# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=131

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

**Page:** 132

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## [Maximum intensity projection video](https://discourse.slicer.org/t/maximum-intensity-projection-video/32568)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 5\
**Last updated:** [November 8, 2023, 11:20am UTC](https://discourse.slicer.org/t/maximum-intensity-projection-video/32568 "2023-11-08T11:20:53Z")

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I don’t use the maximum intensity projection mode very much, but this animation has a really strange artifact. I can’t quite tell whether it is spinning clockwise or counterclockwise after a while (it was supposed to be …

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## [Distorted DICOM images](https://discourse.slicer.org/t/distorted-dicom-images/32638)

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**Author:** [@willi](https://discourse.slicer.org/u/willi)\
**Replies:** 3\
**Last updated:** [November 7, 2023, 10:33pm UTC](https://discourse.slicer.org/t/distorted-dicom-images/32638 "2023-11-07T22:33:48Z")

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Hi all, I have a problem loading some DICOM images recorded as slices of the coronal plane where the axial images show up distorted. Let me give some more information. I have MRI scans of the femur with two different s…

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## [Strange air pockets in segmentation editor, can't mark air pockets as apart of segmentation.](https://discourse.slicer.org/t/strange-air-pockets-in-segmentation-editor-cant-mark-air-pockets-as-apart-of-segmentation/32640)

<div class="topic-metadata">

**Author:** [@GunnarE](https://discourse.slicer.org/u/GunnarE)\
**Replies:** 2\
**Last updated:** [November 7, 2023, 6:18pm UTC](https://discourse.slicer.org/t/strange-air-pockets-in-segmentation-editor-cant-mark-air-pockets-as-apart-of-segmentation/32640 "2023-11-07T18:18:19Z")

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Hi everyone, I seem to have ran into a bug, when using segmentation editor to segment a head in MRI data, I get these air pockets that are not included in segmentation. The goal is to use this segmentation to construct …

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## [Color scheme spontanous change](https://discourse.slicer.org/t/color-scheme-spontanous-change/32617)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 3\
**Last updated:** [November 6, 2023, 5:34pm UTC](https://discourse.slicer.org/t/color-scheme-spontanous-change/32617 "2023-11-06T17:34:15Z")

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i have been noticing this unusual behavior for over 6 months, where the color of volume rendering changes on its own upon saving and opening the file again. it usually gets to this dark scheme. It is not always happenin…

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## [Missing ACPC module 5.4](https://discourse.slicer.org/t/missing-acpc-module-5-4/32586)

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**Author:** [@DennisEx81](https://discourse.slicer.org/u/DennisEx81)\
**Replies:** 2\
**Last updated:** [November 6, 2023, 5:04pm UTC](https://discourse.slicer.org/t/missing-acpc-module-5-4/32586 "2023-11-06T17:04:15Z")

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Hello, Does anyone know what happened to the ACPC transform module in 5.4? Can’t find it under specialized where it used to be. Also tried to install SlicerNeuro but it simply crashed slicer after restart. Thanks

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## [Output the color map of my DICOM file](https://discourse.slicer.org/t/output-the-color-map-of-my-dicom-file/32627)

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**Author:** [@jp\_jp\_jp](https://discourse.slicer.org/u/jp_jp_jp)\
**Replies:** 0\
**Last updated:** [November 6, 2023, 5:01pm UTC](https://discourse.slicer.org/t/output-the-color-map-of-my-dicom-file/32627 "2023-11-06T17:01:51Z")

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Hi, I want to use the color map of my DICOM (different window/level) for my plot of another simulation (visualized in Paraview). So that I can know is my simulation results valid or not, can anyone tell me where to find…

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## [Tool bar options](https://discourse.slicer.org/t/tool-bar-options/32619)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 3\
**Last updated:** [November 6, 2023, 4:55pm UTC](https://discourse.slicer.org/t/tool-bar-options/32619 "2023-11-06T16:55:30Z")

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it would be great if the toolbar could be customizable for the volume rendering module and segmentation module similar to the markup module. would save a lot of back and forth.

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## [Export dcm as a single file](https://discourse.slicer.org/t/export-dcm-as-a-single-file/32618)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 1\
**Last updated:** [November 6, 2023, 3:54pm UTC](https://discourse.slicer.org/t/export-dcm-as-a-single-file/32618 "2023-11-06T15:54:19Z")

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is it possible to export dicom as a single file rather than a directory? thanks

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## [Report a problem with converting stl to nrrd](https://discourse.slicer.org/t/report-a-problem-with-converting-stl-to-nrrd/32620)

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**Author:** [@Chuan](https://discourse.slicer.org/u/Chuan)\
**Replies:** 1\
**Last updated:** [November 6, 2023, 3:47pm UTC](https://discourse.slicer.org/t/report-a-problem-with-converting-stl-to-nrrd/32620 "2023-11-06T15:47:53Z")

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Hi, I would like to report a problem with converting stl file to nrrd.file. The red figure is my stl file of a skeleton model. I would like to convert it to nrrd file, and my process is right click my stl model, and ch…

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## [Cannot save DICOM to NRRD files](https://discourse.slicer.org/t/cannot-save-dicom-to-nrrd-files/32609)

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**Author:** [@maiseld](https://discourse.slicer.org/u/maiseld)\
**Replies:** 3\
**Last updated:** [November 6, 2023, 5:45am UTC](https://discourse.slicer.org/t/cannot-save-dicom-to-nrrd-files/32609 "2023-11-06T05:45:00Z")

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After loading in all of the DICOM files into Slicer, I click to save but do not have the option of saving into NRRD files. I was following this guide: I just downloaded Slicer as of today so I should have the current v…

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## [How to use Python to add header content](https://discourse.slicer.org/t/how-to-use-python-to-add-header-content/32573)

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**Author:** [@sun-wanqing](https://discourse.slicer.org/u/sun-wanqing)\
**Replies:** 2\
**Last updated:** [November 6, 2023, 1:51am UTC](https://discourse.slicer.org/t/how-to-use-python-to-add-header-content/32573 "2023-11-06T01:51:05Z")

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I want to batch import matrices into nrrd. I added a new keys to the header, but it still cannot work. mhd\_path = path + f'\\{name}\\Segmentation\_1\_T1\_lumen.mhd' sitk\_image = sitk.ReadImage(mhd\_path) …

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## [3D registration of 3D microscopy images](https://discourse.slicer.org/t/3d-registration-of-3d-microscopy-images/32204)

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**Author:** [@ylcnkzy](https://discourse.slicer.org/u/ylcnkzy)\
**Replies:** 3\
**Last updated:** [November 5, 2023, 6:13pm UTC](https://discourse.slicer.org/t/3d-registration-of-3d-microscopy-images/32204 "2023-11-05T18:13:46Z")

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Greetings Everyone, In our lab, we have developed a methodology that allows us to stain the same sample for different biological targets at different time points, and enable us to visualize the same sample again and aga…

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## [Customize mouse scroll behavoir](https://discourse.slicer.org/t/customize-mouse-scroll-behavoir/32604)

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**Author:** [@pfrwilson](https://discourse.slicer.org/u/pfrwilson)\
**Replies:** 1\
**Last updated:** [November 4, 2023, 7:45pm UTC](https://discourse.slicer.org/t/customize-mouse-scroll-behavoir/32604 "2023-11-04T19:45:04Z")

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I have an ultrasound cineloop loaded as a sequence with a sequence browser in slicer. I would like to allow the user to be able to scroll through the cineloop playback by using the mouse wheel when hovering over the slic…

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## [Combine 2 ct volumes into one](https://discourse.slicer.org/t/combine-2-ct-volumes-into-one/32580)

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**Author:** [@mijelsan](https://discourse.slicer.org/u/mijelsan)\
**Replies:** 3\
**Last updated:** [November 3, 2023, 7:31pm UTC](https://discourse.slicer.org/t/combine-2-ct-volumes-into-one/32580 "2023-11-03T19:31:44Z")

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I have 2 ct of same patient of 2 half bodys overlapping, one from head to pelvis and second from pelvis to feet. I want to combine them into one, i’m going with this workflow: first i enlarge body section to body\_exten…

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## [Inquiry Regarding TotalSegmentator V2 Compatibility with Rabbit Micro-CT Images for Lung Segmentation](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489)

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**Author:** [@cong\_lu](https://discourse.slicer.org/u/cong_lu)\
**Replies:** 15\
**Last updated:** [November 3, 2023, 6:19pm UTC](https://discourse.slicer.org/t/inquiry-regarding-totalsegmentator-v2-compatibility-with-rabbit-micro-ct-images-for-lung-segmentation/32489 "2023-11-03T18:19:18Z")

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Dear TotalSegmentator Team, Thank you for releasing the updated TotalSegmentator V2 software. I am a Master’s student in medical science, currently focused on the quantitative analysis of micro-CT images in a rabbit mod…

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## [Landmark based rigid alignment](https://discourse.slicer.org/t/landmark-based-rigid-alignment/32354)

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**Author:** [@pkashya](https://discourse.slicer.org/u/pkashya)\
**Replies:** 2\
**Last updated:** [November 3, 2023, 4:13pm UTC](https://discourse.slicer.org/t/landmark-based-rigid-alignment/32354 "2023-11-03T16:13:54Z")

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Hi, I’m trying to run landmark-based rigid alignment on some infant hippocampus shape measures. I am unable to find a fiducials (\*.fcsv) file for doing so. Please advise. Thanks for all the help,

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## [3D Slicer Paint/Draw Tool Issue ](https://discourse.slicer.org/t/3d-slicer-paint-draw-tool-issue/32531)

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**Author:** [@Cameron\_Shepherd](https://discourse.slicer.org/u/Cameron_Shepherd)\
**Replies:** 2\
**Last updated:** [November 3, 2023, 12:08pm UTC](https://discourse.slicer.org/t/3d-slicer-paint-draw-tool-issue/32531 "2023-11-03T12:08:36Z")

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Operating system: Windows 11 Slicer version: 5.0.3 Background: I am a undergraduate working within a research lab and I have been using 3D Slicer for about a year now. This issue is with the paint tool and has happene…

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## [How can I approximate the Noise Reduction Non-Local Means in Amira?](https://discourse.slicer.org/t/how-can-i-approximate-the-noise-reduction-non-local-means-in-amira/32559)

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**Author:** [@Tan](https://discourse.slicer.org/u/Tan)\
**Replies:** 2\
**Last updated:** [November 3, 2023, 3:08am UTC](https://discourse.slicer.org/t/how-can-i-approximate-the-noise-reduction-non-local-means-in-amira/32559 "2023-11-03T03:08:40Z")

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I’ve tried in-build four denoising tools for my micro-ct data, but the results were not ideal. Sometimes the results are even mixed with noise outside the organization. This is my default setting in Amira. How should I a…

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## [Can TotalSegmentator segment maxillofacial CT as well?](https://discourse.slicer.org/t/can-totalsegmentator-segment-maxillofacial-ct-as-well/32484)

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**Author:** [@Tijl](https://discourse.slicer.org/u/Tijl)\
**Replies:** 8\
**Last updated:** [November 3, 2023, 12:51am UTC](https://discourse.slicer.org/t/can-totalsegmentator-segment-maxillofacial-ct-as-well/32484 "2023-11-03T00:51:34Z")

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Is it segmenting maxillofacial ct as well? Met vriendelijke groeten, T.H. van den Berg, Parodontoloog NVvP, Implantoloog NVOI Zijlweg 144 2015 BH Haarlem +31 23 542 01 88

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## [When tracing tissues on MRI sometimes the segment goes past the desired layer onto the next level](https://discourse.slicer.org/t/when-tracing-tissues-on-mri-sometimes-the-segment-goes-past-the-desired-layer-onto-the-next-level/32566)

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**Author:** [@Bryan](https://discourse.slicer.org/u/Bryan)\
**Replies:** 1\
**Last updated:** [November 3, 2023, 12:18am UTC](https://discourse.slicer.org/t/when-tracing-tissues-on-mri-sometimes-the-segment-goes-past-the-desired-layer-onto-the-next-level/32566 "2023-11-03T00:18:24Z")

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I am tracing muscle and leg tissue with a 10 mm separation between each layer. Most of the time I have no issue of tracing the tissues and moving on to the next layer. Sometimes when I draw on one layer it continues to g…

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## [DICOMDIR file creation](https://discourse.slicer.org/t/dicomdir-file-creation/32564)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 1\
**Last updated:** [November 2, 2023, 6:43pm UTC](https://discourse.slicer.org/t/dicomdir-file-creation/32564 "2023-11-02T18:43:50Z")

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Hi: The option “Create a DICOM Series” creates DICOM slices in a specified folder, but it lacks DICOMDIR file. How can I create it? Sincerely, Gonzalo Rojas Costa

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## [Cannot install the SlicerRadiomics Module ](https://discourse.slicer.org/t/cannot-install-the-slicerradiomics-module/32556)

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**Author:** [@melisaocbe](https://discourse.slicer.org/u/melisaocbe)\
**Replies:** 2\
**Last updated:** [November 2, 2023, 4:57pm UTC](https://discourse.slicer.org/t/cannot-install-the-slicerradiomics-module/32556 "2023-11-02T16:57:17Z")

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Hello, community! I have been struggling with 3D Slicer, python, PyRadiomics for days… I’m an oral and maxillofacial radiologist so I’m a total stranger for these topics such as coding and computing. Although, I would l…

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## [Add orientation labels (A, P, S, I, R, L) to 2D slice views](https://discourse.slicer.org/t/add-orientation-labels-a-p-s-i-r-l-to-2d-slice-views/31655)

<div class="topic-metadata">

**Author:** [@moraleda](https://discourse.slicer.org/u/moraleda)\
**Replies:** 7\
**Last updated:** [November 2, 2023, 3:40pm UTC](https://discourse.slicer.org/t/add-orientation-labels-a-p-s-i-r-l-to-2d-slice-views/31655 "2023-11-02T15:40:29Z")

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Hello everyone, I was wondering whether there is a nice way to add the orientation labels into the 2D slice view. In the 3D view, we see these labels (A, P, S, I, R, L) but in the 2D views, we can only use the little m…

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## [How to do the Surface rendering of knee joint](https://discourse.slicer.org/t/how-to-do-the-surface-rendering-of-knee-joint/32557)

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**Author:** [@vidhatrigujela](https://discourse.slicer.org/u/vidhatrigujela)\
**Replies:** 0\
**Last updated:** [November 2, 2023, 1:15pm UTC](https://discourse.slicer.org/t/how-to-do-the-surface-rendering-of-knee-joint/32557 "2023-11-02T13:15:08Z")

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## [How to Open "color bar"](https://discourse.slicer.org/t/how-to-open-color-bar/32543)

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**Author:** [@Jayleen\_Yuri](https://discourse.slicer.org/u/Jayleen_Yuri)\
**Replies:** 2\
**Last updated:** [November 2, 2023, 10:08am UTC](https://discourse.slicer.org/t/how-to-open-color-bar/32543 "2023-11-02T10:08:23Z")

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Operating system:window10 Enterprise Slicer version:4.8.1 Expected behavior: Open “color bar” Actual behavior:No Open by default "Open “color bar” function Dear community experts， I just recently used 3D slicer and…

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## [STL file to fake CT scan/DICOM?](https://discourse.slicer.org/t/stl-file-to-fake-ct-scan-dicom/32524)

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**Author:** [@BlakeSlicer](https://discourse.slicer.org/u/BlakeSlicer)\
**Replies:** 2\
**Last updated:** [November 2, 2023, 3:02am UTC](https://discourse.slicer.org/t/stl-file-to-fake-ct-scan-dicom/32524 "2023-11-02T03:02:55Z")

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I have a STL of a segmented bone. I would like to convert the STL back to a CT scan as a DICOM to be used in another software which processes images. I’ve imported the STL files as a segmentation and can now scroll thou…

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## [CT cranial bone thickness](https://discourse.slicer.org/t/ct-cranial-bone-thickness/32529)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 0\
**Last updated:** [November 1, 2023, 3:38pm UTC](https://discourse.slicer.org/t/ct-cranial-bone-thickness/32529 "2023-11-01T15:38:45Z")

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Hi: I have two different populations (cranial CT images). I want to compute the bone thickness of each one, and then I want to do a comparison between both populations. How can I do that? Any 3D slicer extension? Or oth…

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## [Total Segmentator Extension](https://discourse.slicer.org/t/total-segmentator-extension/32518)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 2\
**Last updated:** [November 1, 2023, 1:50pm UTC](https://discourse.slicer.org/t/total-segmentator-extension/32518 "2023-11-01T13:50:18Z")

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Dear all, I looked at the extension manager description for the total segmentator extension can segment 104, but when I run it, it just only segment 72. How does is it?

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## [How does one find the translation and rotation measurements of one anatomy with respect to another?](https://discourse.slicer.org/t/how-does-one-find-the-translation-and-rotation-measurements-of-one-anatomy-with-respect-to-another/30722)

<div class="topic-metadata">

**Author:** [@Firoza\_Kothari](https://discourse.slicer.org/u/Firoza_Kothari)\
**Replies:** 7\
**Last updated:** [November 1, 2023, 1:46pm UTC](https://discourse.slicer.org/t/how-does-one-find-the-translation-and-rotation-measurements-of-one-anatomy-with-respect-to-another/30722 "2023-11-01T13:46:06Z")

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I would like to find the Translation XYZ and Rotation XYZ of one anatomy with respect to another - say if I would like to consider center of the bone to be the origin and would like to find the above measurements of the …

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## [Is there a way to wait until certain condition are met before continuing and deleting nodes in using a python script](https://discourse.slicer.org/t/is-there-a-way-to-wait-until-certain-condition-are-met-before-continuing-and-deleting-nodes-in-using-a-python-script/6396)

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**Author:** [@Kevin.Kn](https://discourse.slicer.org/u/Kevin.Kn)\
**Replies:** 9\
**Last updated:** [October 31, 2023, 7:53pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-wait-until-certain-condition-are-met-before-continuing-and-deleting-nodes-in-using-a-python-script/6396 "2023-10-31T19:53:27Z")

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I am currently going through directories, grabbing fcsv and image pairs, and then loading them into slicer using a python script. # Image/fcsv loading \[success, markupNode\] = slicer.util.loadMarkupsFiducialList(fcsv, re…

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