# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=137

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

**Page:** 138

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## [Can't Hide Segmentations](https://discourse.slicer.org/t/cant-hide-segmentations/32004)

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**Author:** [@sldamico13](https://discourse.slicer.org/u/sldamico13)\
**Replies:** 3\
**Last updated:** [October 3, 2023, 2:23pm UTC](https://discourse.slicer.org/t/cant-hide-segmentations/32004 "2023-10-03T14:23:15Z")

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Operating system: MacOS Slicer version: 5.4.0 Expected behavior: Segmentations are not visible when hidden in both 3D and sectional views. Actual behavior: Segmentations cannot be hidden. I can only see the background…

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## [Is there an existing "interpolator" in ITK specifically for the Slice-to-Volume registration?](https://discourse.slicer.org/t/is-there-an-existing-interpolator-in-itk-specifically-for-the-slice-to-volume-registration/31955)

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**Author:** [@Shuwei](https://discourse.slicer.org/u/Shuwei)\
**Replies:** 7\
**Last updated:** [October 3, 2023, 1:57pm UTC](https://discourse.slicer.org/t/is-there-an-existing-interpolator-in-itk-specifically-for-the-slice-to-volume-registration/31955 "2023-10-03T13:57:58Z")

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Hi All, I am working on the slice-to-volume registration topic using ITK. Conventionally, slice-to-volume registration (e.g. US-CT) needs to reslice the volume data based on the transformation and then convert it to a 2…

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## [Kernal Crash when extracting voxel based feature map for Wavelet filtered images](https://discourse.slicer.org/t/kernal-crash-when-extracting-voxel-based-feature-map-for-wavelet-filtered-images/32011)

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**Author:** [@nsrao48](https://discourse.slicer.org/u/nsrao48)\
**Replies:** 0\
**Last updated:** [October 3, 2023, 1:43pm UTC](https://discourse.slicer.org/t/kernal-crash-when-extracting-voxel-based-feature-map-for-wavelet-filtered-images/32011 "2023-10-03T13:43:38Z")

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Hi, I was trying to visualize the radiomic features using Voxel based feature map. I am able to extract the feature map for other filtered images except wavelet. Its crashing the kernel. Is it a known issue ? yaml file …

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## [Improving vmtk-centerline detection](https://discourse.slicer.org/t/improving-vmtk-centerline-detection/31935)

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**Author:** [@b\_gop](https://discourse.slicer.org/u/b_gop)\
**Replies:** 6\
**Last updated:** [October 3, 2023, 11:44am UTC](https://discourse.slicer.org/t/improving-vmtk-centerline-detection/31935 "2023-10-03T11:44:09Z")

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I am trying to get the centerline for a very intricate tree-like structure. While the centerline computation gets most of the structure, there are still branches that it does not cover despite there being endpoints on th…

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## [Slicermorph: error when excluding landmarks](https://discourse.slicer.org/t/slicermorph-error-when-excluding-landmarks/31933)

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**Author:** [@Ale](https://discourse.slicer.org/u/Ale)\
**Replies:** 3\
**Last updated:** [October 3, 2023, 11:06am UTC](https://discourse.slicer.org/t/slicermorph-error-when-excluding-landmarks/31933 "2023-10-03T11:06:18Z")

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Hi all, I’m using Slicermorph for GM analyses. The GPA runs fine using all landmarks, but when trying to exclude one landmark e.g. 12, from analysis nothing happens. Python console shows me this error: AttributeError: ‘…

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## [Reconstruct 3d heart model from cine-MRI data](https://discourse.slicer.org/t/reconstruct-3d-heart-model-from-cine-mri-data/31910)

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**Author:** [@Sushil](https://discourse.slicer.org/u/Sushil)\
**Replies:** 2\
**Last updated:** [September 28, 2023, 6:29pm UTC](https://discourse.slicer.org/t/reconstruct-3d-heart-model-from-cine-mri-data/31910 "2023-09-28T18:29:38Z")

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Hi I am trying to reconstruct 3d heart model from cineMRI data. I have followed the steps from " Reconstruct 4D volume from cine-MRI frames". now I have 5 volume sequence exported in .NRRD format AOT trufi cine - 25 …

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## [Make transform visible in slice view](https://discourse.slicer.org/t/make-transform-visible-in-slice-view/31979)

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**Author:** [@Andrew\_Kanawati](https://discourse.slicer.org/u/Andrew_Kanawati)\
**Replies:** 2\
**Last updated:** [October 3, 2023, 3:40am UTC](https://discourse.slicer.org/t/make-transform-visible-in-slice-view/31979 "2023-10-03T03:40:38Z")

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I’ve created a cylinder model using ‘create models’, and I can see it on the 3d view. Is there a way of seeing the cylinder in the slice view before creating it into a segment? Thanks so much

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## [PCA Analysis Spoke Length](https://discourse.slicer.org/t/pca-analysis-spoke-length/31997)

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**Author:** [@umair04](https://discourse.slicer.org/u/umair04)\
**Replies:** 0\
**Last updated:** [October 2, 2023, 5:09pm UTC](https://discourse.slicer.org/t/pca-analysis-spoke-length/31997 "2023-10-02T17:09:36Z")

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I ran a PCA Analysis on multiple skeletal representations and would like to quantify the length of the spokes to determine an average length? Does anyone know how I can do that through 3D Slicer or SlicerSALT?

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## [Markup renaming error loses numbering](https://discourse.slicer.org/t/markup-renaming-error-loses-numbering/31971)

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**Author:** [@slopezal](https://discourse.slicer.org/u/slopezal)\
**Replies:** 6\
**Last updated:** [October 2, 2023, 3:57pm UTC](https://discourse.slicer.org/t/markup-renaming-error-loses-numbering/31971 "2023-10-02T15:57:33Z")

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Hi, I’m running into some sort of bug when renaming a point list. If I start off with a point list that is named using the scheme 7\_1-%d and then I try to remove the underscore to make it 7-%d, the whole numbering scheme…

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## [Time average of sequence of transforms](https://discourse.slicer.org/t/time-average-of-sequence-of-transforms/31927)

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**Author:** [@Zimogre](https://discourse.slicer.org/u/Zimogre)\
**Replies:** 4\
**Last updated:** [October 2, 2023, 3:17pm UTC](https://discourse.slicer.org/t/time-average-of-sequence-of-transforms/31927 "2023-10-02T15:17:31Z")

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Hi all, I am recently working with a time series of volumes. First, I obtained a sequence (Sequence module) of volumes and then registered them using the SequenceRegistration module obtaining the corresponding Transform…

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## [4D Ultrasound (.3dus) to 4D NRRD](https://discourse.slicer.org/t/4d-ultrasound-3dus-to-4d-nrrd/31994)

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**Author:** [@eyalyah](https://discourse.slicer.org/u/eyalyah)\
**Replies:** 2\
**Last updated:** [October 2, 2023, 2:46pm UTC](https://discourse.slicer.org/t/4d-ultrasound-3dus-to-4d-nrrd/31994 "2023-10-02T14:46:25Z")

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I have an 4D ultrasound from a vivid E95 machine, I successfully loaded it the 4D volume to slicer by changing the extension of the file to .3dus when I load it to slicer i have 2 data entries, one is the 3d data and t…

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## [TotalSegmentator not showing in module finder, and cannot be uninstall from extension module](https://discourse.slicer.org/t/totalsegmentator-not-showing-in-module-finder-and-cannot-be-uninstall-from-extension-module/31946)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 22\
**Last updated:** [October 2, 2023, 12:04pm UTC](https://discourse.slicer.org/t/totalsegmentator-not-showing-in-module-finder-and-cannot-be-uninstall-from-extension-module/31946 "2023-10-02T12:04:17Z")

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Hi, I’ve installed TotalSegmentator but it cannot be found in the module finder. When I open the extension module and try to uninstall TotalSegmentator, a prompt appears: “Failed to open extension setting…” please give …

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## [Center of rotation](https://discourse.slicer.org/t/center-of-rotation/31984)

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**Author:** [@ortho3d](https://discourse.slicer.org/u/ortho3d)\
**Replies:** 1\
**Last updated:** [October 2, 2023, 2:54am UTC](https://discourse.slicer.org/t/center-of-rotation/31984 "2023-10-02T02:54:45Z")

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Is it possible to choose a different center of rotation for a model (in transformation app) thanks

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## [Sir can I import 3D slicer file into Ansys Fluent software?](https://discourse.slicer.org/t/sir-can-i-import-3d-slicer-file-into-ansys-fluent-software/31988)

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**Author:** [@Sameer123](https://discourse.slicer.org/u/Sameer123)\
**Replies:** 1\
**Last updated:** [October 2, 2023, 2:51am UTC](https://discourse.slicer.org/t/sir-can-i-import-3d-slicer-file-into-ansys-fluent-software/31988 "2023-10-02T02:51:08Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [How to retraining the whole-body CT segmentation in the MONAI model zoo?](https://discourse.slicer.org/t/how-to-retraining-the-whole-body-ct-segmentation-in-the-monai-model-zoo/31977)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 0\
**Last updated:** [October 1, 2023, 4:52am UTC](https://discourse.slicer.org/t/how-to-retraining-the-whole-body-ct-segmentation-in-the-monai-model-zoo/31977 "2023-10-01T04:52:27Z")

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Hi, i read that we can use MONAI model zoo as replacement of TotalSegmentator by retraining the whole-body CT Segementation from this model-zoo/models/wholeBody\_ct\_segmentation at dev · Project-MONAI/model-zoo · GitHub. …

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## [Error while trying to use monailabel](https://discourse.slicer.org/t/error-while-trying-to-use-monailabel/31975)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 0\
**Last updated:** [October 1, 2023, 3:56am UTC](https://discourse.slicer.org/t/error-while-trying-to-use-monailabel/31975 "2023-10-01T03:56:19Z")

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Hi, i got this error while trying to train the segmentation. What sould i do?

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## [Change color of each model uploaded](https://discourse.slicer.org/t/change-color-of-each-model-uploaded/31966)

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**Author:** [@CharNamIII](https://discourse.slicer.org/u/CharNamIII)\
**Replies:** 2\
**Last updated:** [September 30, 2023, 10:46am UTC](https://discourse.slicer.org/t/change-color-of-each-model-uploaded/31966 "2023-09-30T10:46:28Z")

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Hi, Is there a way to give each model a unique color when uploaded to 3DSlicer? They all come out the same color if I upload them all at once and changing them one by one takes a long time!

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## [Smoothing the meshes generated by the Total Segmentation module](https://discourse.slicer.org/t/smoothing-the-meshes-generated-by-the-total-segmentation-module/31962)

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**Author:** [@Miri\_Trope](https://discourse.slicer.org/u/Miri_Trope)\
**Replies:** 1\
**Last updated:** [September 30, 2023, 4:43am UTC](https://discourse.slicer.org/t/smoothing-the-meshes-generated-by-the-total-segmentation-module/31962 "2023-09-30T04:43:43Z")

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Hello everyone, I’m currently using the Total Segmentation module and gaining valuable insights into the anatomy of different organs. I’m curious about your recommendations for an effective smoothing filter to prevent t…

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## [Rigid Transformation is-- scaling?](https://discourse.slicer.org/t/rigid-transformation-is-scaling/31953)

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**Author:** [@Beth\_Bearce](https://discourse.slicer.org/u/Beth_Bearce)\
**Replies:** 7\
**Last updated:** [September 30, 2023, 4:41am UTC](https://discourse.slicer.org/t/rigid-transformation-is-scaling/31953 "2023-09-30T04:41:18Z")

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Hi there! I have a bit of a workflow to extract the simplified shapes of fish spines from their whole skeletons, and then align them to one another. (I work on scoliosis & spine morphology.) Here is what I typically do: …

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## [Automatic segmentation of low intensity-difference layers](https://discourse.slicer.org/t/automatic-segmentation-of-low-intensity-difference-layers/31941)

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**Author:** [@Windy](https://discourse.slicer.org/u/Windy)\
**Replies:** 5\
**Last updated:** [September 29, 2023, 1:17am UTC](https://discourse.slicer.org/t/automatic-segmentation-of-low-intensity-difference-layers/31941 "2023-09-29T01:17:02Z")

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Hi, I have an image dataset where the color intensity difference of classes in an image is pretty much similar (example given below, contains 4 layers of muscle, hence 4 classes). I tried many semiautomatic algorithms l…

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## [Scale model in gltf](https://discourse.slicer.org/t/scale-model-in-gltf/31639)

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**Author:** [@Caterina](https://discourse.slicer.org/u/Caterina)\
**Replies:** 17\
**Last updated:** [September 28, 2023, 7:01pm UTC](https://discourse.slicer.org/t/scale-model-in-gltf/31639 "2023-09-28T19:01:22Z")

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Good morning, I performed segmentation and I would like to scale the results of segmentation in gltf format. Actually I can scale the model in stl using Surface Toolbox or save the unscaled model in gltf. I need to sc…

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## [3D Slicer not responding but still using maximum CPU](https://discourse.slicer.org/t/3d-slicer-not-responding-but-still-using-maximum-cpu/31924)

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**Author:** [@b\_gop](https://discourse.slicer.org/u/b_gop)\
**Replies:** 6\
**Last updated:** [September 28, 2023, 3:30pm UTC](https://discourse.slicer.org/t/3d-slicer-not-responding-but-still-using-maximum-cpu/31924 "2023-09-28T15:30:41Z")

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I am trying to use vmtk centerline extraction on a model of approximately ~250mb size. \[Even though the file size is not too big, the model is definitely intricate with a lot of branches and would understandably require …

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## [Vertebrae Segmentation Setting on Total Segmentator Module](https://discourse.slicer.org/t/vertebrae-segmentation-setting-on-total-segmentator-module/31947)

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**Author:** [@marcosncosta1](https://discourse.slicer.org/u/marcosncosta1)\
**Replies:** 1\
**Last updated:** [September 28, 2023, 2:21pm UTC](https://discourse.slicer.org/t/vertebrae-segmentation-setting-on-total-segmentator-module/31947 "2023-09-28T14:21:20Z")

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Hello Slicer community, I am trying to segment vertebrae with the TotalSegmentator module and I was wondering if there is a setting where I can add “vertebrae segmentation” to the segmentation task so that I don’t have …

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## [Slicer Memory Leak](https://discourse.slicer.org/t/slicer-memory-leak/22369)

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**Author:** [@Fabyan](https://discourse.slicer.org/u/Fabyan)\
**Replies:** 3\
**Last updated:** [September 28, 2023, 10:02am UTC](https://discourse.slicer.org/t/slicer-memory-leak/22369 "2023-09-28T10:02:46Z")

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Hello. I am working on a slicer module that loads .mha data, applies transformations from a .csv to each frame and displays the separate orientations. Currently I load the data and preprocess it by splitting the differen…

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## [New extensions can not work on Slicer 5.4.0 on MacOS](https://discourse.slicer.org/t/new-extensions-can-not-work-on-slicer-5-4-0-on-macos/31535)

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**Author:** [@wrc](https://discourse.slicer.org/u/wrc)\
**Replies:** 27\
**Last updated:** [September 28, 2023, 7:21am UTC](https://discourse.slicer.org/t/new-extensions-can-not-work-on-slicer-5-4-0-on-macos/31535 "2023-09-28T07:21:28Z")

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Hello, I have just updated Slicer VMTK to 144582e (2023-08-22). It showed the following error: dlopen(/Applications/Slicer 5.4.0.app/Contents/Extensions-31938/SlicerVMTK/lib/Slicer-5.4/qt-loadable-modules/qSlicerBranchC…

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## [How to input and output segments in mhd format in 3D slicers.](https://discourse.slicer.org/t/how-to-input-and-output-segments-in-mhd-format-in-3d-slicers/31943)

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**Author:** [@sun-wanqing](https://discourse.slicer.org/u/sun-wanqing)\
**Replies:** 3\
**Last updated:** [September 28, 2023, 3:21am UTC](https://discourse.slicer.org/t/how-to-input-and-output-segments-in-mhd-format-in-3d-slicers/31943 "2023-09-28T03:21:54Z")

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I currently have T1 data in nrrd format and annotated segmentation data in nrrd format. I hope to convert them into mhd format data. For volume, I can choose the mhd format when saving, but for files in seg.nrrd format, …

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## [How to substract two STL files?](https://discourse.slicer.org/t/how-to-substract-two-stl-files/31888)

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**Author:** [@Inka\_Saraswati](https://discourse.slicer.org/u/Inka_Saraswati)\
**Replies:** 4\
**Last updated:** [September 28, 2023, 2:02am UTC](https://discourse.slicer.org/t/how-to-substract-two-stl-files/31888 "2023-09-28T02:02:55Z")

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I have 2 STLs, one is a model of bone with defect, the other one is an intact one. I want to get a 3D model of the defect (the difference between the two files). I know how to substract with Logical Operators in Segment…

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## [Mask volume in segment editor](https://discourse.slicer.org/t/mask-volume-in-segment-editor/31688)

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**Author:** [@megvdb](https://discourse.slicer.org/u/megvdb)\
**Replies:** 1\
**Last updated:** [September 27, 2023, 8:18pm UTC](https://discourse.slicer.org/t/mask-volume-in-segment-editor/31688 "2023-09-27T20:18:45Z")

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Hi! Previously i have used the mask volume tool to export a segment into volume renderings. However, i found in the newest slicer version (5.4) when i use mask volume nothing is showing up in the volume rendering. any th…

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## [Segment the osteoderm of a lizard](https://discourse.slicer.org/t/segment-the-osteoderm-of-a-lizard/31717)

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**Author:** [@Froggyo](https://discourse.slicer.org/u/Froggyo)\
**Replies:** 1\
**Last updated:** [September 27, 2023, 8:16pm UTC](https://discourse.slicer.org/t/segment-the-osteoderm-of-a-lizard/31717 "2023-09-27T20:16:29Z")

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I’m trying to segment the osteoderm of a lizard from the rest of its skeleton and having difficulty doing so in an efficient manner. Any suggestions? It has about the same density as the skeleton and is even attached at…

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## [Merge Models with Volume](https://discourse.slicer.org/t/merge-models-with-volume/31937)

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**Author:** [@Bahram\_Zargar](https://discourse.slicer.org/u/Bahram_Zargar)\
**Replies:** 3\
**Last updated:** [September 28, 2023, 2:51am UTC](https://discourse.slicer.org/t/merge-models-with-volume/31937 "2023-09-28T02:51:44Z")

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3d Slicer version 5.2.2 OS: Linux Redhat 8 Hello 3D slicer experts, I do have an MRI volume, with 6 models in my 3D Slicer, and can export each of them separately as DICOM file. However what I want to do is to merge a…

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