# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=46

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

**Page:** 47

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## [Imported volumes are not aligned](https://discourse.slicer.org/t/imported-volumes-are-not-aligned/42235)

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**Author:** [@Aidan](https://discourse.slicer.org/u/Aidan)\
**Replies:** 4\
**Last updated:** [March 26, 2025, 10:10pm UTC](https://discourse.slicer.org/t/imported-volumes-are-not-aligned/42235 "2025-03-26T22:10:39Z")

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Hi, I have a very basic issue that I can’t seem to figure out. When I import 2 different NIFTI volumes of the same subject from the same session in Slicer (one is an anatomical 3D MR volume and the other is a function EP…

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## [Burn colorful models into 3d volume and export as DICOM series](https://discourse.slicer.org/t/burn-colorful-models-into-3d-volume-and-export-as-dicom-series/42316)

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**Author:** [@Bahram\_Zargar](https://discourse.slicer.org/u/Bahram_Zargar)\
**Replies:** 2\
**Last updated:** [March 26, 2025, 5:12pm UTC](https://discourse.slicer.org/t/burn-colorful-models-into-3d-volume-and-export-as-dicom-series/42316 "2025-03-26T17:12:15Z")

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Using 3rd party software, I get some volumes and then import them to Slicer as models indifferent colors. I get them all as following in slicer; How could I can export a colorful dicom series with all of those models…

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## [Using matplotlib for voxel by voxel SUV plot](https://discourse.slicer.org/t/using-matplotlib-for-voxel-by-voxel-suv-plot/42315)

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**Author:** [@CSalt](https://discourse.slicer.org/u/CSalt)\
**Replies:** 3\
**Last updated:** [March 26, 2025, 4:18pm UTC](https://discourse.slicer.org/t/using-matplotlib-for-voxel-by-voxel-suv-plot/42315 "2025-03-26T16:18:23Z")

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I have a segmented PET scan for which I am trying to display voxel by voxel SUV data. I am using the Python console in Slicer and was able to code everything I need, but ran into the error: :1: UserWarning: FigureCanvas…

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## [Is BoneTexture Extension abandoned?](https://discourse.slicer.org/t/is-bonetexture-extension-abandoned/39711)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [March 26, 2025, 1:19pm UTC](https://discourse.slicer.org/t/is-bonetexture-extension-abandoned/39711 "2025-03-26T13:19:25Z")

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A colleague of mine needs to use this extension, and it appears that it hasn’t been functioning since v5.0.3. I tried to download that specific release, but the extension catalogue is empty (no extensions are shown). Th…

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## [New Segment Statistics: Oriented Bounding Box, Diameter and More](https://discourse.slicer.org/t/new-segment-statistics-oriented-bounding-box-diameter-and-more/10203)

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**Author:** [@Sunderlandkyl](https://discourse.slicer.org/u/Sunderlandkyl)\
**Replies:** 5\
**Last updated:** [July 21, 2023, 5:50pm UTC](https://discourse.slicer.org/t/new-segment-statistics-oriented-bounding-box-diameter-and-more/10203 "2023-07-21T17:50:32Z")

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New statistics have been added to the Segment Statistics module: Centroid Oriented bounding box Feret diameter Perimeter Roundness Flatness Elongation Principal axes/moments These statistics are not enabled by default…

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## [Segmentation in Slicer extremely slow when using the Scissors tool in slice view](https://discourse.slicer.org/t/segmentation-in-slicer-extremely-slow-when-using-the-scissors-tool-in-slice-view/41930)

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**Author:** [@Russell\_Engelman](https://discourse.slicer.org/u/Russell_Engelman)\
**Replies:** 18\
**Last updated:** [March 26, 2025, 3:25am UTC](https://discourse.slicer.org/t/segmentation-in-slicer-extremely-slow-when-using-the-scissors-tool-in-slice-view/41930 "2025-03-26T03:25:27Z")

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Operating System - Windows 10 Slicer 3D Version - 5.8.0 I am working with a dataset of a (cleaned, so no flesh) skull with the teeth in occlusion, so I have to separate the upper and lower jaws to get the morphological…

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## [How to change Dose (X-axis) increments on a Dose-Volume-Histogram?](https://discourse.slicer.org/t/how-to-change-dose-x-axis-increments-on-a-dose-volume-histogram/41505)

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**Author:** [@Jeremy\_Fockenier](https://discourse.slicer.org/u/Jeremy_Fockenier)\
**Replies:** 1\
**Last updated:** [March 25, 2025, 6:57pm UTC](https://discourse.slicer.org/t/how-to-change-dose-x-axis-increments-on-a-dose-volume-histogram/41505 "2025-03-25T18:57:59Z")

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Hello fellow Slicers, I am currently testing Monte-Carlo simulations on a synthetic lung with a proton beam (all input files are in DICOM) and am trying to output a DVH file. However, since the DVH program seems to only…

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## [How to make 3D Slicer load just a single DICOM file instead of automatically loading the full series?](https://discourse.slicer.org/t/how-to-make-3d-slicer-load-just-a-single-dicom-file-instead-of-automatically-loading-the-full-series/42299)

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**Author:** [@shahzadali](https://discourse.slicer.org/u/shahzadali)\
**Replies:** 3\
**Last updated:** [March 25, 2025, 5:57pm UTC](https://discourse.slicer.org/t/how-to-make-3d-slicer-load-just-a-single-dicom-file-instead-of-automatically-loading-the-full-series/42299 "2025-03-25T17:57:33Z")

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In 3D Slicer (v5.6.2), how can I restrict it to load only a single DICOM (.dcm) file without automatically loading the entire image series it belongs to? I’m trying to inspect just one particular slice, but Slicer keeps …

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## [Total Segmentator liver vasculature?](https://discourse.slicer.org/t/total-segmentator-liver-vasculature/41125)

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**Author:** [@moraleda](https://discourse.slicer.org/u/moraleda)\
**Replies:** 1\
**Last updated:** [March 25, 2025, 5:22pm UTC](https://discourse.slicer.org/t/total-segmentator-liver-vasculature/41125 "2025-03-25T17:22:49Z")

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Hi all, I remember that the previous version of Total Segmentator had an option to segment liver vessels and tumors. This option is not available anymore in v2. Could I somehow downgrade to v1 in the extension to use th…

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## [MorphoSource files not Opening](https://discourse.slicer.org/t/morphosource-files-not-opening/42290)

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**Author:** [@Vincent\_Girgenti](https://discourse.slicer.org/u/Vincent_Girgenti)\
**Replies:** 1\
**Last updated:** [March 25, 2025, 2:28pm UTC](https://discourse.slicer.org/t/morphosource-files-not-opening/42290 "2025-03-25T14:28:48Z")

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Hello! I’m new to 3d Slicer and am looking to use it for models from MorphoSource. I have downloaded the .zip folder and attempt to open it I’m not entirely sure what to do about it so if anyone has tips I’d apprecia…

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## [Vessel segmentation on version 5.8.1 for mac](https://discourse.slicer.org/t/vessel-segmentation-on-version-5-8-1-for-mac/42293)

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**Author:** [@AlexM](https://discourse.slicer.org/u/AlexM)\
**Replies:** 1\
**Last updated:** [March 25, 2025, 2:00pm UTC](https://discourse.slicer.org/t/vessel-segmentation-on-version-5-8-1-for-mac/42293 "2025-03-25T14:00:14Z")

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Hi, I am new to 3D slicer and am trying to segment the abdominal aorta for a study. I have installed the SegmentEditorExtraEffects and SlicerVMTK extensions, and have been following the instructions found in this youtu…

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## [Heat map two timepoint cbct comparison](https://discourse.slicer.org/t/heat-map-two-timepoint-cbct-comparison/42289)

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**Author:** [@Michelle\_cbo](https://discourse.slicer.org/u/Michelle_cbo)\
**Replies:** 0\
**Last updated:** [March 25, 2025, 12:40pm UTC](https://discourse.slicer.org/t/heat-map-two-timepoint-cbct-comparison/42289 "2025-03-25T12:40:47Z")

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Hello, I am interested in generating a heat map to visualize changes in certain structures (preoperation and postoperation) using registered cbct files (nii.gz). I tried model to model distance extension but it didn’t w…

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## [Getting measures off plane or ROI markups](https://discourse.slicer.org/t/getting-measures-off-plane-or-roi-markups/42269)

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**Author:** [@Jordan\_T](https://discourse.slicer.org/u/Jordan_T)\
**Replies:** 1\
**Last updated:** [March 24, 2025, 1:12pm UTC](https://discourse.slicer.org/t/getting-measures-off-plane-or-roi-markups/42269 "2025-03-24T13:12:50Z")

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Hi! I am fairly new to Slicer and I imagine there is an easy solution to this, but I cannot find it. I am trying to measure length and width of a condyle, but because the condyle bows out in places just getting the dis…

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## [Slicer module AREG - problem](https://discourse.slicer.org/t/slicer-module-areg-problem/41289)

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**Author:** [@Ender](https://discourse.slicer.org/u/Ender)\
**Replies:** 1\
**Last updated:** [March 24, 2025, 11:51am UTC](https://discourse.slicer.org/t/slicer-module-areg-problem/41289 "2025-03-24T11:51:13Z")

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I need help with the AREG module. I have footage before and after treatment. I created the DentalSegmenetator module, saving the files as NIFITI. Then, in the AREG module, before adding T1 and T2, the message “does not h…

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## [TotalSegmentator choose organs to be segmented](https://discourse.slicer.org/t/totalsegmentator-choose-organs-to-be-segmented/42270)

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**Author:** [@MihaiPomohaci](https://discourse.slicer.org/u/MihaiPomohaci)\
**Replies:** 0\
**Last updated:** [March 23, 2025, 8:43pm UTC](https://discourse.slicer.org/t/totalsegmentator-choose-organs-to-be-segmented/42270 "2025-03-23T20:43:41Z")

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Operating system: Windows 11 Slicer version: 5.8.1 Hello, First of all I would like to thank you guys for this app that makes my life so much easier, and also a huge thanks to the TotalSegmentator team! I am doing a …

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## [Cartilage/Ligament/Tendon Segmentation and Reconstruction from MRI](https://discourse.slicer.org/t/cartilage-ligament-tendon-segmentation-and-reconstruction-from-mri/42265)

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**Author:** [@ckr](https://discourse.slicer.org/u/ckr)\
**Replies:** 0\
**Last updated:** [March 23, 2025, 5:00pm UTC](https://discourse.slicer.org/t/cartilage-ligament-tendon-segmentation-and-reconstruction-from-mri/42265 "2025-03-23T17:00:11Z")

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Hi - I’m a completely new to 3D slicer person so any guidance would be helpful. I have a handful of whole body, knee, hip, shoulder, and elbow MRIs (with both T1/T2/PD sequences). I only care about the bones, articular c…

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## [Maxilla and mandibula segmentation with Dental Segmentator](https://discourse.slicer.org/t/maxilla-and-mandibula-segmentation-with-dental-segmentator/42254)

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**Author:** [@Orsolya\_Varga](https://discourse.slicer.org/u/Orsolya_Varga)\
**Replies:** 0\
**Last updated:** [March 22, 2025, 11:51am UTC](https://discourse.slicer.org/t/maxilla-and-mandibula-segmentation-with-dental-segmentator/42254 "2025-03-22T11:51:08Z")

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Hello! Do you have idea how to segmentate the CT differently with 3D slicer? I want to balse plate be a separate segment ( as maxilla, mandibula and nerve canal) I’m creating all on 4 surgical guide. Thx

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## [Bone recontruction planner help](https://discourse.slicer.org/t/bone-recontruction-planner-help/41202)

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**Author:** [@Enkh-Orchlon\_Batbaya](https://discourse.slicer.org/u/Enkh-Orchlon_Batbaya)\
**Replies:** 6\
**Last updated:** [March 21, 2025, 3:30pm UTC](https://discourse.slicer.org/t/bone-recontruction-planner-help/41202 "2025-03-21T15:30:04Z")

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Hello? How to resolve this problem? when I try to update fibula planner over fibula line, this error keeps coming? Thank you very much

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## [Save the reformat image in Slicer](https://discourse.slicer.org/t/save-the-reformat-image-in-slicer/24221)

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**Author:** [@Shahin](https://discourse.slicer.org/u/Shahin)\
**Replies:** 5\
**Last updated:** [March 21, 2025, 1:43pm UTC](https://discourse.slicer.org/t/save-the-reformat-image-in-slicer/24221 "2025-03-21T13:43:36Z")

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After spinning an image in different axes, how to save the reformatted image as a .nii file?

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## [Information regarding 3D Slicer for a literature review paper](https://discourse.slicer.org/t/information-regarding-3d-slicer-for-a-literature-review-paper/42153)

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**Author:** [@aronosterlund](https://discourse.slicer.org/u/aronosterlund)\
**Replies:** 2\
**Last updated:** [March 21, 2025, 9:50am UTC](https://discourse.slicer.org/t/information-regarding-3d-slicer-for-a-literature-review-paper/42153 "2025-03-21T09:50:25Z")

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Hey, I am writing a systematic review paper about body composition analysis (BCA) software tools for CT and MRI. The review is going to be published in a peer reviewed journal paper in addition to being a part of my bac…

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## [Split tolerance in two values in Guided Artery Segmentation Module](https://discourse.slicer.org/t/split-tolerance-in-two-values-in-guided-artery-segmentation-module/41059)

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**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\
**Replies:** 1\
**Last updated:** [March 20, 2025, 9:27pm UTC](https://discourse.slicer.org/t/split-tolerance-in-two-values-in-guided-artery-segmentation-module/41059 "2025-03-20T21:27:05Z")

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Hi! I was trying some Slicer’s modules and I found the Guided Artery Segmentation Module, which is truly interesting to segment specific zone with relative precision. To make it more functional, I’m thinking that split …

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## [Tutorial maker extension issues](https://discourse.slicer.org/t/tutorial-maker-extension-issues/42203)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [March 20, 2025, 5:06pm UTC](https://discourse.slicer.org/t/tutorial-maker-extension-issues/42203 "2025-03-20T17:06:40Z")

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Tutorial maker seems like a very useful module and would like to give a try, but I can’t seem to get it to work on preview using the example on the source repo. My interface doesn’t look like the example. There is no run…

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## ["Application has run out of memory"](https://discourse.slicer.org/t/application-has-run-out-of-memory/42154)

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**Author:** [@TChild](https://discourse.slicer.org/u/TChild)\
**Replies:** 4\
**Last updated:** [March 20, 2025, 4:15pm UTC](https://discourse.slicer.org/t/application-has-run-out-of-memory/42154 "2025-03-20T16:15:32Z")

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Operating system: Microsoft Windows Slicer version: 5.8.1 Expected behavior: File saving when “Save” is pressed; able to edit/mark scene Actual behavior: On four different normally working computers, an error message …

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## [Module in different category in Slicer than in documentation](https://discourse.slicer.org/t/module-in-different-category-in-slicer-than-in-documentation/42218)

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**Author:** [@robertf](https://discourse.slicer.org/u/robertf)\
**Replies:** 4\
**Last updated:** [March 20, 2025, 1:04am UTC](https://discourse.slicer.org/t/module-in-different-category-in-slicer-than-in-documentation/42218 "2025-03-20T01:04:17Z")

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The modules Resample DTI Volume and Resample Scalar/Vector/DWI Volume are under Diffusion \> Utilities in the Slicer GUI, but are under Converters at Modules — 3D Slicer documentation. Is that intentional? Am I missing s…

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## [Segment Editor: Draw Tube - it makes octagonal prisms instead of smooth cylinders](https://discourse.slicer.org/t/segment-editor-draw-tube-it-makes-octagonal-prisms-instead-of-smooth-cylinders/42223)

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**Author:** [@bobcieri](https://discourse.slicer.org/u/bobcieri)\
**Replies:** 2\
**Last updated:** [March 19, 2025, 8:19pm UTC](https://discourse.slicer.org/t/segment-editor-draw-tube-it-makes-octagonal-prisms-instead-of-smooth-cylinders/42223 "2025-03-19T20:19:31Z")

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I am using the draw tube feature in the segment editor. It is great, except that it is drawing octagonal prisms instead of cylinders/tubes. This is much more apparent when the radius is increased to above 10. Can the num…

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## [Use of displacementJacobianFilter](https://discourse.slicer.org/t/use-of-displacementjacobianfilter/42220)

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**Author:** [@Posiz](https://discourse.slicer.org/u/Posiz)\
**Replies:** 1\
**Last updated:** [March 19, 2025, 8:17pm UTC](https://discourse.slicer.org/t/use-of-displacementjacobianfilter/42220 "2025-03-19T20:17:54Z")

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Hi experts. I am trying to use the displacementJacobianFilter within simple filters for a displacement field obtained from a deformable registration. The problem is that it seems that the simple filter does not accept v…

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## [Locking a segment for edits](https://discourse.slicer.org/t/locking-a-segment-for-edits/35156)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 10\
**Last updated:** [March 19, 2025, 6:57pm UTC](https://discourse.slicer.org/t/locking-a-segment-for-edits/35156 "2025-03-19T18:57:37Z")

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Would it be possible to implement a function that will lock a segment for further edits (regardless whether it is set to visible or not, and overriding all other editable area settings)? Sometimes I overlook my editable…

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## [Issue with Installing Extensions in Slicer Custom App](https://discourse.slicer.org/t/issue-with-installing-extensions-in-slicer-custom-app/42214)

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**Author:** [@software](https://discourse.slicer.org/u/software)\
**Replies:** 2\
**Last updated:** [March 19, 2025, 6:58pm UTC](https://discourse.slicer.org/t/issue-with-installing-extensions-in-slicer-custom-app/42214 "2025-03-19T18:58:10Z")

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I turned Slicer\_BUILD\_EXTENSIONMANAGER\_SUPPORT ON in the top-level CMakeLists.txt, then configured and generated the project using CMake GUI. After that, I opened the project from CMake GUI in Visual Studio and built All…

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## [Segmentation File saving as 4 dimensions in new version instead of 3](https://discourse.slicer.org/t/segmentation-file-saving-as-4-dimensions-in-new-version-instead-of-3/42224)

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**Author:** [@acoggins](https://discourse.slicer.org/u/acoggins)\
**Replies:** 5\
**Last updated:** [March 19, 2025, 6:52pm UTC](https://discourse.slicer.org/t/segmentation-file-saving-as-4-dimensions-in-new-version-instead-of-3/42224 "2025-03-19T18:52:52Z")

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Using the new version of slicer my segmentation files (.seg.nrrd) are saving as 4 dimensions: dimension: 4 space: left-posterior-superior sizes: 2 512 512 156 In previous versions, my segmentation files save as 3 dim…

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## [Converting a set of dicom files of one serie to nrrd using python API](https://discourse.slicer.org/t/converting-a-set-of-dicom-files-of-one-serie-to-nrrd-using-python-api/26387)

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**Author:** [@Leyla\_Ebrahimpour](https://discourse.slicer.org/u/Leyla_Ebrahimpour)\
**Replies:** 9\
**Last updated:** [March 19, 2025, 5:13pm UTC](https://discourse.slicer.org/t/converting-a-set-of-dicom-files-of-one-serie-to-nrrd-using-python-api/26387 "2025-03-19T17:13:42Z")

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Hi. I wonder if anyone can help me with this. I am using about 400 studies (each study includes couple of series. The DICOM SEG file is also included. Imagine that I have downloaded all the data and I have found the seri…

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