# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=98

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

**Page:** 99

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## [Intersection lines not show up](https://discourse.slicer.org/t/intersection-lines-not-show-up/35851)

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**Author:** [@Ben\_Fong](https://discourse.slicer.org/u/Ben_Fong)\
**Replies:** 7\
**Last updated:** [May 2, 2024, 12:57pm UTC](https://discourse.slicer.org/t/intersection-lines-not-show-up/35851 "2024-05-02T12:57:15Z")

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I am a novice user. I tried “basic + intersection” or “small basic + intersection”, the crosshair showed up, but the intersection did not, what should I do? Please help. Thanks. (Windows 10 & Mac Sonoma, version 5.6.2).

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## [Not able to select masks for registration in elastix](https://discourse.slicer.org/t/not-able-to-select-masks-for-registration-in-elastix/35870)

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**Author:** [@Chih-Ying-Huang](https://discourse.slicer.org/u/Chih-Ying-Huang)\
**Replies:** 0\
**Last updated:** [May 2, 2024, 12:48pm UTC](https://discourse.slicer.org/t/not-able-to-select-masks-for-registration-in-elastix/35870 "2024-05-02T12:48:34Z")

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Operating system: Windows10 Slicer version: 5.6.2 Expected behavior: Registration between 2 abdominal CT image with masks Actual behavior: After import my binary mask as segmentations in slicer, I was not able to fin…

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## [I need help to count number of pixels](https://discourse.slicer.org/t/i-need-help-to-count-number-of-pixels/35865)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 0\
**Last updated:** [May 2, 2024, 8:24am UTC](https://discourse.slicer.org/t/i-need-help-to-count-number-of-pixels/35865 "2024-05-02T08:24:23Z")

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i finally i segmented ct cubic dicom file in 3d box there is output segmented image there is extra circle i put in this image i need to segment extra line in image after i want to count number of pixel of air(black) a…

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## [2D image of .dcm file to 3D Volume](https://discourse.slicer.org/t/2d-image-of-dcm-file-to-3d-volume/12771)

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**Author:** [@Madelene\_Habib](https://discourse.slicer.org/u/Madelene_Habib)\
**Replies:** 9\
**Last updated:** [May 2, 2024, 12:50am UTC](https://discourse.slicer.org/t/2d-image-of-dcm-file-to-3d-volume/12771 "2024-05-02T00:50:26Z")

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Hi, I’ve received a .dcm file that only displays on the axial view as a 2D image of a sonogram. Is it possible to convert this into a 3D volume for segmentation? I’ve tried increasing the volumes using the Volumes modul…

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## [Get US whole volume reconstruction](https://discourse.slicer.org/t/get-us-whole-volume-reconstruction/35661)

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**Author:** [@LeidyMoraV](https://discourse.slicer.org/u/LeidyMoraV)\
**Replies:** 4\
**Last updated:** [May 1, 2024, 9:37pm UTC](https://discourse.slicer.org/t/get-us-whole-volume-reconstruction/35661 "2024-05-01T21:37:19Z")

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Hi, I want to reconstruct the whole vertebrae volume based on the ultrasound reconstruction (Img 1). for this I’m using the module ALPACA-SlicerMorph having as source other vertebrae reconstructed from CT(Img. 2), but w…

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## [Segmentation have CT dicom file of 238 slices of cubic and there is only 2 density in cu](https://discourse.slicer.org/t/segmentation-have-ct-dicom-file-of-238-slices-of-cubic-and-there-is-only-2-density-in-cu/35845)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 1\
**Last updated:** [May 1, 2024, 7:02pm UTC](https://discourse.slicer.org/t/segmentation-have-ct-dicom-file-of-238-slices-of-cubic-and-there-is-only-2-density-in-cu/35845 "2024-05-01T19:02:18Z")

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i have CT dicom file of 238 slices of cubic and there is only 2 density in cubic 1st is Air and 2nd is lattice , so i want to segment lattice and air or convert into volume image can anybody help me please , after i …

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## [3D image comparison](https://discourse.slicer.org/t/3d-image-comparison/35847)

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**Author:** [@Miri\_Trope](https://discourse.slicer.org/u/Miri_Trope)\
**Replies:** 2\
**Last updated:** [May 1, 2024, 6:19pm UTC](https://discourse.slicer.org/t/3d-image-comparison/35847 "2024-05-01T18:19:48Z")

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Hi, sorry if this question has been asked frequently, but I’ve been unable to find a satisfactory answer. Here’s my question: I have two 3D MRI images from different years for the same patient, and I want to assess wheth…

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## [Pop-up window not working on Bone Angle Meter](https://discourse.slicer.org/t/pop-up-window-not-working-on-bone-angle-meter/35848)

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**Author:** [@Rosamv](https://discourse.slicer.org/u/Rosamv)\
**Replies:** 4\
**Last updated:** [May 1, 2024, 1:12pm UTC](https://discourse.slicer.org/t/pop-up-window-not-working-on-bone-angle-meter/35848 "2024-05-01T13:12:31Z")

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Hello, I am using the Bone Angle Meter plug-in, which requires that a pop-up window be created when the measurements right/left function is called upon. Unfortunately, the pop-up window does not show up on my MacBook Pr…

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## [How to get the boundary/edges of organs instead of the filled with color?](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836)

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**Author:** [@Js165](https://discourse.slicer.org/u/Js165)\
**Replies:** 7\
**Last updated:** [May 1, 2024, 4:06am UTC](https://discourse.slicer.org/t/how-to-get-the-boundary-edges-of-organs-instead-of-the-filled-with-color/26836 "2024-05-01T04:06:25Z")

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How to get the boundary/edges of organs instead of the filled with color?

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## [Find absolute shortest distance between 2 objects](https://discourse.slicer.org/t/find-absolute-shortest-distance-between-2-objects/35842)

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**Author:** [@bw3232](https://discourse.slicer.org/u/bw3232)\
**Replies:** 0\
**Last updated:** [April 30, 2024, 11:06pm UTC](https://discourse.slicer.org/t/find-absolute-shortest-distance-between-2-objects/35842 "2024-04-30T23:06:37Z")

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I am trying to take measurements, finding the absolute shortest distance between two objects on a CT scan. I have been scrolling to find what appears to be the closest point, but is there a way to use segmentation to fin…

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## [Error when Performing Registration in Slicelets \> Gel Dosimetry Analysis](https://discourse.slicer.org/t/error-when-performing-registration-in-slicelets-gel-dosimetry-analysis/35478)

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**Author:** [@sieunmiin96](https://discourse.slicer.org/u/sieunmiin96)\
**Replies:** 1\
**Last updated:** [April 30, 2024, 12:10pm UTC](https://discourse.slicer.org/t/error-when-performing-registration-in-slicelets-gel-dosimetry-analysis/35478 "2024-04-30T12:10:59Z")

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I’m trying to perform gamma analysis of my data, but every time I press perform registration in 2.1 Register planning CT to CBCT of Gel Dosimetry Analysis under Slicelet, nothing happens and the loading icon by the mouse…

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## [How to get the position of the DICOM from the Mesh generated?](https://discourse.slicer.org/t/how-to-get-the-position-of-the-dicom-from-the-mesh-generated/35804)

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**Author:** [@guilherme-francisco](https://discourse.slicer.org/u/guilherme-francisco)\
**Replies:** 5\
**Last updated:** [April 30, 2024, 2:34am UTC](https://discourse.slicer.org/t/how-to-get-the-position-of-the-dicom-from-the-mesh-generated/35804 "2024-04-30T02:34:18Z")

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I’d like to know how the 3D Slicer gets the position of the CT images from the position of the 3d model generated. Exactly like the following image: Thanks in advance!

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## [Trouble loading vff file](https://discourse.slicer.org/t/trouble-loading-vff-file/35608)

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**Author:** [@sieunmiin96](https://discourse.slicer.org/u/sieunmiin96)\
**Replies:** 4\
**Last updated:** [April 29, 2024, 5:39pm UTC](https://discourse.slicer.org/t/trouble-loading-vff-file/35608 "2024-04-29T17:39:40Z")

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When I try to import my vff file into 3D slicer, I get the following error message: LoadVffFile: The values for the origin must each be greater than or equal to 0. LoadVffFile: Incorrect parameters or required paramete…

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## [How to make a portable slicer with Monai Auto3Dseg extension](https://discourse.slicer.org/t/how-to-make-a-portable-slicer-with-monai-auto3dseg-extension/35815)

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**Author:** [@Osson4](https://discourse.slicer.org/u/Osson4)\
**Replies:** 1\
**Last updated:** [April 29, 2024, 8:44pm UTC](https://discourse.slicer.org/t/how-to-make-a-portable-slicer-with-monai-auto3dseg-extension/35815 "2024-04-29T20:44:26Z")

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Using the latest preview of slicer (5.7.0 revision 32834 built 2024-04-28) on a Windows system, I would like to try the new extension on a offline, hospital computer with limited space and writing rights but with good GP…

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## [Segmentation by threshold and surrounding segment](https://discourse.slicer.org/t/segmentation-by-threshold-and-surrounding-segment/35729)

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**Author:** [@FraP](https://discourse.slicer.org/u/FraP)\
**Replies:** 6\
**Last updated:** [April 29, 2024, 8:01pm UTC](https://discourse.slicer.org/t/segmentation-by-threshold-and-surrounding-segment/35729 "2024-04-29T20:01:25Z")

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I would like to close the lumen of vessels of which I am able to select (partially or completely) the wall, having a solid cylinder and not hollow tube. However, the colour of the lumen is similar to that surrounding the…

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## [Suggested change to the Markups module- multiple export](https://discourse.slicer.org/t/suggested-change-to-the-markups-module-multiple-export/35658)

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**Author:** [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)\
**Replies:** 9\
**Last updated:** [April 29, 2024, 7:11pm UTC](https://discourse.slicer.org/t/suggested-change-to-the-markups-module-multiple-export/35658 "2024-04-29T19:11:43Z")

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Hi all, In my cursory search, I did not find older posts suggesting this, so I thought it would be nice to bring it up. @lassoan would it be possible to add an additional export selection or option to the Markups module…

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## [Automatize model generation from segmentation](https://discourse.slicer.org/t/automatize-model-generation-from-segmentation/35355)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 5\
**Last updated:** [April 29, 2024, 4:20pm UTC](https://discourse.slicer.org/t/automatize-model-generation-from-segmentation/35355 "2024-04-29T16:20:30Z")

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Hi, I would like to automatically generate 3D-models from segmented 3D-data. The segmented data is stored as \*.nrrd, and the segmentation was performed with an external program. The idea is to store the segmented dat…

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## [How to do skull stripping using SwissSkullStriper Extension](https://discourse.slicer.org/t/how-to-do-skull-stripping-using-swissskullstriper-extension/35799)

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**Author:** [@dorsa](https://discourse.slicer.org/u/dorsa)\
**Replies:** 1\
**Last updated:** [April 29, 2024, 2:15pm UTC](https://discourse.slicer.org/t/how-to-do-skull-stripping-using-swissskullstriper-extension/35799 "2024-04-29T14:15:51Z")

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Hi All, I’m trying to process Brain MRI images. and the first thing I would like to is to remove the Skull using the SwissSkullstripping extension but Unfortunately I can’t find any guide on how to do it from scratch an…

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## [Create standard terminology for new segmentation project](https://discourse.slicer.org/t/create-standard-terminology-for-new-segmentation-project/35798)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 9\
**Last updated:** [April 26, 2024, 3:52pm UTC](https://discourse.slicer.org/t/create-standard-terminology-for-new-segmentation-project/35798 "2024-04-26T15:52:21Z")

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The key is to use a project-independent, universal, archival quality segmentation file format. For example, .seg.nrrd file with terminology or DICOM Segmentation Object can both fulfill this role. You can perform a ver…

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## [Help with setting up MONAILabel](https://discourse.slicer.org/t/help-with-setting-up-monailabel/35796)

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**Author:** [@diazandr3s](https://discourse.slicer.org/u/diazandr3s)\
**Replies:** 1\
**Last updated:** [April 29, 2024, 8:44am UTC](https://discourse.slicer.org/t/help-with-setting-up-monailabel/35796 "2024-04-29T08:44:13Z")

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I have a problem with Monai label. With great difficulty I installed succesfully the Monai Label, so everything is ok, I able to connect to the server in the Slicer extension. My big problem is, that I want to use the Ta…

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## [Dose comparison module](https://discourse.slicer.org/t/dose-comparison-module/35665)

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**Author:** [@azam](https://discourse.slicer.org/u/azam)\
**Replies:** 1\
**Last updated:** [April 29, 2024, 11:43am UTC](https://discourse.slicer.org/t/dose-comparison-module/35665 "2024-04-29T11:43:57Z")

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Hi every one slicer version: 5.2.2 I have 2 RT Dos exported from the treatment planning system. I want to compare these 2 dose distributions using the Dose Comparison module in 3 D slicer. my CT slice thickness is 5mm…

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## [Pulmonary vessels segmentation with MONAI](https://discourse.slicer.org/t/pulmonary-vessels-segmentation-with-monai/35788)

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**Author:** [@Killmaro](https://discourse.slicer.org/u/Killmaro)\
**Replies:** 0\
**Last updated:** [April 29, 2024, 5:42am UTC](https://discourse.slicer.org/t/pulmonary-vessels-segmentation-with-monai/35788 "2024-04-29T05:42:45Z")

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Hi All By selecting MONAI’s automatic segmentation “lung” tool I obtain this result, which is rather satisfactory, however there is significant aliasing. Is there a way to modify the sampling settings to obtain a model …

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## [Question about system requirements on Mac](https://discourse.slicer.org/t/question-about-system-requirements-on-mac/35784)

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**Author:** [@Rosamv](https://discourse.slicer.org/u/Rosamv)\
**Replies:** 2\
**Last updated:** [April 28, 2024, 8:56pm UTC](https://discourse.slicer.org/t/question-about-system-requirements-on-mac/35784 "2024-04-28T20:56:57Z")

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Hello, I am new to Slicer and recently downloaded the software to use a bone measurement plugin (Bone Angle Meter). I am having trouble with the software running very slow during 3D rendering manipulations, to the point…

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## [Json markups colors do not work](https://discourse.slicer.org/t/json-markups-colors-do-not-work/35739)

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**Author:** [@FatihSogukpinar](https://discourse.slicer.org/u/FatihSogukpinar)\
**Replies:** 8\
**Last updated:** [April 28, 2024, 5:37pm UTC](https://discourse.slicer.org/t/json-markups-colors-do-not-work/35739 "2024-04-28T17:37:39Z")

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Hi all, I am trying to show a bunch of markup points using json file. The points are being loaded, and their positions are correct. However, I am also trying to set their colors and sizes, but somehow, slicer uses the d…

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## [Generate animations easily based on keyframes in Slicer](https://discourse.slicer.org/t/generate-animations-easily-based-on-keyframes-in-slicer/35778)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 0\
**Last updated:** [April 28, 2024, 4:01am UTC](https://discourse.slicer.org/t/generate-animations-easily-based-on-keyframes-in-slicer/35778 "2024-04-28T04:01:36Z")

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SlicerMorph has a module called Animator that allows creating movies that are not possible to do with default Screen Capture module. eg. It includes things like cropping volumes, interpolating between diffe…

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## [Exporting a segmentation paired to a custom colortable](https://discourse.slicer.org/t/exporting-a-segmentation-paired-to-a-custom-colortable/35719)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 8\
**Last updated:** [April 27, 2024, 10:20pm UTC](https://discourse.slicer.org/t/exporting-a-segmentation-paired-to-a-custom-colortable/35719 "2024-04-27T22:20:08Z")

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Hi, I’ve been reading the threads about naming/numbering and the colormaps for segmentations: Export Segmentation as Labeled LabelMap Copying segment names/colors from one segmentation to another I am not sure to be …

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## [Point on 2D CT slice image to RAS coordinate transformation](https://discourse.slicer.org/t/point-on-2d-ct-slice-image-to-ras-coordinate-transformation/35770)

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**Author:** [@joanne40226](https://discourse.slicer.org/u/joanne40226)\
**Replies:** 0\
**Last updated:** [April 27, 2024, 12:57pm UTC](https://discourse.slicer.org/t/point-on-2d-ct-slice-image-to-ras-coordinate-transformation/35770 "2024-04-27T12:57:38Z")

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Hi community, I encounter problems when doing point on 2D CT slice image to RAS coordinate. I have screen shot an 2D CT image as shown below. i check some imformation for example the actual size of the image in mm is :…

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## [Broken centerline model with continuous voronoi diagram](https://discourse.slicer.org/t/broken-centerline-model-with-continuous-voronoi-diagram/35755)

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**Author:** [@ruili](https://discourse.slicer.org/u/ruili)\
**Replies:** 3\
**Last updated:** [April 27, 2024, 11:36am UTC](https://discourse.slicer.org/t/broken-centerline-model-with-continuous-voronoi-diagram/35755 "2024-04-27T11:36:08Z")

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Hello, I have been using the Extract Centerline module to extract the centerlines from some vessel segmentation. However, I have been struggling to get a fully connected centerline model even though the segmentation is …

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## [Slicer 3D view not displaying labels of markup curves properly](https://discourse.slicer.org/t/slicer-3d-view-not-displaying-labels-of-markup-curves-properly/34364)

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**Author:** [@ruili](https://discourse.slicer.org/u/ruili)\
**Replies:** 5\
**Last updated:** [April 26, 2024, 4:16pm UTC](https://discourse.slicer.org/t/slicer-3d-view-not-displaying-labels-of-markup-curves-properly/34364 "2024-04-26T16:16:40Z")

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Hello, I am writing to report what seems to be a bug with the labelling of centerline curves or markup curves in general in the 3D view. The details of this bug can be found in a previous discussion here. But to summari…

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## [Cannot find Slicer Radiomics in extensions library](https://discourse.slicer.org/t/cannot-find-slicer-radiomics-in-extensions-library/35749)

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**Author:** [@Celina\_Hallal](https://discourse.slicer.org/u/Celina_Hallal)\
**Replies:** 1\
**Last updated:** [April 26, 2024, 2:49pm UTC](https://discourse.slicer.org/t/cannot-find-slicer-radiomics-in-extensions-library/35749 "2024-04-26T14:49:23Z")

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I’m trying to install Radiomics extension, but I can’t find it. Tried to install from file also, with no success. I’m currently using v5.7-2024-04-22 in a MacOS. Thanks in advance!

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