# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=273

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

**Page:** 274

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## [individual muscle - manual segmentation](https://discourse.slicer.org/t/individual-muscle-manual-segmentation/18360)

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**Author:** [@ryan-t](https://discourse.slicer.org/u/ryan-t)\
**Replies:** 1\
**Last updated:** [June 28, 2021, 12:57pm UTC](https://discourse.slicer.org/t/individual-muscle-manual-segmentation/18360 "2021-06-28T12:57:33Z")

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Operating system: Windows Slicer version: 4.10.2 Hi, I am looking to find the best way to manually segement multiple slices and multiple muscles and then export the data. For example I have MRI of the thigh and I wan…

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## [ALPACA Scale issue](https://discourse.slicer.org/t/alpaca-scale-issue/18355)

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**Author:** [@seanchoi0519](https://discourse.slicer.org/u/seanchoi0519)\
**Replies:** 7\
**Last updated:** [June 28, 2021, 4:49am UTC](https://discourse.slicer.org/t/alpaca-scale-issue/18355 "2021-06-28T04:49:26Z")

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I have 2 models I am aligning with ALPACA extension. They are same in size. I have clicked “skip scaling” option and only went up to “Run subsampling, run rigid alignment” stage (without CPD non-rigid registration/deform…

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## [How to export dicom file after I use transformation?](https://discourse.slicer.org/t/how-to-export-dicom-file-after-i-use-transformation/18297)

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**Author:** [@yllgl](https://discourse.slicer.org/u/yllgl)\
**Replies:** 8\
**Last updated:** [June 27, 2021, 1:54pm UTC](https://discourse.slicer.org/t/how-to-export-dicom-file-after-i-use-transformation/18297 "2021-06-27T13:54:34Z")

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I import my local dicom dataset. There are two study of one patient : one about CT, the other about MR. Then I use registration between them, and automatically generate a linear transformation and apply on CT. Now I want…

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## [Slicelet vs Guidelet](https://discourse.slicer.org/t/slicelet-vs-guidelet/18336)

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**Author:** [@seanchoi0519](https://discourse.slicer.org/u/seanchoi0519)\
**Replies:** 2\
**Last updated:** [June 27, 2021, 1:13pm UTC](https://discourse.slicer.org/t/slicelet-vs-guidelet/18336 "2021-06-27T13:13:53Z")

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Hello i’m looking to create a custom module now that I’ve established the workflow of my project. It involves connecting the functionalities of the ALPACA, then processed by Model-to-Model distance, then analyzed by Sha…

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## [sEEG trajectories and viewing](https://discourse.slicer.org/t/seeg-trajectories-and-viewing/18220)

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**Author:** [@mubafz](https://discourse.slicer.org/u/mubafz)\
**Replies:** 7\
**Last updated:** [June 27, 2021, 1:04am UTC](https://discourse.slicer.org/t/seeg-trajectories-and-viewing/18220 "2021-06-27T01:04:37Z")

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Hi, I am a new clinican user to 3dSlicer and it looks great. Is there a way to quickly construct electrode trajectories based on DIXI parameters from post-implant CT/MRI co-ordinates. As well is there a way to view slic…

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## [Model-to-model distance module questions](https://discourse.slicer.org/t/model-to-model-distance-module-questions/3481)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 7\
**Last updated:** [June 18, 2019, 7:30pm UTC](https://discourse.slicer.org/t/model-to-model-distance-module-questions/3481 "2019-06-18T19:30:28Z")

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Operating system: Slicer version:4.8.1 Expected behavior: Actual behavior: hello 3D slicer experts, I made two models and calculated the distance between them with the model to model distance module , then I ran it’…

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## [Export coordinate points of markups to the predefined folder](https://discourse.slicer.org/t/export-coordinate-points-of-markups-to-the-predefined-folder/18216)

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**Author:** [@Serg](https://discourse.slicer.org/u/Serg)\
**Replies:** 8\
**Last updated:** [June 26, 2021, 7:36pm UTC](https://discourse.slicer.org/t/export-coordinate-points-of-markups-to-the-predefined-folder/18216 "2021-06-26T19:36:03Z")

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I’m pretty sure that this is a very simple, but can’t find an answer in the Support category. I need to export the RAS of the markups table to the predefined folder just with one click of the “Export” button to avoid th…

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## [SlicerSimpleWorkflow](https://discourse.slicer.org/t/slicersimpleworkflow/18337)

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**Author:** [@seanchoi0519](https://discourse.slicer.org/u/seanchoi0519)\
**Replies:** 1\
**Last updated:** [June 25, 2021, 5:54pm UTC](https://discourse.slicer.org/t/slicersimpleworkflow/18337 "2021-06-25T17:54:55Z")

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Hi, if I want to test/explore a slicelet such as the following: How can I load them on Slicer? How can I launch it? Sincerely

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## [Fit an ellipse to a cross-section slice](https://discourse.slicer.org/t/fit-an-ellipse-to-a-cross-section-slice/18331)

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**Author:** [@joannecallow](https://discourse.slicer.org/u/joannecallow)\
**Replies:** 6\
**Last updated:** [June 26, 2021, 1:39am UTC](https://discourse.slicer.org/t/fit-an-ellipse-to-a-cross-section-slice/18331 "2021-06-26T01:39:30Z")

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Hello. I was wondering if there is a way to fit an ellipse to a cross section slice? I have a shape that is close to an ellipse, but not perfect. I would like to fit an ellipse to the structure and find the major and min…

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## [Export segmentation as DICOM](https://discourse.slicer.org/t/export-segmentation-as-dicom/13970)

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**Author:** [@Jan\_Alexander](https://discourse.slicer.org/u/Jan_Alexander)\
**Replies:** 9\
**Last updated:** [June 25, 2021, 11:02pm UTC](https://discourse.slicer.org/t/export-segmentation-as-dicom/13970 "2021-06-25T23:02:53Z")

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Hello, I try to do the same discussed above and as is shown in this tutorial. Unfortunately, this does not work. I believe the extensions SlicerRT and Quantitave reporting are correctly installed, but I do not even ge…

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## [Hdf5 to NRRD to SEQ.NRRD](https://discourse.slicer.org/t/hdf5-to-nrrd-to-seq-nrrd/18277)

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**Author:** [@Jamal\_K](https://discourse.slicer.org/u/Jamal_K)\
**Replies:** 3\
**Last updated:** [June 25, 2021, 10:23pm UTC](https://discourse.slicer.org/t/hdf5-to-nrrd-to-seq-nrrd/18277 "2021-06-25T22:23:02Z")

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I have an hdf5 4D Volume rendering with 1 dimension begin time. I transformed this file using python into an NRRD for Slicer to read it. I then added the ‘seq’ label to the file as mentioned here (Documentation/4.10/Exte…

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## [Understanding image registration process](https://discourse.slicer.org/t/understanding-image-registration-process/18314)

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**Author:** [@marianaslicer](https://discourse.slicer.org/u/marianaslicer)\
**Replies:** 1\
**Last updated:** [June 25, 2021, 6:29pm UTC](https://discourse.slicer.org/t/understanding-image-registration-process/18314 "2021-06-25T18:29:43Z")

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Hi, I’m getting an unexpected behavior in the image registration process. I’m using Elastix registration to register two 4DCT frames of the popi-model data dir\_validation\_data - Rayonnement, Images, Oncologie (insa-lyon…

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## [Project a segmentation onto another segmentation](https://discourse.slicer.org/t/project-a-segmentation-onto-another-segmentation/18318)

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**Author:** [@Cody\_Xie](https://discourse.slicer.org/u/Cody_Xie)\
**Replies:** 1\
**Last updated:** [June 25, 2021, 6:20pm UTC](https://discourse.slicer.org/t/project-a-segmentation-onto-another-segmentation/18318 "2021-06-25T18:20:40Z")

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Hi to all, I was wondering if there is a way to project a segmentation onto another segmentation. For example, here we have two segmentations (see the figures below): A heart left ventricle (red) and a target (blue). A…

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## [Draw specific dimensions in markup module](https://discourse.slicer.org/t/draw-specific-dimensions-in-markup-module/18221)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 40\
**Last updated:** [June 25, 2021, 5:59pm UTC](https://discourse.slicer.org/t/draw-specific-dimensions-in-markup-module/18221 "2021-06-25T17:59:08Z")

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Hello all, How can I use the markup module to draw closed shapes with specific dimensions? Such as a circle with a specific radius, or a rectangle with a specific width/height? Thanks in advance.

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## [Segment registration is Voxelbase registration？](https://discourse.slicer.org/t/segment-registration-is-voxelbase-registration/18338)

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**Author:** [@lili-yu22](https://discourse.slicer.org/u/lili-yu22)\
**Replies:** 1\
**Last updated:** [June 25, 2021, 5:41pm UTC](https://discourse.slicer.org/t/segment-registration-is-voxelbase-registration/18338 "2021-06-25T17:41:59Z")

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Operating system:windows Slicer version:3Dslicer4.11.20210226 Expected behavior:May I ask the segment registration is the Voxelbase registration？What’s the principle of the surface registration？ Actual behavior:

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## [Create a voxel based mesh](https://discourse.slicer.org/t/create-a-voxel-based-mesh/18324)

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**Author:** [@ellismckenzielee](https://discourse.slicer.org/u/ellismckenzielee)\
**Replies:** 6\
**Last updated:** [June 25, 2021, 1:46pm UTC](https://discourse.slicer.org/t/create-a-voxel-based-mesh/18324 "2021-06-25T13:46:03Z")

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Hi there, I was wondering if it is possible to create a 3D mesh, where each voxel is an element using 3Dslicer? I have tried using the segmentmesher plugin but to no avail. At this point in time, I only need the mesh to…

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## [Cannot start Slicer on LInux - cannot connect to X server](https://discourse.slicer.org/t/cannot-start-slicer-on-linux-cannot-connect-to-x-server/18302)

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**Author:** [@Fabio\_Geraci](https://discourse.slicer.org/u/Fabio_Geraci)\
**Replies:** 2\
**Last updated:** [June 25, 2021, 2:05am UTC](https://discourse.slicer.org/t/cannot-start-slicer-on-linux-cannot-connect-to-x-server/18302 "2021-06-25T02:05:18Z")

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this is my output ~/Slicer-4.11.20210226-linux-amd64/Slicer Slicer: cannot connect to X server 192.168.0.1 fec0:0:0:ffff::1 fec0:0:0:ffff::2:0

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## [Consultation on the feasibility of developing an extension for 3DSlicer](https://discourse.slicer.org/t/consultation-on-the-feasibility-of-developing-an-extension-for-3dslicer/18285)

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**Author:** [@CharlesChen](https://discourse.slicer.org/u/CharlesChen)\
**Replies:** 8\
**Last updated:** [June 24, 2021, 11:18pm UTC](https://discourse.slicer.org/t/consultation-on-the-feasibility-of-developing-an-extension-for-3dslicer/18285 "2021-06-24T23:18:22Z")

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Hello, I’m new to 3DSlicer, I’d like to ask a few questions about the feasibility of developing an extension/module for calculating the volume proportion of the confocal region in volume rendering. The measurement of c…

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## [Another Extensions Manager problem](https://discourse.slicer.org/t/another-extensions-manager-problem/18272)

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**Author:** [@MikaelO](https://discourse.slicer.org/u/MikaelO)\
**Replies:** 7\
**Last updated:** [June 24, 2021, 9:41pm UTC](https://discourse.slicer.org/t/another-extensions-manager-problem/18272 "2021-06-24T21:41:27Z")

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Hi all, I have read through posts dealing with Extension Manager problems, but I can’t say I’ve found one with my particular problem (apologies if I’ve overlooked a previosly posted solution). When I open the extension…

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## [Slicer IGT Multiple Tools, Plus ToolKit](https://discourse.slicer.org/t/slicer-igt-multiple-tools-plus-toolkit/18328)

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**Author:** [@jasmine-lou](https://discourse.slicer.org/u/jasmine-lou)\
**Replies:** 1\
**Last updated:** [June 24, 2021, 8:45pm UTC](https://discourse.slicer.org/t/slicer-igt-multiple-tools-plus-toolkit/18328 "2021-06-24T20:45:38Z")

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Hi all, I had a question about how to implement tracking multiple tools using the NDI Aurora EM system and multiple coils. Right now, it seems that the first tool/coil is working fine but the Plus/Slicer connection does…

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## [Slicer Stable 4.11.20210226 issue with scipy package in Linux](https://discourse.slicer.org/t/slicer-stable-4-11-20210226-issue-with-scipy-package-in-linux/16354)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 5\
**Last updated:** [June 24, 2021, 8:18pm UTC](https://discourse.slicer.org/t/slicer-stable-4-11-20210226-issue-with-scipy-package-in-linux/16354 "2021-06-24T20:18:53Z")

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There is a problem with scipy package in linux in the new Slicer stable: from scipy import signal File "/home/alex/Programas/Slicer3D/lib/Python/lib/python3.6/site-packages/scipy/signal/\_\_init\_\_.py", line 289, in \<mod…

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## [Calculating Simple Areas](https://discourse.slicer.org/t/calculating-simple-areas/5435)

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**Author:** [@Caroline\_Tomas](https://discourse.slicer.org/u/Caroline_Tomas)\
**Replies:** 9\
**Last updated:** [June 24, 2021, 6:34pm UTC](https://discourse.slicer.org/t/calculating-simple-areas/5435 "2021-06-24T18:34:47Z")

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I want to be able to calculate the area of total muscle on a single axial slice. When I run the segmentation statistics, it does give me “surface area” but I think it’s processing the entire CT scan instead of that singl…

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## [Ellipse measurement tool](https://discourse.slicer.org/t/ellipse-measurement-tool/7485)

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**Author:** [@Joshua\_Broder](https://discourse.slicer.org/u/Joshua_Broder)\
**Replies:** 1\
**Last updated:** [December 9, 2020, 5:04pm UTC](https://discourse.slicer.org/t/ellipse-measurement-tool/7485 "2020-12-09T17:04:55Z")

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Operating system: Windows Slicer version: Any Does Slicer have an elliptical measurement tool? I need to measure the circumference of structures which may be perfect circles or ellipses.

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## [Regarding image stacking](https://discourse.slicer.org/t/regarding-image-stacking/18319)

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**Author:** [@anitakh1](https://discourse.slicer.org/u/anitakh1)\
**Replies:** 1\
**Last updated:** [June 24, 2021, 5:35pm UTC](https://discourse.slicer.org/t/regarding-image-stacking/18319 "2021-06-24T17:35:23Z")

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hello sir. I am really stuck at one point. I loaded png images (more than 5000 images) and converted them to .tif format (which was successful). then i copied 1600 images out of this folder in another folder and tried to…

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## [Write a python CLI module but do not show in the slicer app](https://discourse.slicer.org/t/write-a-python-cli-module-but-do-not-show-in-the-slicer-app/18287)

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**Author:** [@bywbilly](https://discourse.slicer.org/u/bywbilly)\
**Replies:** 9\
**Last updated:** [June 24, 2021, 4:49pm UTC](https://discourse.slicer.org/t/write-a-python-cli-module-but-do-not-show-in-the-slicer-app/18287 "2021-06-24T16:49:23Z")

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Hi, I implemented an interactive python loadable module but it requires a heavy computation to do something with the volume. To avoid this heavy computation stuff to block the main slicer app, (after some search) I fin…

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## [Loading annotations/labels in python for training](https://discourse.slicer.org/t/loading-annotations-labels-in-python-for-training/18236)

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**Author:** [@Dhruba](https://discourse.slicer.org/u/Dhruba)\
**Replies:** 1\
**Last updated:** [June 24, 2021, 4:01pm UTC](https://discourse.slicer.org/t/loading-annotations-labels-in-python-for-training/18236 "2021-06-24T16:01:29Z")

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I want to load my nii.gz file and corresponding ROI annotations (.csv) in python for training purposes. I am not sure the right way to do that. Can you give me some reference code or documentation on loading annotations?…

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## [Missing Create surface function in segment editor](https://discourse.slicer.org/t/missing-create-surface-function-in-segment-editor/15332)

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**Author:** [@vjysnkr58](https://discourse.slicer.org/u/vjysnkr58)\
**Replies:** 5\
**Last updated:** [June 24, 2021, 12:51pm UTC](https://discourse.slicer.org/t/missing-create-surface-function-in-segment-editor/15332 "2021-06-24T12:51:34Z")

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Hi, When I open segment editor , I don’t see a create surface tool in the window. How can I get this option, which extension to be downloaded. Thank you. Capture|467x500

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## [Apply transformation change the image size](https://discourse.slicer.org/t/apply-transformation-change-the-image-size/17768)

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**Author:** [@marianaslicer](https://discourse.slicer.org/u/marianaslicer)\
**Replies:** 2\
**Last updated:** [May 25, 2021, 10:37am UTC](https://discourse.slicer.org/t/apply-transformation-change-the-image-size/17768 "2021-05-25T10:37:35Z")

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Hi everyone, I’m using the 3D Slicer version 4.13 and when I apply a b-spline transformation to an image it changes the original size. Original size = 512 x 512 x 140 After apply the transformation: transformLogi…

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## [Get new fiducial position after transform](https://discourse.slicer.org/t/get-new-fiducial-position-after-transform/18205)

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**Author:** [@sandyaa0313](https://discourse.slicer.org/u/sandyaa0313)\
**Replies:** 2\
**Last updated:** [June 24, 2021, 6:45am UTC](https://discourse.slicer.org/t/get-new-fiducial-position-after-transform/18205 "2021-06-24T06:45:31Z")

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Operating system:Windows10 Slicer version:4.11.20200930 Expected behavior: Actual behavior: I want to do some functions similar to fiducial registeration wizard in SlicerIGT by my own python module. Now I can retrie…

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## [MarkupsToModel : can it strictly follow the placed points?](https://discourse.slicer.org/t/markupstomodel-can-it-strictly-follow-the-placed-points/18256)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 3\
**Last updated:** [June 23, 2021, 4:35pm UTC](https://discourse.slicer.org/t/markupstomodel-can-it-strictly-follow-the-placed-points/18256 "2021-06-23T16:35:10Z")

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The image below show the model created by MarkupsToModel. Some points get ignored if others create a concave trajectory. The final model has always a convex surface. I suppose it’s the intended algorithm in use. I wi…

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