 myelography sessions, which included the fluoroscopy (sp?) and fast CT imaging. Are there any tutorials, or other documentation regarding myelography? It…

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## [New user-stuck getting segment editor tools to work](https://discourse.slicer.org/t/new-user-stuck-getting-segment-editor-tools-to-work/26472)

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**Author:** [@Lohi](https://discourse.slicer.org/u/Lohi)\
**Replies:** 17\
**Last updated:** [December 3, 2022, 5:08pm UTC](https://discourse.slicer.org/t/new-user-stuck-getting-segment-editor-tools-to-work/26472 "2022-12-03T17:08:19Z")

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well, super-basic stuff… i can’t seem to get tools to work, at all…clearly something basic missing; i tried a little tutorial, which included a data set to download in a tar.gz format…this seemed to open into three views…

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## [Closed curves - centroid and eplipse long and short axis](https://discourse.slicer.org/t/closed-curves-centroid-and-eplipse-long-and-short-axis/26761)

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**Author:** [@Igor\_S](https://discourse.slicer.org/u/Igor_S)\
**Replies:** 2\
**Last updated:** [December 16, 2022, 8:27pm UTC](https://discourse.slicer.org/t/closed-curves-centroid-and-eplipse-long-and-short-axis/26761 "2022-12-16T20:27:32Z")

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Hello, I’ve drawn a closed curve on DICOM image. How do you calculate centroid of closed curve? Can you approximate ellipse from closed curve and calculate longest and short axis of this ellipse? I would like to imple…

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## [Matching CBCT scans and calculating the volume difference after bone augmentation](https://discourse.slicer.org/t/matching-cbct-scans-and-calculating-the-volume-difference-after-bone-augmentation/26767)

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**Author:** [@Johanna\_Caca](https://discourse.slicer.org/u/Johanna_Caca)\
**Replies:** 1\
**Last updated:** [December 16, 2022, 7:39pm UTC](https://discourse.slicer.org/t/matching-cbct-scans-and-calculating-the-volume-difference-after-bone-augmentation/26767 "2022-12-16T19:39:27Z")

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Hello, I´m looking for a software which can match cbct scans from before and after bone augmentation of the jaw bone and calculate the volume difference in the region of interest in the jaw bone. Is this possible with 3…

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