# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=276

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

**Page:** 277

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## [Slicer Security](https://discourse.slicer.org/t/slicer-security/18082)

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**Author:** [@spycolyf](https://discourse.slicer.org/u/spycolyf)\
**Replies:** 1\
**Last updated:** [June 11, 2021, 8:28pm UTC](https://discourse.slicer.org/t/slicer-security/18082 "2021-06-11T20:28:12Z")

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In light of the recent ransomware incidents, physicians are concerned about the security if Slicer and modules developed using it. Do you have any information on how you protect yourselves from being hacked and the secur…

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## [Help with rendering labelmap](https://discourse.slicer.org/t/help-with-rendering-labelmap/18067)

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**Author:** [@sannpeterson](https://discourse.slicer.org/u/sannpeterson)\
**Replies:** 4\
**Last updated:** [June 11, 2021, 6:49pm UTC](https://discourse.slicer.org/t/help-with-rendering-labelmap/18067 "2021-06-11T18:49:24Z")

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When I load a labeled segmentation, the colors on the rendered volume shows up differently from the original. What am I doing wrong?

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## [Calculating the RMSE](https://discourse.slicer.org/t/calculating-the-rmse/17326)

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**Author:** [@toyama](https://discourse.slicer.org/u/toyama)\
**Replies:** 4\
**Last updated:** [June 11, 2021, 8:51am UTC](https://discourse.slicer.org/t/calculating-the-rmse/17326 "2021-06-11T08:51:36Z")

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I would like to get the RMSE, which is the evaluation criteria for DIR. I looked at the Slicer community and found the Fiducials To Model Distance modelu and the Fiducials To Model Registration module to be useful. I w…

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## [Measuring surface characteristics/compare shapes of bone surfaces](https://discourse.slicer.org/t/measuring-surface-characteristics-compare-shapes-of-bone-surfaces/17975)

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**Author:** [@OrthopedicsSeb](https://discourse.slicer.org/u/OrthopedicsSeb)\
**Replies:** 4\
**Last updated:** [June 10, 2021, 2:44pm UTC](https://discourse.slicer.org/t/measuring-surface-characteristics-compare-shapes-of-bone-surfaces/17975 "2021-06-10T14:44:18Z")

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Operating system: Windows 10 Slicer version: 4.11 Expected behavior: Measure and display the surface of a bone and calculate the mean angle (if its convex or concave shape), compare it to other specimens, size of the a…

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## [How merge two segmentations?](https://discourse.slicer.org/t/how-merge-two-segmentations/18065)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [June 10, 2021, 2:05pm UTC](https://discourse.slicer.org/t/how-merge-two-segmentations/18065 "2021-06-10T14:05:28Z")

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I have created two segmentations in segment editor and I want to merge them into a single volume. How can I do this?

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## [About pedicle triangle](https://discourse.slicer.org/t/about-pedicle-triangle/18014)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 19\
**Last updated:** [June 10, 2021, 11:23am UTC](https://discourse.slicer.org/t/about-pedicle-triangle/18014 "2021-06-10T11:23:15Z")

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PedicleScrewSimulator About the Pedicle Tirangle The author mainly made improvements to LandmarksStep.py of this project.We proposed the concept of the Pedicle Tirangle, which refers to the three points of the same verte…

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## [Editable intensity range](https://discourse.slicer.org/t/editable-intensity-range/17845)

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**Author:** [@H.Khasawneh](https://discourse.slicer.org/u/H.Khasawneh)\
**Replies:** 4\
**Last updated:** [June 10, 2021, 11:00am UTC](https://discourse.slicer.org/t/editable-intensity-range/17845 "2021-06-10T11:00:55Z")

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I am trying to use the Editable intensity range option for editing pre-existing segmentation masks to crop around our region of interest however it is not working properly. We have attempted multiple ranges without suc…

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## [Extract the coronary and aorta](https://discourse.slicer.org/t/extract-the-coronary-and-aorta/17998)

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**Author:** [@smm9886](https://discourse.slicer.org/u/smm9886)\
**Replies:** 4\
**Last updated:** [June 10, 2021, 5:55am UTC](https://discourse.slicer.org/t/extract-the-coronary-and-aorta/17998 "2021-06-10T05:55:15Z")

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Operating system: Windows 64 bit Slicer version: 4.11.20210226 r29738 / 7a593c8 Expected behavior: Actual behavior: Hi all, I could get to know about the Slicer about 2 weeks ago. So far I could read several of the …

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## [How to select a portion of volume through sphere?](https://discourse.slicer.org/t/how-to-select-a-portion-of-volume-through-sphere/18051)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [June 10, 2021, 5:38am UTC](https://discourse.slicer.org/t/how-to-select-a-portion-of-volume-through-sphere/18051 "2021-06-10T05:38:53Z")

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How can I select a portion of a volume using a sphere from a volume in three d window?And then how to get the data of the selected portion?

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## [How to disable right click Zoom function](https://discourse.slicer.org/t/how-to-disable-right-click-zoom-function/17782)

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**Author:** [@luxiaoyang9999](https://discourse.slicer.org/u/luxiaoyang9999)\
**Replies:** 3\
**Last updated:** [June 9, 2021, 9:42pm UTC](https://discourse.slicer.org/t/how-to-disable-right-click-zoom-function/17782 "2021-06-09T21:42:17Z")

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Hello everyone, I want to implement my right click function in slicer. however, when I use observer to active my right click function, the default zoom function will also be activated and it cannot be closed. interact…

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## [Segmentation has changed images resolution](https://discourse.slicer.org/t/segmentation-has-changed-images-resolution/18043)

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**Author:** [@Antonio\_Giulio\_Genna](https://discourse.slicer.org/u/Antonio_Giulio_Genna)\
**Replies:** 1\
**Last updated:** [June 9, 2021, 8:59pm UTC](https://discourse.slicer.org/t/segmentation-has-changed-images-resolution/18043 "2021-06-09T20:59:09Z")

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Operating system: Windows 8.1 Slicer version: 4.11.20210226 Expected behavior: Use the same resolution as volume images Actual behavior: The segmentation has higher image resolution compared to native T1 volume H…

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## [How can I write a python CLI code using slicer internal module](https://discourse.slicer.org/t/how-can-i-write-a-python-cli-code-using-slicer-internal-module/18023)

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**Author:** [@bywbilly](https://discourse.slicer.org/u/bywbilly)\
**Replies:** 7\
**Last updated:** [June 9, 2021, 8:16pm UTC](https://discourse.slicer.org/t/how-can-i-write-a-python-cli-code-using-slicer-internal-module/18023 "2021-06-09T20:16:23Z")

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Hi, I am new to slice and working on incorporating our own 3D segmentation model with slicer. And we would like to assume the slicer user does not know anything about code, so intend to write a python CLI code to do eve…

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## [Unable to install Slicer in c:\\Program Files](https://discourse.slicer.org/t/unable-to-install-slicer-in-c-program-files/18020)

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**Author:** [@edboas](https://discourse.slicer.org/u/edboas)\
**Replies:** 2\
**Last updated:** [June 9, 2021, 5:43pm UTC](https://discourse.slicer.org/t/unable-to-install-slicer-in-c-program-files/18020 "2021-06-09T17:43:23Z")

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When I try to install Slicer 4.11 on Windows 10, I get the following error message: “Error opening file for writing: C:\\Program Files\\Slicer 4.11.20210226\\Slicer.exe”

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## [How to transform the CoordinateSystem from LPS to RAS](https://discourse.slicer.org/t/how-to-transform-the-coordinatesystem-from-lps-to-ras/17872)

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**Author:** [@rongqi\_lin](https://discourse.slicer.org/u/rongqi_lin)\
**Replies:** 1\
**Last updated:** [June 9, 2021, 2:02pm UTC](https://discourse.slicer.org/t/how-to-transform-the-coordinatesystem-from-lps-to-ras/17872 "2021-06-09T14:02:15Z")

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Hi! I am a new 3D Slicer user, I want to ask how to tranform CoordinateSystem from LPS to RAS in 3D Slicer 4.11. I use the 3D Slicer to locate the depth electrodes, and I found the CoordinateSystem in 3D slicer was RAS…

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## [Resample DWI Volume](https://discourse.slicer.org/t/resample-dwi-volume/17941)

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**Author:** [@Nadya\_Shusharina](https://discourse.slicer.org/u/Nadya_Shusharina)\
**Replies:** 9\
**Last updated:** [June 9, 2021, 1:56pm UTC](https://discourse.slicer.org/t/resample-dwi-volume/17941 "2021-06-09T13:56:04Z")

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I am using Resample Scalar/Vector/DWI Volume module to simply upsample the image. The Apply button runs the process of resampling with the status “Completed” after about 25 sec. However, the output resampled volume is no…

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## [ELF load command address/offset not properly aligned](https://discourse.slicer.org/t/elf-load-command-address-offset-not-properly-aligned/18039)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [June 9, 2021, 1:10pm UTC](https://discourse.slicer.org/t/elf-load-command-address-offset-not-properly-aligned/18039 "2021-06-09T13:10:35Z")

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This is not a slicer issue per se, but perhaps someone on the forum might suggest what this errors means. This happens inside a docker instance of SlicerMorph. So some sort of a missing library might be at play, but not…

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## [Resizing Mask - Error during Feature extraction](https://discourse.slicer.org/t/resizing-mask-error-during-feature-extraction/18036)

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**Author:** [@tduplessis](https://discourse.slicer.org/u/tduplessis)\
**Replies:** 0\
**Last updated:** [June 9, 2021, 12:29pm UTC](https://discourse.slicer.org/t/resizing-mask-error-during-feature-extraction/18036 "2021-06-09T12:29:28Z")

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Hallo I am extracting features from 2D x-rays. The segmentation model I used created png masks of 256x256 pixels. My original x-rays are 1024x1024 pixels. So I have increased the masks with a simple python function, np…

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## [Subtract unhealthy tissue from area of box around a tumor](https://discourse.slicer.org/t/subtract-unhealthy-tissue-from-area-of-box-around-a-tumor/17609)

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**Author:** [@Mostafa2020](https://discourse.slicer.org/u/Mostafa2020)\
**Replies:** 12\
**Last updated:** [June 8, 2021, 11:38pm UTC](https://discourse.slicer.org/t/subtract-unhealthy-tissue-from-area-of-box-around-a-tumor/17609 "2021-06-08T23:38:19Z")

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Operating system:macOS Slicer version:4.11 Expected behavior: Actual behavior: Hi all, I am trying to subtract unhealthy tissue from the area of the box surrounding the tumor. I used the Markups module, put a box…

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## [About the angle threshold for DTI?](https://discourse.slicer.org/t/about-the-angle-threshold-for-dti/17965)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 1\
**Last updated:** [June 8, 2021, 8:15pm UTC](https://discourse.slicer.org/t/about-the-angle-threshold-for-dti/17965 "2021-06-08T20:15:53Z")

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Just as the pic, Can I set the angel in slicer?

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## [Export fibers from DTI with full color](https://discourse.slicer.org/t/export-fibers-from-dti-with-full-color/17953)

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**Author:** [@Pawel\_Ozga](https://discourse.slicer.org/u/Pawel_Ozga)\
**Replies:** 3\
**Last updated:** [June 8, 2021, 8:14pm UTC](https://discourse.slicer.org/t/export-fibers-from-dti-with-full-color/17953 "2021-06-08T20:14:47Z")

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Hi, does any body have an idea how to export fibers (from DTI) but in full color? I suppose VRML format would be best, but I don’t have an Idea how to do it? Paul

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## [Specific thickness for segmentation](https://discourse.slicer.org/t/specific-thickness-for-segmentation/17945)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 5\
**Last updated:** [June 8, 2021, 7:59pm UTC](https://discourse.slicer.org/t/specific-thickness-for-segmentation/17945 "2021-06-08T19:59:51Z")

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Hello all, Is there possible to set one dimension of a segmentation (such as the thickness of a thin structure) to be a constant value in the slicer? Thanks

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## [Existing Web application integration with 3D Slicer](https://discourse.slicer.org/t/existing-web-application-integration-with-3d-slicer/17813)

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**Author:** [@klm-1992](https://discourse.slicer.org/u/klm-1992)\
**Replies:** 8\
**Last updated:** [June 8, 2021, 7:16pm UTC](https://discourse.slicer.org/t/existing-web-application-integration-with-3d-slicer/17813 "2021-06-08T19:16:31Z")

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I have an existing web application where we are able to search for images and display it in OHIF viewer. We have a new requirement where we need to integrate the 3D slicer viewer as well. Can I know how can I run it in t…

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## [Open3d pip\_install issue](https://discourse.slicer.org/t/open3d-pip-install-issue/16377)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 10\
**Last updated:** [June 8, 2021, 6:44pm UTC](https://discourse.slicer.org/t/open3d-pip-install-issue/16377 "2021-06-08T18:44:27Z")

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Posting on behalf of a user. They had a difficulty installing SlicerMorph extension. When we looked into it, the computer is in Greek locale (and the user folder contain greek alphabet letters). We tried installing C:\\S…

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## [Convert segmentation to CAD surface](https://discourse.slicer.org/t/convert-segmentation-to-cad-surface/18015)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 4\
**Last updated:** [June 8, 2021, 6:28pm UTC](https://discourse.slicer.org/t/convert-segmentation-to-cad-surface/18015 "2021-06-08T18:28:36Z")

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Hello all, With current developments of the slice, are there any possibilities to convert a model/segmentation to a CAD file?

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## [DMRI module: visualization](https://discourse.slicer.org/t/dmri-module-visualization/17866)

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**Author:** [@Nadya\_Shusharina](https://discourse.slicer.org/u/Nadya_Shusharina)\
**Replies:** 3\
**Last updated:** [June 8, 2021, 5:27pm UTC](https://discourse.slicer.org/t/dmri-module-visualization/17866 "2021-06-08T17:27:40Z")

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Is it possible to visualize specific individual components of the diffusion tensor? Could you please point me to the code?

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## [Analysis of plant stem, roots and froots](https://discourse.slicer.org/t/analysis-of-plant-stem-roots-and-froots/17999)

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**Author:** [@sreenivasalluri](https://discourse.slicer.org/u/sreenivasalluri)\
**Replies:** 3\
**Last updated:** [June 8, 2021, 5:21pm UTC](https://discourse.slicer.org/t/analysis-of-plant-stem-roots-and-froots/17999 "2021-06-08T17:21:14Z")

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Can we analyze the plant roots and stems and fruits? Dr. Sreenivas Alluri

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## [Veselness filter](https://discourse.slicer.org/t/veselness-filter/17739)

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**Author:** [@Winet\_Azer](https://discourse.slicer.org/u/Winet_Azer)\
**Replies:** 9\
**Last updated:** [June 8, 2021, 4:23pm UTC](https://discourse.slicer.org/t/veselness-filter/17739 "2021-06-08T16:23:08Z")

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Operating system: windows Slicer version: 4.11.20200930 Hello, In my project I use the VMTK plug in for segmentation. When creating the centerline I wonder if there is a possibility to export the data concerning the d…

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## [difficulty with finding cross sectional area of skeletal muscle at l3 for assessing sarcopenia](https://discourse.slicer.org/t/difficulty-with-finding-cross-sectional-area-of-skeletal-muscle-at-l3-for-assessing-sarcopenia/17982)

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**Author:** [@aman](https://discourse.slicer.org/u/aman)\
**Replies:** 10\
**Last updated:** [June 8, 2021, 2:55pm UTC](https://discourse.slicer.org/t/difficulty-with-finding-cross-sectional-area-of-skeletal-muscle-at-l3-for-assessing-sarcopenia/17982 "2021-06-08T14:55:47Z")

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Operating system: win 64 Slicer version: 4.13.0 Expected behavior: Actual behavior: sir i am unable to take out the cross sectional area of dicom images i have taken the cross sectional area and volume come out to b…

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## [What tool was used to place landmarks in slicermorph ALPACA video?](https://discourse.slicer.org/t/what-tool-was-used-to-place-landmarks-in-slicermorph-alpaca-video/18013)

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**Author:** [@bcolbert](https://discourse.slicer.org/u/bcolbert)\
**Replies:** 1\
**Last updated:** [June 8, 2021, 1:07pm UTC](https://discourse.slicer.org/t/what-tool-was-used-to-place-landmarks-in-slicermorph-alpaca-video/18013 "2021-06-08T13:07:22Z")

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The slicermorph ALPACA video shows a lion femur with landmarks along surface. Does anyone know what tool was used to place those?

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## [SegmentEditor Islands effect keeps the islands in the original segment](https://discourse.slicer.org/t/segmenteditor-islands-effect-keeps-the-islands-in-the-original-segment/8037)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 16\
**Last updated:** [June 8, 2021, 5:41am UTC](https://discourse.slicer.org/t/segmenteditor-islands-effect-keeps-the-islands-in-the-original-segment/8037 "2021-06-08T05:41:17Z")

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I am trying to do use the islands effect to separate individual bones. While, it finishes correctly, it still retains the new created islands/segments in the original segment. I thought the behavior was to move them to t…

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