# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=307

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

**Page:** 308

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## [Multi-segment workflow?](https://discourse.slicer.org/t/multi-segment-workflow/13780)

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**Author:** [@jax200](https://discourse.slicer.org/u/jax200)\
**Replies:** 1\
**Last updated:** [December 9, 2020, 4:57pm UTC](https://discourse.slicer.org/t/multi-segment-workflow/13780 "2020-12-09T16:57:28Z")

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Hi As a new user exercise, I am attempting to segment out bone, cardiovasculature and liver in one presentation. Using the Slicer sample CTACardio data, I can get good segmentation for cv (default artery color) and li…

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## [The image after registration is distorted](https://discourse.slicer.org/t/the-image-after-registration-is-distorted/14783)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 2\
**Last updated:** [December 9, 2020, 4:56pm UTC](https://discourse.slicer.org/t/the-image-after-registration-is-distorted/14783 "2020-12-09T16:56:47Z")

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This is a MRI scan of the pituitary gland and a CT scan of a complete brain. In order to perform registration, I first crop volume the MRI and then use Elastix to register. The resulting image is distorted. How to deal w…

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## [Hire someone to extract Skull + Mandible + wires and plates](https://discourse.slicer.org/t/hire-someone-to-extract-skull-mandible-wires-and-plates/14511)

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**Author:** [@brockgs](https://discourse.slicer.org/u/brockgs)\
**Replies:** 1\
**Last updated:** [December 9, 2020, 4:54pm UTC](https://discourse.slicer.org/t/hire-someone-to-extract-skull-mandible-wires-and-plates/14511 "2020-12-09T16:54:51Z")

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Hello, I have two studies. One of myself pre-surgery, one, post-surgery. I would like to find someone who I can hire to get nice clean extracted models from the data to enable 3D printing a before and after skull. I’m m…

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## [Inferior dental nerve tracing](https://discourse.slicer.org/t/inferior-dental-nerve-tracing/14956)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 2\
**Last updated:** [December 9, 2020, 4:43pm UTC](https://discourse.slicer.org/t/inferior-dental-nerve-tracing/14956 "2020-12-09T16:43:15Z")

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I would appreciate if someone could share their ways (recipes) of segmenting the IDN Canal on CBCT and CTs. What is the most balanced way (speed and accuracy) that you have found for this? thanks

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## [How to get an artery from a curve](https://discourse.slicer.org/t/how-to-get-an-artery-from-a-curve/14964)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [December 9, 2020, 3:16pm UTC](https://discourse.slicer.org/t/how-to-get-an-artery-from-a-curve/14964 "2020-12-09T15:16:33Z")

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If this curve is the center line of a blood vessel or tube, I know the diameter and how to create a blood vessel or tube. What I mean is how to use the center line to get a solid tube model.

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## [View segmentation without background volume](https://discourse.slicer.org/t/view-segmentation-without-background-volume/14945)

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**Author:** [@iboeth](https://discourse.slicer.org/u/iboeth)\
**Replies:** 2\
**Last updated:** [December 9, 2020, 11:55am UTC](https://discourse.slicer.org/t/view-segmentation-without-background-volume/14945 "2020-12-09T11:55:04Z")

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Hello! I put a segmentation into 3D-Slicer, but the “pictures” are not visible… I also restarted 3D-Slicer, but it is still the same. What have I done wrong?

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## [Masking: "Overwrite visible" allowing overlap instead of overwriting](https://discourse.slicer.org/t/masking-overwrite-visible-allowing-overlap-instead-of-overwriting/14857)

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**Author:** [@sioussou](https://discourse.slicer.org/u/sioussou)\
**Replies:** 8\
**Last updated:** [December 9, 2020, 6:08am UTC](https://discourse.slicer.org/t/masking-overwrite-visible-allowing-overlap-instead-of-overwriting/14857 "2020-12-09T06:08:36Z")

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Problem report for Slicer 4.11.20200930 win-amd64: in segment editor, I’ve set the masking option “Modify other segments” to “Overwrite visible” before applying smoothing \[closing (fill holes) - 1.00mm\]. If any of my seg…

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## [How can I add planes in 5mm intervals along the short-axis of a heart from apex to base?](https://discourse.slicer.org/t/how-can-i-add-planes-in-5mm-intervals-along-the-short-axis-of-a-heart-from-apex-to-base/14929)

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**Author:** [@jsalas424](https://discourse.slicer.org/u/jsalas424)\
**Replies:** 5\
**Last updated:** [December 9, 2020, 1:38am UTC](https://discourse.slicer.org/t/how-can-i-add-planes-in-5mm-intervals-along-the-short-axis-of-a-heart-from-apex-to-base/14929 "2020-12-09T01:38:31Z")

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Hello, I’ve generated a 3D shell of the left ventricle of a heart using the IGT → Markups to Model module. I have fiducial points marked in the model that correspond to points of scientific interest in an excised heart…

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## [Remove dental fillings artifacts from CT scan](https://discourse.slicer.org/t/remove-dental-fillings-artifacts-from-ct-scan/14941)

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**Author:** [@jess](https://discourse.slicer.org/u/jess)\
**Replies:** 3\
**Last updated:** [December 8, 2020, 8:58pm UTC](https://discourse.slicer.org/t/remove-dental-fillings-artifacts-from-ct-scan/14941 "2020-12-08T20:58:21Z")

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I’m new to 3D Slicer and medical imaging in general. I have a CT scan of my head and wanted to extract a clean 3d model of my skull. My dental fillings appear to cause some kind of reflections that show as rays in the sc…

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## [Add "Create new segment" or "Clone segment" feature to Segment Editor](https://discourse.slicer.org/t/add-create-new-segment-or-clone-segment-feature-to-segment-editor/14947)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [December 8, 2020, 9:18pm UTC](https://discourse.slicer.org/t/add-create-new-segment-or-clone-segment-feature-to-segment-editor/14947 "2020-12-08T21:18:59Z")

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Would it be possible to modify the Segment Editor effects such that: Output of a segmentation can be set as a new segment as oppose to changing the existing one. For example a setting of “Modify other segments” can be …

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## [Help with "Grow from Seeds"](https://discourse.slicer.org/t/help-with-grow-from-seeds/14939)

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**Author:** [@Enya\_Nora2020](https://discourse.slicer.org/u/Enya_Nora2020)\
**Replies:** 0\
**Last updated:** [December 8, 2020, 3:05pm UTC](https://discourse.slicer.org/t/help-with-grow-from-seeds/14939 "2020-12-08T15:05:01Z")

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Hi, I would like to determine the volume of the tibia cartilage. For this I am currently working with the “Grow from Seeds” feature (If you recommend another option please tell me). Unfortunately my result is very unclea…

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## [Failing to download extension with Slicer-4.11 stable](https://discourse.slicer.org/t/failing-to-download-extension-with-slicer-4-11-stable/14928)

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**Author:** [@tbillah](https://discourse.slicer.org/u/tbillah)\
**Replies:** 4\
**Last updated:** [December 8, 2020, 1:25pm UTC](https://discourse.slicer.org/t/failing-to-download-extension-with-slicer-4-11-stable/14928 "2020-12-08T13:25:53Z")

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Hi all, Is this a familar error? A cookie associated with a cross-site resource at http://www.nitrc.org/ was set without the SameSite attrute. A future release of Chrome will only deliver cookies with cross-site reque…

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## [Extension service is down](https://discourse.slicer.org/t/extension-service-is-down/14914)

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**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 3\
**Last updated:** [December 8, 2020, 1:25pm UTC](https://discourse.slicer.org/t/extension-service-is-down/14914 "2020-12-08T13:25:27Z")

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It looks like midas is half-broken. The metadata can be retrieved but the downloaded files are empty. Can someone reboot it? "Retrieving extension metadata \[ extensionId: 405842\]" "Downloading extension \[ itemId: 5484…

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## [Creating Volume from Numpy](https://discourse.slicer.org/t/creating-volume-from-numpy/658)

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**Author:** [@hph10128](https://discourse.slicer.org/u/hph10128)\
**Replies:** 18\
**Last updated:** [December 8, 2020, 7:17am UTC](https://discourse.slicer.org/t/creating-volume-from-numpy/658 "2020-12-08T07:17:26Z")

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Hi all, I have slicer version 4.7.0-2017-07-07 r26146 installed. I am trying to convert a numpy 3d array into a new volume. I tried the following as listed in the nightly documentation: resultVolumeNode = getNode(‘…

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## [Threshold range in 3D Slicer is \[0, 99\]](https://discourse.slicer.org/t/threshold-range-in-3d-slicer-is-0-99/7760)

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**Author:** [@mli](https://discourse.slicer.org/u/mli)\
**Replies:** 19\
**Last updated:** [December 8, 2020, 2:03am UTC](https://discourse.slicer.org/t/threshold-range-in-3d-slicer-is-0-99/7760 "2020-12-08T02:03:06Z")

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Hi guys, I am trying to segment CT image. The data format is .nrrd and I can import it to Slicer successfully. I checked the import data and the voxel value is HU, which is from about -1000 to 1000. However, when I use…

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## [Draw a fixed sized segment](https://discourse.slicer.org/t/draw-a-fixed-sized-segment/14930)

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**Author:** [@tenzin\_kunkyab](https://discourse.slicer.org/u/tenzin_kunkyab)\
**Replies:** 1\
**Last updated:** [December 8, 2020, 1:22am UTC](https://discourse.slicer.org/t/draw-a-fixed-sized-segment/14930 "2020-12-08T01:22:43Z")

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Hi Andras, Is there a way to make a cubic segmentation of size 2 cm by 2 cm by 2 cm (just an example) in terms of its dimension? the symmetric option in scissor effect is not giving me what I need to do. thank you so m…

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## [Retrieving Transform Matrix From Transforms Module](https://discourse.slicer.org/t/retrieving-transform-matrix-from-transforms-module/14924)

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**Author:** [@YBurakD](https://discourse.slicer.org/u/YBurakD)\
**Replies:** 1\
**Last updated:** [December 7, 2020, 10:15pm UTC](https://discourse.slicer.org/t/retrieving-transform-matrix-from-transforms-module/14924 "2020-12-07T22:15:44Z")

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Hi, I have 3D images that I need to rotate and to do this I am using the transforms module. I want to do the rotation in the gui with sliders and retrieve the transform matrix via python code to apply the transform with…

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## [Old FreeSurfer color lookup table](https://discourse.slicer.org/t/old-freesurfer-color-lookup-table/13184)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 4\
**Last updated:** [December 7, 2020, 10:05pm UTC](https://discourse.slicer.org/t/old-freesurfer-color-lookup-table/13184 "2020-12-07T22:05:55Z")

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In older Slicer releases, there was a color map called “FreeSurfer Labels”. In more recent nightly releases, this color map is gone, and I see new ones called “SPL-BrainAtlas-2009-ColorFile”, “SPL-BrainAtlas-2012-ColorF…

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## [MarkupsCurve with Endoscopy error message](https://discourse.slicer.org/t/markupscurve-with-endoscopy-error-message/14862)

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**Author:** [@torquil](https://discourse.slicer.org/u/torquil)\
**Replies:** 9\
**Last updated:** [December 7, 2020, 4:16pm UTC](https://discourse.slicer.org/t/markupscurve-with-endoscopy-error-message/14862 "2020-12-07T16:16:44Z")

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In the Endoscopy module it is possible to choose a MarkupsCurve as the “Input Fiducials”. However, nothing happens when clicking on “Create path”. In addition, I have seven cameras with the same name, so I’m not really s…

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## [3D slicer No reaction after clicked INSTALL](https://discourse.slicer.org/t/3d-slicer-no-reaction-after-clicked-install/14926)

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**Author:** [@BarnettZhang](https://discourse.slicer.org/u/BarnettZhang)\
**Replies:** 1\
**Last updated:** [December 7, 2020, 3:35pm UTC](https://discourse.slicer.org/t/3d-slicer-no-reaction-after-clicked-install/14926 "2020-12-07T15:35:47Z")

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Hi, I’m using 3D slicer version 4.11.20200930 (the stable release) on Windows and trying to install Jupyter Notebook extension. But every time I clicked on INSTALL and the green notifications show up, but not the instal…

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## [Segmenting goes across 3 slices](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079)

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**Author:** [@tnguyen](https://discourse.slicer.org/u/tnguyen)\
**Replies:** 8\
**Last updated:** [December 6, 2020, 4:57pm UTC](https://discourse.slicer.org/t/segmenting-goes-across-3-slices/2079 "2020-12-06T16:57:09Z")

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Hi everyone, I was using Paint Effect in Segment Editor and I noticed that the area that I painted on 1 slice also appears on the next two adjacent slices (if I try to erase this area on these two slices, it will also e…

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## [Problem with Bone texture analysis extension](https://discourse.slicer.org/t/problem-with-bone-texture-analysis-extension/14382)

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**Author:** [@isibeal](https://discourse.slicer.org/u/isibeal)\
**Replies:** 1\
**Last updated:** [December 6, 2020, 12:45pm UTC](https://discourse.slicer.org/t/problem-with-bone-texture-analysis-extension/14382 "2020-12-06T12:45:10Z")

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Operating system: windows 64 bit Slicer version: 4.11.20200930 Expected behavior: Actual behavior: Hi! I have started a new project where I want to measure changes in distal part of mice femur. I want to know hot t…

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## [What is the command in python to apply surface smoothing to 3D object?](https://discourse.slicer.org/t/what-is-the-command-in-python-to-apply-surface-smoothing-to-3d-object/14889)

<div class="topic-metadata">

**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 1\
**Last updated:** [December 6, 2020, 11:29am UTC](https://discourse.slicer.org/t/what-is-the-command-in-python-to-apply-surface-smoothing-to-3d-object/14889 "2020-12-06T11:29:56Z")

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What is the command to apply this?

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## [Load markups curve from file](https://discourse.slicer.org/t/load-markups-curve-from-file/14905)

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**Author:** [@yee](https://discourse.slicer.org/u/yee)\
**Replies:** 3\
**Last updated:** [December 6, 2020, 6:58am UTC](https://discourse.slicer.org/t/load-markups-curve-from-file/14905 "2020-12-06T06:58:26Z")

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Hi! When I input " curveNode = slicer.util.loadMarkupsCurve('some/folder/MarkupsCurve.fcsv')", I just get makups node. How can I get the markupcurve? Thank you in advance ! And if i use Edoscopy ,I just got this. {E5…

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## [LongitudinalPETCT extension fails to read DICOM files](https://discourse.slicer.org/t/longitudinalpetct-extension-fails-to-read-dicom-files/14902)

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**Author:** [@Mgi](https://discourse.slicer.org/u/Mgi)\
**Replies:** 0\
**Last updated:** [December 3, 2020, 7:05pm UTC](https://discourse.slicer.org/t/longitudinalpetct-extension-fails-to-read-dicom-files/14902 "2020-12-03T19:05:07Z")

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Thank you, this solve my problem. I have another question because now with the version 4.11.2 is not compatible “LongitudinalPETCT” extension, and when I tried to load the dicom with images appear the message: “Coud not …

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## [Set color cut-offs for volume](https://discourse.slicer.org/t/set-color-cut-offs-for-volume/14819)

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**Author:** [@Even](https://discourse.slicer.org/u/Even)\
**Replies:** 1\
**Last updated:** [December 5, 2020, 8:31pm UTC](https://discourse.slicer.org/t/set-color-cut-offs-for-volume/14819 "2020-12-05T20:31:36Z")

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Hi! I have two volumes: One with a common MNI brain and one with specific scalar values. The goal is to overlay the volume with specific values on top of the MNI brain. Both volumes have the same dimensions. I want to c…

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## [Is 3D Slicer available for a tablet?](https://discourse.slicer.org/t/is-3d-slicer-available-for-a-tablet/14802)

<div class="topic-metadata">

**Author:** [@aldoSanchez](https://discourse.slicer.org/u/aldoSanchez)\
**Replies:** 11\
**Last updated:** [December 5, 2020, 8:07pm UTC](https://discourse.slicer.org/t/is-3d-slicer-available-for-a-tablet/14802 "2020-12-05T20:07:28Z")

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I want to edit the segments on a tablet because I think is easier to use a pen. or it’s another tool to do it fast.

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## [PET/CT Standardized\_uptake\_value\_body\_weight series](https://discourse.slicer.org/t/pet-ct-standardized-uptake-value-body-weight-series/14898)

<div class="topic-metadata">

**Author:** [@Jakub\_Mitura](https://discourse.slicer.org/u/Jakub_Mitura)\
**Replies:** 3\
**Last updated:** [December 5, 2020, 6:43pm UTC](https://discourse.slicer.org/t/pet-ct-standardized-uptake-value-body-weight-series/14898 "2020-12-05T18:43:08Z")

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Hello When I upload the PET/CT dicom data (exported from syngo via) I get Standardized\_uptake\_value\_body\_weight series that is not in the series i imported - so I presume it is genereted by slicer - so just to be sure e…

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## [Smoothing effect only in 1 axis](https://discourse.slicer.org/t/smoothing-effect-only-in-1-axis/14613)

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**Author:** [@NoobForSlicer](https://discourse.slicer.org/u/NoobForSlicer)\
**Replies:** 15\
**Last updated:** [December 5, 2020, 4:27pm UTC](https://discourse.slicer.org/t/smoothing-effect-only-in-1-axis/14613 "2020-12-05T16:27:16Z")

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is it possible to have smoothing effect only affect the one axis, the one that vertically goes through slices. In other words, if the resolution of a slice is good but slices were spaced a lot, if the 2mm or 3mm smooth…

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## [Segmentation by thresholding doesnt correspond to HU units](https://discourse.slicer.org/t/segmentation-by-thresholding-doesnt-correspond-to-hu-units/14900)

<div class="topic-metadata">

**Author:** [@Cesar\_Puga](https://discourse.slicer.org/u/Cesar_Puga)\
**Replies:** 1\
**Last updated:** [December 5, 2020, 4:14pm UTC](https://discourse.slicer.org/t/segmentation-by-thresholding-doesnt-correspond-to-hu-units/14900 "2020-12-05T16:14:04Z")

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Hello Everyone, Im trying to segment the bones from a set of CT scans, actually i’ve done this actions both in Slicer and in Python, i have read the segmentation recipes for extracting skeletons but when i apply a thres…

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