# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=43

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

**Page:** 44

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## [SlicerMorph - semilandmarks](https://discourse.slicer.org/t/slicermorph-semilandmarks/34331)

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**Author:** [@Katya\_Stansfield](https://discourse.slicer.org/u/Katya_Stansfield)\
**Replies:** 5\
**Last updated:** [April 23, 2025, 7:13pm UTC](https://discourse.slicer.org/t/slicermorph-semilandmarks/34331 "2025-04-23T19:13:16Z")

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Hello – may I ask for help with semilandmark projection using either Alpaca or ProjectSemiLM. I have fairly simple surface objects so that Alpaca struggles to superimpose meshes without errors. Sometime it works just fi…

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## [Growth plate segmentation - same intensity as surrounding tissues](https://discourse.slicer.org/t/growth-plate-segmentation-same-intensity-as-surrounding-tissues/42602)

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**Author:** [@mariammtch](https://discourse.slicer.org/u/mariammtch)\
**Replies:** 2\
**Last updated:** [April 22, 2025, 10:32am UTC](https://discourse.slicer.org/t/growth-plate-segmentation-same-intensity-as-surrounding-tissues/42602 "2025-04-22T10:32:32Z")

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Hi. I have 7 different timepoint (so variable in size) CT data without contrast. I need to mark the gap (meant to be a growth plate) between the bony parts (marked in beige in the screenshot) . It is not uniform so 3D pa…

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## [Using SkyScanReconImport - do I need to change my .log file?](https://discourse.slicer.org/t/using-skyscanreconimport-do-i-need-to-change-my-log-file/42644)

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**Author:** [@atay5510](https://discourse.slicer.org/u/atay5510)\
**Replies:** 2\
**Last updated:** [April 22, 2025, 8:28am UTC](https://discourse.slicer.org/t/using-skyscanreconimport-do-i-need-to-change-my-log-file/42644 "2025-04-22T08:28:10Z")

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I have scanned some specimens on a Bruker SkyScan 2214 MicroCT. I have transferred these scans into a separate computer from the machine I used to acquire the images. As such, in the .log file, the Home Directory and Da…

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## [Set the view perpendicular on each tooth](https://discourse.slicer.org/t/set-the-view-perpendicular-on-each-tooth/42636)

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**Author:** [@Yasser\_Ahmad](https://discourse.slicer.org/u/Yasser_Ahmad)\
**Replies:** 1\
**Last updated:** [April 21, 2025, 12:56pm UTC](https://discourse.slicer.org/t/set-the-view-perpendicular-on-each-tooth/42636 "2025-04-21T12:56:23Z")

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I have a 3D dental model which I can rotate in infinite directions and angles. But, I want to be able to set a view where I will be looking directly at the facial surface of each tooth What I’ve tried to do is: Draw …

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## [If I wanna do white and gray matter segmentation on PET-CT images, how could I ](https://discourse.slicer.org/t/if-i-wanna-do-white-and-gray-matter-segmentation-on-pet-ct-images-how-could-i/42643)

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**Author:** [@Carole\_Abouomar](https://discourse.slicer.org/u/Carole_Abouomar)\
**Replies:** 0\
**Last updated:** [April 21, 2025, 11:34am UTC](https://discourse.slicer.org/t/if-i-wanna-do-white-and-gray-matter-segmentation-on-pet-ct-images-how-could-i/42643 "2025-04-21T11:34:18Z")

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If I wanna do white and gray matter segmentation on PET-CT images, how could I

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## [Register MRI with CT by Elastix](https://discourse.slicer.org/t/register-mri-with-ct-by-elastix/42624)

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**Author:** [@Asparagine](https://discourse.slicer.org/u/Asparagine)\
**Replies:** 2\
**Last updated:** [April 21, 2025, 5:36am UTC](https://discourse.slicer.org/t/register-mri-with-ct-by-elastix/42624 "2025-04-21T05:36:12Z")

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Hello everyone. I’m new to slicer and now using elastix to register the MRI to CT (about temporomandibular joint), but I found it is not that accurate using presets generic (all) and generic rigid (all). I read the pape…

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## [Add a keyboard shortcut to close the application](https://discourse.slicer.org/t/add-a-keyboard-shortcut-to-close-the-application/42615)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 4\
**Last updated:** [April 19, 2025, 6:24pm UTC](https://discourse.slicer.org/t/add-a-keyboard-shortcut-to-close-the-application/42615 "2025-04-19T18:24:32Z")

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Many applications can be closed by the “CTRL + Q” keyboard shortcut. This combination does not seem to be used in Slicer. I am aware that custom keyboard shortcuts can be assigned, just wondering if it could be built-in. …

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## [Cleaner bone segmentation](https://discourse.slicer.org/t/cleaner-bone-segmentation/42560)

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**Author:** [@JT\_GAUD](https://discourse.slicer.org/u/JT_GAUD)\
**Replies:** 5\
**Last updated:** [April 18, 2025, 7:56pm UTC](https://discourse.slicer.org/t/cleaner-bone-segmentation/42560 "2025-04-18T19:56:47Z")

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Hello ! I’m currently trying to have some cleans bones and i would like to know how to have a cleaner version of my hand (without holes, noises, sponge spongy bones), like the second photo (from what i’ve searched…

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## [Sending images over socket/pyigtl takes very long in 3D Slicer](https://discourse.slicer.org/t/sending-images-over-socket-pyigtl-takes-very-long-in-3d-slicer/42569)

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**Author:** [@Daniel\_L](https://discourse.slicer.org/u/Daniel_L)\
**Replies:** 2\
**Last updated:** [April 18, 2025, 8:58am UTC](https://discourse.slicer.org/t/sending-images-over-socket-pyigtl-takes-very-long-in-3d-slicer/42569 "2025-04-18T08:58:21Z")

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Hello everyone! I am using a Raspberry Pi with an Intel Realsense to send images to 3D Slicer over a socket connection to create a point cloud out of them. Now sometimes it takes a very long time until the image is rece…

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## [Issue Loading TensorFlow .h5 Model in 3D Slicer – "Unknown Layer: 'TensorFlowOpLayer](https://discourse.slicer.org/t/issue-loading-tensorflow-h5-model-in-3d-slicer-unknown-layer-tensorflowoplayer/42583)

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**Author:** [@software](https://discourse.slicer.org/u/software)\
**Replies:** 11\
**Last updated:** [April 18, 2025, 7:15am UTC](https://discourse.slicer.org/t/issue-loading-tensorflow-h5-model-in-3d-slicer-unknown-layer-tensorflowoplayer/42583 "2025-04-18T07:15:02Z")

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Hi everyone, I’m currently working on integrating an acute stroke detection model (originally trained in TensorFlow and saved as a .h5 file) into the 3D Slicer environment. I tried running it within my Slicer module, b…

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## [SlicerFreeSurfer runs out of memory to load wmparc.mgz](https://discourse.slicer.org/t/slicerfreesurfer-runs-out-of-memory-to-load-wmparc-mgz/42608)

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**Author:** [@tbillah](https://discourse.slicer.org/u/tbillah)\
**Replies:** 1\
**Last updated:** [April 17, 2025, 8:05pm UTC](https://discourse.slicer.org/t/slicerfreesurfer-runs-out-of-memory-to-load-wmparc-mgz/42608 "2025-04-17T20:05:30Z")

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Slicer-5.6.1 @pieper asked us to use SlicerFreeSurfer extension. We installed it. But when trying to load a wmparc.mgz file, we get the following: Console error is: Slicer has caught an application error, please s…

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## [BoneTexture Extension Understanding](https://discourse.slicer.org/t/bonetexture-extension-understanding/42609)

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**Author:** [@SurgiCADS](https://discourse.slicer.org/u/SurgiCADS)\
**Replies:** 0\
**Last updated:** [April 17, 2025, 7:48pm UTC](https://discourse.slicer.org/t/bonetexture-extension-understanding/42609 "2025-04-17T19:48:22Z")

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I’m quite novice here for the CODING, LANGUAGES & Deep IMAGE PROCESSING. Yet, I have one task, where I have come to know about BoneTexture Extension. I want to evaluate the Ossointegration/BoneGrowth of IMPLANT with th…

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## [Simultaneously display a sequence at different indices](https://discourse.slicer.org/t/simultaneously-display-a-sequence-at-different-indices/42588)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 12\
**Last updated:** [April 17, 2025, 4:56pm UTC](https://discourse.slicer.org/t/simultaneously-display-a-sequence-at-different-indices/42588 "2025-04-17T16:56:56Z")

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How would I go about displaying a sequence in the slice views where one 2D slice viewer is displaying the sequence at a given index and another 2D slicer viewer is displaying the same sequence at a different index? Cons…

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## [Model registration](https://discourse.slicer.org/t/model-registration/8177)

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**Author:** [@Jainey](https://discourse.slicer.org/u/Jainey)\
**Replies:** 6\
**Last updated:** [April 17, 2025, 2:05pm UTC](https://discourse.slicer.org/t/model-registration/8177 "2025-04-17T14:05:47Z")

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Hi Thank you for all the previous inputs; this seems to be working. One more question- When I register two models the mean distance appear in decimals , say 0.65 but when I check the translations on the transforms modu…

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## [MONAI Auto3DSeg Segmentation Error](https://discourse.slicer.org/t/monai-auto3dseg-segmentation-error/42594)

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**Author:** [@ShoopD](https://discourse.slicer.org/u/ShoopD)\
**Replies:** 1\
**Last updated:** [April 17, 2025, 12:55pm UTC](https://discourse.slicer.org/t/monai-auto3dseg-segmentation-error/42594 "2025-04-17T12:55:46Z")

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Greetings. I did a whole-body segmentation with the MONAI Auto3DSeg (Whole body segmentation TS1) and exported it in the RTSTRUCT format. There were a few missing parts after the segmentation, especially in the brain pa…

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## [SUVR in PET brain images](https://discourse.slicer.org/t/suvr-in-pet-brain-images/42587)

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**Author:** [@Gonzalo\_Rojas\_Costa](https://discourse.slicer.org/u/Gonzalo_Rojas_Costa)\
**Replies:** 0\
**Last updated:** [April 16, 2025, 4:52pm UTC](https://discourse.slicer.org/t/suvr-in-pet-brain-images/42587 "2025-04-16T16:52:36Z")

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How can I compute the SUVR in some PET brain images? Sincerely Gonzalo Rojas Costa

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## [Interactive Lobe Segmentation hhorizontal fissure on Chest Imaging Platform](https://discourse.slicer.org/t/interactive-lobe-segmentation-hhorizontal-fissure-on-chest-imaging-platform/42584)

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**Author:** [@Devanish](https://discourse.slicer.org/u/Devanish)\
**Replies:** 0\
**Last updated:** [April 16, 2025, 11:50am UTC](https://discourse.slicer.org/t/interactive-lobe-segmentation-hhorizontal-fissure-on-chest-imaging-platform/42584 "2025-04-16T11:50:07Z")

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Operating system: Windows 11 Slicer version: 5.6.2 Expected behavior: Trying to use Interactive Lung Segmentation of Chest Imaging Platform. Placed fiducials as suggested here: It seemed to work fine 2 weeks ago. A…

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## [MonaiLabel internal server error when running the model](https://discourse.slicer.org/t/monailabel-internal-server-error-when-running-the-model/42578)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 2\
**Last updated:** [April 16, 2025, 3:56am UTC](https://discourse.slicer.org/t/monailabel-internal-server-error-when-running-the-model/42578 "2025-04-16T03:56:06Z")

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Hi, I successfully trained a model using MonaiLabel for a simple skull segmentation. However, when I tested running the model on a volume, it reported Status: 500; Response: Internal Server Error Traceback (most recent…

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## [Imported segmentation does not show on DICOM file image](https://discourse.slicer.org/t/imported-segmentation-does-not-show-on-dicom-file-image/42538)

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**Author:** [@maysan1](https://discourse.slicer.org/u/maysan1)\
**Replies:** 1\
**Last updated:** [April 15, 2025, 2:33pm UTC](https://discourse.slicer.org/t/imported-segmentation-does-not-show-on-dicom-file-image/42538 "2025-04-15T14:33:25Z")

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Hello, I am using Slicer 5.9.0. I have created a segmentation on one dicom file of a certain volume. Then saved it as a seg.nrrd file. I am now trying to import it to another dicom file of another volume. It can be impo…

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## [Installing SlicerRadiomics Extension](https://discourse.slicer.org/t/installing-slicerradiomics-extension/41397)

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**Author:** [@pprior99999](https://discourse.slicer.org/u/pprior99999)\
**Replies:** 2\
**Last updated:** [April 15, 2025, 2:09pm UTC](https://discourse.slicer.org/t/installing-slicerradiomics-extension/41397 "2025-04-15T14:09:00Z")

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Hi, I’m struggling to install SlicerRadiomics extension in 3D Slicer 5.6.2 using the Extension Manager within slicer. I get the following warning, " Failed to open extensions settings file: C:/ProgramData/slicer.org/Sli…

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## [Problem installing radiology app of MonaiLabel in conda environment](https://discourse.slicer.org/t/problem-installing-radiology-app-of-monailabel-in-conda-environment/42567)

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**Author:** [@chz31](https://discourse.slicer.org/u/chz31)\
**Replies:** 1\
**Last updated:** [April 15, 2025, 6:33am UTC](https://discourse.slicer.org/t/problem-installing-radiology-app-of-monailabel-in-conda-environment/42567 "2025-04-15T06:33:32Z")

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Hi, I tried to reinstall monailabel in a fresh conda environment in Windows 11. Previously, I successfully installed monai and radiology app in a conda envrionment and ran in Slicer with no issue, but it suddenly could …

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## [Beginner question: Resample scalar volume giving enlarged image size](https://discourse.slicer.org/t/beginner-question-resample-scalar-volume-giving-enlarged-image-size/42550)

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**Author:** [@Chamini](https://discourse.slicer.org/u/Chamini)\
**Replies:** 5\
**Last updated:** [April 15, 2025, 12:12am UTC](https://discourse.slicer.org/t/beginner-question-resample-scalar-volume-giving-enlarged-image-size/42550 "2025-04-15T00:12:08Z")

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Hi all, I used the ‘Resample Scalar Volume’ module to change the resolution of my dataset. However, the output volume has much higher dimensions than the original. How can I maintain the same image dimensions while only …

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## [slicer.mrmlScene.Clear() not working](https://discourse.slicer.org/t/slicer-mrmlscene-clear-not-working/42556)

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**Author:** [@dpvaldes](https://discourse.slicer.org/u/dpvaldes)\
**Replies:** 5\
**Last updated:** [April 14, 2025, 5:28pm UTC](https://discourse.slicer.org/t/slicer-mrmlscene-clear-not-working/42556 "2025-04-14T17:28:14Z")

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I’m running Slicer 5.8.1 on Windows 11. Inputting slicer.mrmlScene.Clear() in the python console is not clearing it as before. Is this an issue or is it just me? Is there another way of clearing it?

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## [Image Distorted](https://discourse.slicer.org/t/image-distorted/42515)

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**Author:** [@amelia.eastham](https://discourse.slicer.org/u/amelia.eastham)\
**Replies:** 8\
**Last updated:** [April 14, 2025, 12:46pm UTC](https://discourse.slicer.org/t/image-distorted/42515 "2025-04-14T12:46:46Z")

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Does anyone know why this has suddenly happened to one of my files please?

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## [SlicerRVXLiverSegmentation display question](https://discourse.slicer.org/t/slicerrvxliversegmentation-display-question/42505)

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**Author:** [@feiyu](https://discourse.slicer.org/u/feiyu)\
**Replies:** 3\
**Last updated:** [April 14, 2025, 10:52am UTC](https://discourse.slicer.org/t/slicerrvxliversegmentation-display-question/42505 "2025-04-14T10:52:40Z")

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I’m really excited to encounter such an excellent liver segmentation module while attempting liver segmentation - it’s awesome! It achieves perfect segmentation in just 3 seconds. However, I’m facing an issue: When …

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## [Apple M1 Max vs CUDA on chest analysis pack](https://discourse.slicer.org/t/apple-m1-max-vs-cuda-on-chest-analysis-pack/42294)

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**Author:** [@kirion](https://discourse.slicer.org/u/kirion)\
**Replies:** 2\
**Last updated:** [April 14, 2025, 9:56am UTC](https://discourse.slicer.org/t/apple-m1-max-vs-cuda-on-chest-analysis-pack/42294 "2025-04-14T09:56:18Z")

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Hi, I am running the chest platform on a Mac M1 Max, but it seems too slow as it looks for CUDA instead of the MPS. Does anyone knows how to set it for apple M1 Max processors, please?

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## [An X-Ray DICOM file that Slicer won't open](https://discourse.slicer.org/t/an-x-ray-dicom-file-that-slicer-wont-open/42514)

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**Author:** [@shai-ikko](https://discourse.slicer.org/u/shai-ikko)\
**Replies:** 3\
**Last updated:** [April 14, 2025, 8:56am UTC](https://discourse.slicer.org/t/an-x-ray-dicom-file-that-slicer-wont-open/42514 "2025-04-14T08:56:24Z")

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Hello, I have a series of X-Ray files which Slicer refuses to open. I can open them in other DICOM viewers, and I can do some processing in tools like pydicom or the dcm\* and gdcm\* CLI suites. This seems a lot like See…

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## [I meet a problem when I use the modal of totalsegmentater](https://discourse.slicer.org/t/i-meet-a-problem-when-i-use-the-modal-of-totalsegmentater/42549)

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**Author:** [@rlx\_Yi](https://discourse.slicer.org/u/rlx_Yi)\
**Replies:** 0\
**Last updated:** [April 14, 2025, 1:57am UTC](https://discourse.slicer.org/t/i-meet-a-problem-when-i-use-the-modal-of-totalsegmentater/42549 "2025-04-14T01:57:34Z")

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\[DEBUG\]\[Qt\] 13.04.2025 13:11:17 (unknown:0) - Session start time …: 20250413\_131117 \[DEBUG\]\[Qt\] 13.04.2025 13:11:17 (unknown:0) - Slicer version …: 5.8.1 (revision 33241 / 11eaf62) win-amd64 - installed release \[DEBU…

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## [The extension is excellent, but there are bugs during use!](https://discourse.slicer.org/t/the-extension-is-excellent-but-there-are-bugs-during-use/42544)

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**Author:** [@feiyu](https://discourse.slicer.org/u/feiyu)\
**Replies:** 0\
**Last updated:** [April 13, 2025, 1:14am UTC](https://discourse.slicer.org/t/the-extension-is-excellent-but-there-are-bugs-during-use/42544 "2025-04-13T01:14:16Z")

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I’m really excited to encounter such an excellent liver segmentation module while attempting liver segmentation - it’s awesome! It achieves perfect segmentation in just 3 seconds. However, I’m facing an issue: When using…

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## [Help Needed: Removing PHI from Raw DICOM (3D TEE) Files for Research Collaboration. De-identification](https://discourse.slicer.org/t/help-needed-removing-phi-from-raw-dicom-3d-tee-files-for-research-collaboration-de-identification/42541)

<div class="topic-metadata">

**Author:** [@federica-pixel](https://discourse.slicer.org/u/federica-pixel)\
**Replies:** 1\
**Last updated:** [April 12, 2025, 7:12pm UTC](https://discourse.slicer.org/t/help-needed-removing-phi-from-raw-dicom-3d-tee-files-for-research-collaboration-de-identification/42541 "2025-04-12T19:12:13Z")

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Hi everyone, I’m currently working on a research project involving 3D transesophageal echocardiography (TEE) data. I’ve exported raw DICOM files from hospital imaging systems (GE and/or Philips), and these datasets are …

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