# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=270

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

**Page:** 271

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## [Fly through view not showing up](https://discourse.slicer.org/t/fly-through-view-not-showing-up/18652)

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**Author:** [@JohnnyXie13](https://discourse.slicer.org/u/JohnnyXie13)\
**Replies:** 2\
**Last updated:** [July 12, 2021, 8:01pm UTC](https://discourse.slicer.org/t/fly-through-view-not-showing-up/18652 "2021-07-12T20:01:23Z")

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Dear Experts, I’m facing a problem with the Fly through in Endoscopy. Here’s what I did: I loaded all the slices and use volume rendering to create a clean volume. I created several fiducial points in Markups (I dragg…

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## [Segmentation of teeth](https://discourse.slicer.org/t/segmentation-of-teeth/18645)

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**Author:** [@Lucky\_Girish](https://discourse.slicer.org/u/Lucky_Girish)\
**Replies:** 1\
**Last updated:** [July 12, 2021, 5:47pm UTC](https://discourse.slicer.org/t/segmentation-of-teeth/18645 "2021-07-12T17:47:59Z")

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Hi, I want to extract teeth from a cbct, as different layers inside the teeth along with the nerves like here : Enamel,Dentin, Pulp, Nerves, Gum as diferent layers such that to carry out the stress analysis If yes …

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## [How do you create and extend trajectories on Slicer?](https://discourse.slicer.org/t/how-do-you-create-and-extend-trajectories-on-slicer/18583)

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**Author:** [@Timothy\_Minicozzi\_20](https://discourse.slicer.org/u/Timothy_Minicozzi_20)\
**Replies:** 3\
**Last updated:** [July 12, 2021, 5:01pm UTC](https://discourse.slicer.org/t/how-do-you-create-and-extend-trajectories-on-slicer/18583 "2021-07-12T17:01:54Z")

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Operating system: Windows 10 Slicer version: 4.11 Expected behavior: I would like to try to extend a line from the end of a stylus tip modeled by a needle (in order to see the trajectory that is planned by the stylus a…

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## [Loss of contours after Applying Rotation](https://discourse.slicer.org/t/loss-of-contours-after-applying-rotation/18616)

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**Author:** [@MichaelCHL](https://discourse.slicer.org/u/MichaelCHL)\
**Replies:** 2\
**Last updated:** [July 12, 2021, 3:32pm UTC](https://discourse.slicer.org/t/loss-of-contours-after-applying-rotation/18616 "2021-07-12T15:32:20Z")

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Hi all, I’ve applied transformation (rotation about the red target in my phantom) to both the CT scans and the contours (RT strucutures), hardened it and export it to DICOM After the rotation, some of the contours ar…

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## [Transform & Resample Contours/RTStructures?](https://discourse.slicer.org/t/transform-resample-contours-rtstructures/18594)

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**Author:** [@MichaelCHL](https://discourse.slicer.org/u/MichaelCHL)\
**Replies:** 7\
**Last updated:** [July 12, 2021, 3:31pm UTC](https://discourse.slicer.org/t/transform-resample-contours-rtstructures/18594 "2021-07-12T15:31:51Z")

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Hi all, I am new to 3D Slicer :smiley:. For a project I am working on, I need to transform some CT scans alongside with the contours from Eclipse and reimport them back into Eclipse afterwards. To read the contours (RTS…

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## [Bone model registration for navigation](https://discourse.slicer.org/t/bone-model-registration-for-navigation/18642)

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**Author:** [@qiqi5210](https://discourse.slicer.org/u/qiqi5210)\
**Replies:** 1\
**Last updated:** [July 12, 2021, 2:56pm UTC](https://discourse.slicer.org/t/bone-model-registration-for-navigation/18642 "2021-07-12T14:56:31Z")

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Hi, Mr. Lasso! Sorry to reopen this question, I recently met the same problem. I have a head model and a bone model, I want to make the relative position of the two models in the 3D view same with the real world(The bone…

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## [Segmenting Cranial Bones](https://discourse.slicer.org/t/segmenting-cranial-bones/18565)

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**Author:** [@jamieawren](https://discourse.slicer.org/u/jamieawren)\
**Replies:** 1\
**Last updated:** [July 12, 2021, 2:38pm UTC](https://discourse.slicer.org/t/segmenting-cranial-bones/18565 "2021-07-12T14:38:29Z")

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Hi everyone, I am trying to segment the individual cranial bones of human skulls, approximately 350 or so. I’m currently using volume rendering to show the 3D skull and then using threshold masking to apply the paint ef…

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## [Contour propagation problems](https://discourse.slicer.org/t/contour-propagation-problems/18628)

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**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 1\
**Last updated:** [July 12, 2021, 2:35pm UTC](https://discourse.slicer.org/t/contour-propagation-problems/18628 "2021-07-12T14:35:00Z")

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Hello, I have a CT image (CT1-moving image) with a manual contour (RT structure-dicom format), and another CT image (CT2-fixed image) with no contour. I have registered CT1 to CT2 using Elastix extension and got the dis…

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## [Trajectories in the brain](https://discourse.slicer.org/t/trajectories-in-the-brain/18633)

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**Author:** [@diego](https://discourse.slicer.org/u/diego)\
**Replies:** 2\
**Last updated:** [July 12, 2021, 12:16pm UTC](https://discourse.slicer.org/t/trajectories-in-the-brain/18633 "2021-07-12T12:16:59Z")

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I’m working on projectile wound trajectory tracking in the brain using DICOM CT in Slicer. I wonder if there is a module / that allows 3D Slicer tracking to establish possible projectile routes

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## [  How does this module  VMTK vmtkbranchsections work?](https://discourse.slicer.org/t/how-does-this-module-vmtk-vmtkbranchsections-work/18622)

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**Author:** [@ouyangxin](https://discourse.slicer.org/u/ouyangxin)\
**Replies:** 1\
**Last updated:** [July 12, 2021, 4:22am UTC](https://discourse.slicer.org/t/how-does-this-module-vmtk-vmtkbranchsections-work/18622 "2021-07-12T04:22:54Z")

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vmtkbranchsections How to use this module? I import the divided center line and surface, but I get a series of points (x, y, z). There is no parameter described in this module

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## [Volume rendering preset to dicom or NIFTI](https://discourse.slicer.org/t/volume-rendering-preset-to-dicom-or-nifti/18605)

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**Author:** [@tpereira](https://discourse.slicer.org/u/tpereira)\
**Replies:** 1\
**Last updated:** [July 12, 2021, 4:13am UTC](https://discourse.slicer.org/t/volume-rendering-preset-to-dicom-or-nifti/18605 "2021-07-12T04:13:40Z")

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I have a CT scan and I am using the volume rendering preset CT-Bones. I want to save that into a dicom or a nifti or some other format. It could also be helpful if could segment based on the rendering preset or create a …

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## [Animator function making choppy gifs](https://discourse.slicer.org/t/animator-function-making-choppy-gifs/18627)

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**Author:** [@bcolbert](https://discourse.slicer.org/u/bcolbert)\
**Replies:** 4\
**Last updated:** [July 12, 2021, 3:26am UTC](https://discourse.slicer.org/t/animator-function-making-choppy-gifs/18627 "2021-07-12T03:26:47Z")

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I am using the animator function to create a 5-10 second gif. The gifs all end up being very choppy regardless of what size they are. Any suggestions? Looking to create a gif to put in a presentation.

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## [Customization of right-click context menu is being reset to default unexpectedly](https://discourse.slicer.org/t/customization-of-right-click-context-menu-is-being-reset-to-default-unexpectedly/18603)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 8\
**Last updated:** [July 9, 2021, 8:01pm UTC](https://discourse.slicer.org/t/customization-of-right-click-context-menu-is-being-reset-to-default-unexpectedly/18603 "2021-07-09T20:01:18Z")

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I’m trying to modify visible options of the right-click context menu, but my customization is not being maintained. I haven’t figured out what causes it by it ultimately returns to the default right-click context menu an…

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## [Measuring Error between desired and current trajectories](https://discourse.slicer.org/t/measuring-error-between-desired-and-current-trajectories/18585)

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**Author:** [@Ahmet\_Yildiz](https://discourse.slicer.org/u/Ahmet_Yildiz)\
**Replies:** 3\
**Last updated:** [July 10, 2021, 4:39pm UTC](https://discourse.slicer.org/t/measuring-error-between-desired-and-current-trajectories/18585 "2021-07-10T16:39:32Z")

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I am working on designing and following pre-defined and in real-time trajectories in brain interventions in Slicer. I am wondering whether there is a module/way to calculate in real-time the error between desired and cu…

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## [Unexpected behavior of color when using LUT with color count \< 255](https://discourse.slicer.org/t/unexpected-behavior-of-color-when-using-lut-with-color-count-255/18542)

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**Author:** [@squll1](https://discourse.slicer.org/u/squll1)\
**Replies:** 2\
**Last updated:** [July 10, 2021, 6:38am UTC](https://discourse.slicer.org/t/unexpected-behavior-of-color-when-using-lut-with-color-count-255/18542 "2021-07-10T06:38:11Z")

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Hello: The issue is first noted when I tried to reproduce a specific LUT in a commercial workstation by creating a custom LUT with 10 colors, and use it in a subtracted CT volume with standardized window and level ( ba…

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## [Extract Green or Yellow slices as a stacked tif or gif or DICOM files](https://discourse.slicer.org/t/extract-green-or-yellow-slices-as-a-stacked-tif-or-gif-or-dicom-files/15197)

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**Author:** [@qubalee](https://discourse.slicer.org/u/qubalee)\
**Replies:** 8\
**Last updated:** [July 10, 2021, 4:03am UTC](https://discourse.slicer.org/t/extract-green-or-yellow-slices-as-a-stacked-tif-or-gif-or-dicom-files/15197 "2021-07-10T04:03:14Z")

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Hi, I am trying to export both green and yellow views (as separated files) from a 3D volume, but I could not do it. When I convert it to DICOM, I got it from the Red view only. Is there any one can help in this? thanks…

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## [Save segmented images](https://discourse.slicer.org/t/save-segmented-images/18523)

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**Author:** [@refrangioni](https://discourse.slicer.org/u/refrangioni)\
**Replies:** 4\
**Last updated:** [July 10, 2021, 1:56am UTC](https://discourse.slicer.org/t/save-segmented-images/18523 "2021-07-10T01:56:48Z")

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I need to use segmented images in a program that uses segmented slices in .bmp format I can also use segmented images in DICOM format and then transform them to .bmp what is the best way. and how to save segmented ​​sl…

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## [Saving DICOM format](https://discourse.slicer.org/t/saving-dicom-format/18414)

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**Author:** [@refrangioni](https://discourse.slicer.org/u/refrangioni)\
**Replies:** 5\
**Last updated:** [July 10, 2021, 1:53am UTC](https://discourse.slicer.org/t/saving-dicom-format/18414 "2021-07-10T01:53:41Z")

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I need to segment CT images for include such images in TOMO\_MC program to dosimetric simulating in MCNP . The TOMO\_MC program only accept bitmap files. I think save the segmented images in DICOM format to convert in .b…

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## [Cranial and caudal directions are opposite when loading sequence of DICOM images](https://discourse.slicer.org/t/cranial-and-caudal-directions-are-opposite-when-loading-sequence-of-dicom-images/17428)

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**Author:** [@xackey](https://discourse.slicer.org/u/xackey)\
**Replies:** 23\
**Last updated:** [July 10, 2021, 1:44am UTC](https://discourse.slicer.org/t/cranial-and-caudal-directions-are-opposite-when-loading-sequence-of-dicom-images/17428 "2021-07-10T01:44:16Z")

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Hi. When loading sequence of DICOM images (“Load Data”\<\<Chose File(s) to Add"), loading order of files is different between version 4.10.2 and nightly version (4.13.0). I think version 4.10.2 is correct, but caudal and …

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## [Extracting the three 2d slices of data shown by the 3 planes defined in 3d Slicer](https://discourse.slicer.org/t/extracting-the-three-2d-slices-of-data-shown-by-the-3-planes-defined-in-3d-slicer/18383)

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**Author:** [@elarson](https://discourse.slicer.org/u/elarson)\
**Replies:** 6\
**Last updated:** [July 9, 2021, 3:14pm UTC](https://discourse.slicer.org/t/extracting-the-three-2d-slices-of-data-shown-by-the-3-planes-defined-in-3d-slicer/18383 "2021-07-09T15:14:26Z")

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I can manipulate the 3 2d planes in 3d slicer and visualize the the planes of data I want to extract. The data is 3d+t ultrasound data. Ideally I would like to export the data as 2d ultrasound multi-frame data to 3 sep…

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## [qSlicerMarkupsPlaceWidget - How to delete all mark-ups](https://discourse.slicer.org/t/qslicermarkupsplacewidget-how-to-delete-all-mark-ups/18405)

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**Author:** [@seanchoi0519](https://discourse.slicer.org/u/seanchoi0519)\
**Replies:** 18\
**Last updated:** [July 9, 2021, 3:07pm UTC](https://discourse.slicer.org/t/qslicermarkupsplacewidget-how-to-delete-all-mark-ups/18405 "2021-07-09T15:07:13Z")

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Trying to learn the qSlicerMarkupsPlaceWidget Class (Slicer: qSlicerMarkupsPlaceWidget Class Reference). Everything is good however I’d like to modify the delete button so that it deletes ALL mark-ups instead of just th…

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## [Do projection from polydata to a model surface](https://discourse.slicer.org/t/do-projection-from-polydata-to-a-model-surface/18451)

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**Author:** [@sandyaa0313](https://discourse.slicer.org/u/sandyaa0313)\
**Replies:** 6\
**Last updated:** [July 9, 2021, 2:56pm UTC](https://discourse.slicer.org/t/do-projection-from-polydata-to-a-model-surface/18451 "2021-07-09T14:56:56Z")

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Operating system: windows10 Slicer version:4.11.20200930 I want to do the orthogonal projection (or just the simplest projection) from a polydata array to a model surface. The input polydata is the edge of another mode…

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## [Model distorts when using logical operators](https://discourse.slicer.org/t/model-distorts-when-using-logical-operators/18576)

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**Author:** [@t0ons80](https://discourse.slicer.org/u/t0ons80)\
**Replies:** 4\
**Last updated:** [July 9, 2021, 2:50pm UTC](https://discourse.slicer.org/t/model-distorts-when-using-logical-operators/18576 "2021-07-09T14:50:26Z")

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Hello, I’m trying to create a mould using a dicom structure (as the hole) and an imported STL model as the mould itself. Currently I change the dicom structure into a binary label map, I then import an STL (the mould ca…

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## [Slicer models node number](https://discourse.slicer.org/t/slicer-models-node-number/18593)

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**Author:** [@F.A](https://discourse.slicer.org/u/F.A)\
**Replies:** 3\
**Last updated:** [July 9, 2021, 2:46pm UTC](https://discourse.slicer.org/t/slicer-models-node-number/18593 "2021-07-09T14:46:39Z")

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Hi, I have been using 3D Slicer to create a FE model from CT images. I meshed the model and used “probe volume with model” module to get HU and coordinates of each node. I imported the probe’s output to Abaqus using Para…

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## [Save ultrasound images in mha format](https://discourse.slicer.org/t/save-ultrasound-images-in-mha-format/18449)

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**Author:** [@Qianqian\_Cai](https://discourse.slicer.org/u/Qianqian_Cai)\
**Replies:** 3\
**Last updated:** [July 9, 2021, 2:42pm UTC](https://discourse.slicer.org/t/save-ultrasound-images-in-mha-format/18449 "2021-07-09T14:42:18Z")

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I loaded my ultrasound frames with the “load data” button and tried to save them with the “save data” button but it doesn’t give the option to save as .mha file. I checked the format of mha file or mhd file. It looks th…

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## [Set "by default view" after SetSliceToRASByNTP](https://discourse.slicer.org/t/set-by-default-view-after-setslicetorasbyntp/18601)

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**Author:** [@siaeleni](https://discourse.slicer.org/u/siaeleni)\
**Replies:** 1\
**Last updated:** [July 9, 2021, 2:38pm UTC](https://discourse.slicer.org/t/set-by-default-view-after-setslicetorasbyntp/18601 "2021-07-09T14:38:04Z")

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Hello, I set SetSliceToRASByNTP to set a different view for a specific purpose. My question is: Is there any way to go back to the “by default” view after setting a different one? Does SetOrientationToDefault() would …

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## [PET SUV with labels](https://discourse.slicer.org/t/pet-suv-with-labels/18496)

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**Author:** [@Josef\_Yu](https://discourse.slicer.org/u/Josef_Yu)\
**Replies:** 3\
**Last updated:** [July 9, 2021, 11:49am UTC](https://discourse.slicer.org/t/pet-suv-with-labels/18496 "2021-07-09T11:49:37Z")

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Hi people, I was trying to figure out, how the easiest way, I can readout the SUV values (mean, max) of PET images. After segmentation, which are saved in the packaged file .mrb, I tried PET indic, but fail to choose t…

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## [New "Apply to all segments" checkbox available in "Margin", "Hollow", "Smoothing" and "Scissors" effect](https://discourse.slicer.org/t/new-apply-to-all-segments-checkbox-available-in-margin-hollow-smoothing-and-scissors-effect/18587)

<div class="topic-metadata">

**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 1\
**Last updated:** [July 9, 2021, 7:39am UTC](https://discourse.slicer.org/t/new-apply-to-all-segments-checkbox-available-in-margin-hollow-smoothing-and-scissors-effect/18587 "2021-07-09T07:39:08Z")

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As a result of ideas born during the 35th Project Week, a new "Apply to all segment checkbox was implemented in the “Margin”, “Hollow”, “Smoothing”, and “Scissors” effects of Slicer’s Segment Editor. By checking thi…

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## [How to change slicer splash screen and loading screen?](https://discourse.slicer.org/t/how-to-change-slicer-splash-screen-and-loading-screen/18598)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [July 9, 2021, 6:06am UTC](https://discourse.slicer.org/t/how-to-change-slicer-splash-screen-and-loading-screen/18598 "2021-07-09T06:06:09Z")

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I am trying to change slicer splash screen and loading screen. When I replaced the splash image with another image it worked. But the loading screen image is not changing. I replaced the watermark image too. That didn’t …

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## [How to change origin of dicom to 0,0,0 in RAS?](https://discourse.slicer.org/t/how-to-change-origin-of-dicom-to-0-0-0-in-ras/18567)

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**Author:** [@akshay\_pillai](https://discourse.slicer.org/u/akshay_pillai)\
**Replies:** 4\
**Last updated:** [July 9, 2021, 5:51am UTC](https://discourse.slicer.org/t/how-to-change-origin-of-dicom-to-0-0-0-in-ras/18567 "2021-07-09T05:51:25Z")

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Operating system: windows 10 I want to use a set of dicoms as input for image processing using deep learning models and in order for me to feed these images I want them all to have the same orientation. All my dicom fil…

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