# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=249

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

**Page:** 250

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## [dicom data shows non isotropic volume](https://discourse.slicer.org/t/dicom-data-shows-non-isotropic-volume/20749)

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**Author:** [@SONALIGHAICHOUDHURY](https://discourse.slicer.org/u/SONALIGHAICHOUDHURY)\
**Replies:** 1\
**Last updated:** [November 23, 2021, 6:32pm UTC](https://discourse.slicer.org/t/dicom-data-shows-non-isotropic-volume/20749 "2021-11-23T18:32:05Z")

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Operating system: carestream, my cs3D imaging system shows non isotropic volume of dicom data imported from new tom slicer. why? i am unable to use my cs software for analysis.

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## [Don't know how to use Fast marching](https://discourse.slicer.org/t/dont-know-how-to-use-fast-marching/20721)

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**Author:** [@Gabriella-Rus](https://discourse.slicer.org/u/Gabriella-Rus)\
**Replies:** 3\
**Last updated:** [November 23, 2021, 5:19pm UTC](https://discourse.slicer.org/t/dont-know-how-to-use-fast-marching/20721 "2021-11-23T17:19:32Z")

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Hi! I try to work with “fast marching” from segmentation extension but when I press initialize button, nothing happens. What I am doing wrong?

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## [3D Slicer Registration QA](https://discourse.slicer.org/t/3d-slicer-registration-qa/20725)

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**Author:** [@Harpreetkaur](https://discourse.slicer.org/u/Harpreetkaur)\
**Replies:** 1\
**Last updated:** [November 23, 2021, 5:13pm UTC](https://discourse.slicer.org/t/3d-slicer-registration-qa/20725 "2021-11-23T17:13:59Z")

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Hi All, I am planning to commission our Deformable Registration Software. I wanted to know whether anyone tried Registration QA extension before? I need some guiding document for the process. Many Thanks!!!

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## [Final value of registration cost function metric](https://discourse.slicer.org/t/final-value-of-registration-cost-function-metric/20731)

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**Author:** [@bz78](https://discourse.slicer.org/u/bz78)\
**Replies:** 3\
**Last updated:** [November 23, 2021, 2:22pm UTC](https://discourse.slicer.org/t/final-value-of-registration-cost-function-metric/20731 "2021-11-23T14:22:05Z")

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Hi Slicer Forum, Is there a way to get the final value of the cost function (default being MattesMutualInformation, I believe) when registering volumes from Jupyter? For a set of CTs, we are looping through a ton of MR…

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## [Wrong centerline extracted](https://discourse.slicer.org/t/wrong-centerline-extracted/20705)

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**Author:** [@Francesca\_Pittoni](https://discourse.slicer.org/u/Francesca_Pittoni)\
**Replies:** 1\
**Last updated:** [November 19, 2021, 7:44pm UTC](https://discourse.slicer.org/t/wrong-centerline-extracted/20705 "2021-11-19T19:44:31Z")

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Hi, I’m trying to extract the centerline of this piece of aorta, but this is my result. I followed all the steps of the tutorial on youtube (Vessel segmentation and centerline extraction using 3D Slicer and VMTK - Y…

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## [3D model to segmentation](https://discourse.slicer.org/t/3d-model-to-segmentation/5135)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 9\
**Last updated:** [June 13, 2020, 4:27am UTC](https://discourse.slicer.org/t/3d-model-to-segmentation/5135 "2020-06-13T04:27:04Z")

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I would like to able to clean some 3D models from surface scanner. Currently, what I do is to import the model as a segmentation node, and then export the resultant segmentation node as a label map, which I use it as the…

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## [Visualize the difference between two meshes](https://discourse.slicer.org/t/visualize-the-difference-between-two-meshes/20729)

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**Author:** [@suranga](https://discourse.slicer.org/u/suranga)\
**Replies:** 1\
**Last updated:** [November 23, 2021, 7:07am UTC](https://discourse.slicer.org/t/visualize-the-difference-between-two-meshes/20729 "2021-11-23T07:07:31Z")

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I have two volumetric liver meshes in .vtk format (i.e. ground-truth and predicted versions) and I want to plot the error i.e., for example, the difference between the ground-truth and the predicted liver meshes on the p…

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## [segmentation output by model does dot align with the volume when loaded into Slicer ](https://discourse.slicer.org/t/segmentation-output-by-model-does-dot-align-with-the-volume-when-loaded-into-slicer/20726)

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**Author:** [@function2](https://discourse.slicer.org/u/function2)\
**Replies:** 1\
**Last updated:** [November 22, 2021, 6:48pm UTC](https://discourse.slicer.org/t/segmentation-output-by-model-does-dot-align-with-the-volume-when-loaded-into-slicer/20726 "2021-11-22T18:48:13Z")

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Hello, the 3D Slicer Community, Sorry if this question has been asked many times. I’ve trained a segmentation model for some brain tumor, and I want to review the results in Slicer. When I load them into the Slicer, the…

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## [Logarithmic Color scale Bar](https://discourse.slicer.org/t/logarithmic-color-scale-bar/20656)

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**Author:** [@MathiasBrucker](https://discourse.slicer.org/u/MathiasBrucker)\
**Replies:** 4\
**Last updated:** [November 22, 2021, 11:40am UTC](https://discourse.slicer.org/t/logarithmic-color-scale-bar/20656 "2021-11-22T11:40:05Z")

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Slicer version: 4.11.202 Operating system: Windows 10 x64 Software: Jupyter Notebook with Slicer Kernel 4.11 Is it possible to generate a Color Scale Bar with Logarithmic Values. Since I am working with low distances…

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## [Script for resampling scalar volumes](https://discourse.slicer.org/t/script-for-resampling-scalar-volumes/20717)

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**Author:** [@nthach17](https://discourse.slicer.org/u/nthach17)\
**Replies:** 1\
**Last updated:** [November 22, 2021, 9:52am UTC](https://discourse.slicer.org/t/script-for-resampling-scalar-volumes/20717 "2021-11-22T09:52:45Z")

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Hello, I’m new to the developer aspect of 3D Slicer and would like to compile a Python script for resampling batch of scalar volumes. While looking at the documentation for the ResampleVolume module, Modules:ResampleVol…

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## [Clipping effect](https://discourse.slicer.org/t/clipping-effect/20712)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 1\
**Last updated:** [November 22, 2021, 12:25am UTC](https://discourse.slicer.org/t/clipping-effect/20712 "2021-11-22T00:25:14Z")

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I frequently end up using cbct with significant artifacts . Any suggested protocol or steps to eliminate those annoying artifacts ? Thanks

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## [Preset for masks in segmentation](https://discourse.slicer.org/t/preset-for-masks-in-segmentation/20414)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 15\
**Last updated:** [November 20, 2021, 6:00pm UTC](https://discourse.slicer.org/t/preset-for-masks-in-segmentation/20414 "2021-11-20T18:00:53Z")

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i would like to suggest putting the option to save presets for MASKS in segmentation . i struggle to fine tune a mask with threshold or other effects im using , but the frustrating part is that i need to go back and fo…

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## [Movement of an organ ](https://discourse.slicer.org/t/movement-of-an-organ/20698)

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**Author:** [@Felic](https://discourse.slicer.org/u/Felic)\
**Replies:** 5\
**Last updated:** [November 20, 2021, 8:39am UTC](https://discourse.slicer.org/t/movement-of-an-organ/20698 "2021-11-20T08:39:14Z")

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Operating system: Windows 10 Slicer version: 4.10.2 Expected behavior: I would like to animate the stomach in the 3D-Version, so that the stomach is moving in the segmentation. Actual behavior: The registration is com…

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## [Help with landmark registration/Fiducial registration](https://discourse.slicer.org/t/help-with-landmark-registration-fiducial-registration/20684)

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**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 10\
**Last updated:** [November 19, 2021, 9:22pm UTC](https://discourse.slicer.org/t/help-with-landmark-registration-fiducial-registration/20684 "2021-11-19T21:22:40Z")

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Hello, friends. I am trying to perform a rigid alignment between a 2D gray-scale Image and a LABEL image, or a segmentation image. I set up both moving and fixed fiducials (as in the picture), define saving transform, …

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## [can I calculate the volume of  of the tumor by shape features ?](https://discourse.slicer.org/t/can-i-calculate-the-volume-of-of-the-tumor-by-shape-features/20694)

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**Author:** [@mina](https://discourse.slicer.org/u/mina)\
**Replies:** 3\
**Last updated:** [November 19, 2021, 8:51pm UTC](https://discourse.slicer.org/t/can-i-calculate-the-volume-of-of-the-tumor-by-shape-features/20694 "2021-11-19T20:51:18Z")

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Hello, I am doing a radiomics project in 3D Slicer and I am new to all the things. I have a problem. I need to have the volume of the tumor, but in the extracted features (Shape features), there is no Volume and no c…

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## [Use Markups to Model outside of 3D Slicer](https://discourse.slicer.org/t/use-markups-to-model-outside-of-3d-slicer/20697)

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**Author:** [@helenawill95](https://discourse.slicer.org/u/helenawill95)\
**Replies:** 1\
**Last updated:** [November 19, 2021, 2:59pm UTC](https://discourse.slicer.org/t/use-markups-to-model-outside-of-3d-slicer/20697 "2021-11-19T14:59:58Z")

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I found a similar feed but it wasn’t clear if the module was a public fn yet outside of the 3d slicer gui. I am looking to use markups to model features, of translating several surface points, into a 3D mesh and then a …

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## [Surface to surface distance](https://discourse.slicer.org/t/surface-to-surface-distance/20672)

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**Author:** [@archamb4](https://discourse.slicer.org/u/archamb4)\
**Replies:** 6\
**Last updated:** [November 19, 2021, 1:25pm UTC](https://discourse.slicer.org/t/surface-to-surface-distance/20672 "2021-11-19T13:25:27Z")

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Hello, I am searching for guidance on using ParaView or a similar software as done in a research paper. I attached the figures from the paper. I want to use point cloud analysis to calculate linear deviation from a scan…

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## [Problem to save a segmentation](https://discourse.slicer.org/t/problem-to-save-a-segmentation/20659)

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**Author:** [@Lise\_Kasperski](https://discourse.slicer.org/u/Lise_Kasperski)\
**Replies:** 2\
**Last updated:** [November 19, 2021, 11:58am UTC](https://discourse.slicer.org/t/problem-to-save-a-segmentation/20659 "2021-11-19T11:58:14Z")

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Operating system: Windows 10 Slicer version: 4.11.20210226 Actual behavior: I have a problem with how Slicer saves my files. I can’t save my segmentation with click on save icon after I creat the model. So, I can save …

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## [Docker Container - failing to run the proper Python Environnment](https://discourse.slicer.org/t/docker-container-failing-to-run-the-proper-python-environnment/20685)

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**Author:** [@sebastien\_goffart](https://discourse.slicer.org/u/sebastien_goffart)\
**Replies:** 2\
**Last updated:** [November 19, 2021, 7:42am UTC](https://discourse.slicer.org/t/docker-container-failing-to-run-the-proper-python-environnment/20685 "2021-11-19T07:42:03Z")

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Good Morning, I’m quite new to 3Dslicer and I’m trying to set up 3D slicer in a container so I can use python scripts in the Python environment of 3D Slicer. I follow then several guidelines and based myself on the slic…

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## [Model Points from files and display](https://discourse.slicer.org/t/model-points-from-files-and-display/20693)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 1\
**Last updated:** [November 19, 2021, 4:27am UTC](https://discourse.slicer.org/t/model-points-from-files-and-display/20693 "2021-11-19T04:27:47Z")

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I have a couple, probably, stupid questions, but I was wondering how you import a typical model file programmatically in python into 3D Slicer, how to access/display the point cloud and wire mesh from the model for disp…

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## [Change the background color black to white? in red, yellow and green slices?](https://discourse.slicer.org/t/change-the-background-color-black-to-white-in-red-yellow-and-green-slices/17715)

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**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 4\
**Last updated:** [November 18, 2021, 3:47pm UTC](https://discourse.slicer.org/t/change-the-background-color-black-to-white-in-red-yellow-and-green-slices/17715 "2021-11-18T15:47:17Z")

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Would it be possible to somehow change the background color to white rather than having it black? Thanks…

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## [Exporting orthogonal projections as DICOM](https://discourse.slicer.org/t/exporting-orthogonal-projections-as-dicom/20686)

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**Author:** [@alan](https://discourse.slicer.org/u/alan)\
**Replies:** 2\
**Last updated:** [November 18, 2021, 2:48pm UTC](https://discourse.slicer.org/t/exporting-orthogonal-projections-as-dicom/20686 "2021-11-18T14:48:37Z")

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Hello, I’m looking to: import thin (0.5 mm) slice CT DICOM series (multiple per patient) in the axial projection create orthogonal coronal and sagittal views of each series export as DICOM files so can be viewed in al…

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## [The latest Slicer PreRelease Linux version is empty](https://discourse.slicer.org/t/the-latest-slicer-prerelease-linux-version-is-empty/20680)

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**Author:** [@syxz0628](https://discourse.slicer.org/u/syxz0628)\
**Replies:** 1\
**Last updated:** [November 18, 2021, 1:42pm UTC](https://discourse.slicer.org/t/the-latest-slicer-prerelease-linux-version-is-empty/20680 "2021-11-18T13:42:30Z")

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When I download the latest Prerelease Linux version(30407, 18 Nov 2021). The zip file is only 22 Byte. Seams it is empty.

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## [How to change the GPU or CPU？](https://discourse.slicer.org/t/how-to-change-the-gpu-or-cpu/20675)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [November 18, 2021, 1:34pm UTC](https://discourse.slicer.org/t/how-to-change-the-gpu-or-cpu/20675 "2021-11-18T13:34:53Z")

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About the VolumeRendering module, when I select GPU as render, no image can appear in 3D view, but when I select CPU rendering, it can appear, but when I change other computer, the result is the opposite.

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## [Segmenting Finer Blood Vessels in the Arm](https://discourse.slicer.org/t/segmenting-finer-blood-vessels-in-the-arm/20586)

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**Author:** [@DPMM3D](https://discourse.slicer.org/u/DPMM3D)\
**Replies:** 3\
**Last updated:** [November 18, 2021, 7:07am UTC](https://discourse.slicer.org/t/segmenting-finer-blood-vessels-in-the-arm/20586 "2021-11-18T07:07:32Z")

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Hello! I am working with angiogram data of the arm and need to be able to segment the finer blood vessels throughout the forearm. It is not high contrast imaging, making it very difficult to see in the slices, (hopefull…

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## [3D view ruler doesn't change units suffix](https://discourse.slicer.org/t/3d-view-ruler-doesnt-change-units-suffix/20669)

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**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 2\
**Last updated:** [November 18, 2021, 12:19am UTC](https://discourse.slicer.org/t/3d-view-ruler-doesnt-change-units-suffix/20669 "2021-11-18T00:19:00Z")

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Hi, When I add volume and change units from mm to say m I can see no difference on the ruler but in the same time the slice control widget’s spinbox changes units to meter. I suspect this is a bug? Here is the code …

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## [How to run Slicer on the cloud and access in a web browser](https://discourse.slicer.org/t/how-to-run-slicer-on-the-cloud-and-access-in-a-web-browser/16401)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 14\
**Last updated:** [November 17, 2021, 6:52pm UTC](https://discourse.slicer.org/t/how-to-run-slicer-on-the-cloud-and-access-in-a-web-browser/16401 "2021-11-17T18:52:06Z")

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How could I not know about this Binder :slight\_smile: ?? Amazing

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## [ITK Filter... reporting broken?](https://discourse.slicer.org/t/itk-filter-reporting-broken/20668)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 0\
**Last updated:** [November 17, 2021, 6:41pm UTC](https://discourse.slicer.org/t/itk-filter-reporting-broken/20668 "2021-11-17T18:41:41Z")

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Hello, I am following this workflow, but the BinaryThinningImageFilter takes an incredible amount of time to process without any indication of progress. I found a post from 2020 that talked about the issue, but no clear…

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## [How to crop nifti files](https://discourse.slicer.org/t/how-to-crop-nifti-files/6065)

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**Author:** [@rjortiz2](https://discourse.slicer.org/u/rjortiz2)\
**Replies:** 9\
**Last updated:** [November 17, 2021, 3:00pm UTC](https://discourse.slicer.org/t/how-to-crop-nifti-files/6065 "2021-11-17T15:00:41Z")

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I know this may be a simple solution, but how does one crop a nifti file of a brain? I am trying to remove the skull and I’ve been stuck at this issue for quite some time. I have used segmentation wizard (or segmentation…

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## [VR connection to steam/HTC VIVe](https://discourse.slicer.org/t/vr-connection-to-steam-htc-vive/5645)

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**Author:** [@gptruncus](https://discourse.slicer.org/u/gptruncus)\
**Replies:** 6\
**Last updated:** [November 17, 2021, 6:35am UTC](https://discourse.slicer.org/t/vr-connection-to-steam-htc-vive/5645 "2021-11-17T06:35:25Z")

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Apologies if this has been asked and answered, when we hit the VR button to connect, a screen shows up within VR headset with 3 little dashes “thinking” and trying to connect, but never connect and show whats on 3D slice…

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