# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=64

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

**Page:** 65

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## [Registering mri with ct](https://discourse.slicer.org/t/registering-mri-with-ct/40347)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 0\
**Last updated:** [November 23, 2024, 3:33pm UTC](https://discourse.slicer.org/t/registering-mri-with-ct/40347 "2024-11-23T15:33:16Z")

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any advice on registering mri with ct ? facial bone ct and tmj mri i want to superimpose

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## [Lost segmentation data](https://discourse.slicer.org/t/lost-segmentation-data/40343)

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**Author:** [@Hannnonk](https://discourse.slicer.org/u/Hannnonk)\
**Replies:** 0\
**Last updated:** [November 23, 2024, 11:55am UTC](https://discourse.slicer.org/t/lost-segmentation-data/40343 "2024-11-23T11:55:46Z")

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Windows 11. Created and saved a segmentation. Went to reopen file in 3D slicer and this is what the data window looks like. When I click on the eye it the contents of the segmentation “disappear”. I did a search for…

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## [Slicer on a cluster using a virtual desktop](https://discourse.slicer.org/t/slicer-on-a-cluster-using-a-virtual-desktop/40316)

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**Author:** [@mandorodriguez](https://discourse.slicer.org/u/mandorodriguez)\
**Replies:** 2\
**Last updated:** [November 22, 2024, 8:01pm UTC](https://discourse.slicer.org/t/slicer-on-a-cluster-using-a-virtual-desktop/40316 "2024-11-22T20:01:18Z")

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Greetings, We users that would like to use Slicer 3D on our compute cluster which has a virtual desktop. We install apps to a common area that they load via a module system (lmod). Are there any examples of someone else…

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## [General registration\_(ANTs)](https://discourse.slicer.org/t/general-registration-ants/40333)

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**Author:** [@Bor\_Antolic](https://discourse.slicer.org/u/Bor_Antolic)\
**Replies:** 1\
**Last updated:** [November 22, 2024, 7:41pm UTC](https://discourse.slicer.org/t/general-registration-ants/40333 "2024-11-22T19:41:48Z")

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I used the general registration (ANTs) with success until a few days ago. It started reporting error: /AppData/Local/Temp/Slicer/CBGEE\_vtkMRMLScalarVolumeNodeH.nrrd does not exist I tried reinstaling the SlicerANTs plug…

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## [CT scan Dicom 3D rendering not displayed](https://discourse.slicer.org/t/ct-scan-dicom-3d-rendering-not-displayed/40321)

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**Author:** [@Dimitri\_Gouvoussis](https://discourse.slicer.org/u/Dimitri_Gouvoussis)\
**Replies:** 5\
**Last updated:** [November 22, 2024, 6:28pm UTC](https://discourse.slicer.org/t/ct-scan-dicom-3d-rendering-not-displayed/40321 "2024-11-22T18:28:17Z")

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Hello, I have a confocal, spatial, and axial view but I cannot get a 3D view to render. What step am I missing?

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## [Best Way to Compare MRI Scans Over Time?](https://discourse.slicer.org/t/best-way-to-compare-mri-scans-over-time/40228)

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**Author:** [@noobslicer](https://discourse.slicer.org/u/noobslicer)\
**Replies:** 7\
**Last updated:** [November 22, 2024, 4:08pm UTC](https://discourse.slicer.org/t/best-way-to-compare-mri-scans-over-time/40228 "2024-11-22T16:08:13Z")

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Operating system: Windows 10 Slicer version: 5.6.2 Hi everyone, I have about 10 MRI scans of a family member, taken from the early 2000s to now, covering the brain and the spine. I want to compare these scans over the…

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## [3D dose visualization from RTdose DICOM file](https://discourse.slicer.org/t/3d-dose-visualization-from-rtdose-dicom-file/40324)

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**Author:** [@wlstraube](https://discourse.slicer.org/u/wlstraube)\
**Replies:** 3\
**Last updated:** [November 21, 2024, 10:43pm UTC](https://discourse.slicer.org/t/3d-dose-visualization-from-rtdose-dicom-file/40324 "2024-11-21T22:43:23Z")

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Is it possible to show a 3D dose distribution with a 3D view of CTs and Contours?

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## [Crop Volume module returning empty volume](https://discourse.slicer.org/t/crop-volume-module-returning-empty-volume/40323)

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**Author:** [@Dboerma](https://discourse.slicer.org/u/Dboerma)\
**Replies:** 1\
**Last updated:** [November 21, 2024, 10:25pm UTC](https://discourse.slicer.org/t/crop-volume-module-returning-empty-volume/40323 "2024-11-21T22:25:39Z")

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Hello Slicer team! OS: Windows 10 (22H2) Slicer Version: 5.6.2 RAM: 128 GB Data: DICOMs (12.4 GB) Expected Behavior: When using an ROI to define a cropping region (both in the Crop Volumes module and when using the …

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## [Superimposition of mandibular canal tracings ](https://discourse.slicer.org/t/superimposition-of-mandibular-canal-tracings/40322)

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**Author:** [@Swarna\_Yerebairapura](https://discourse.slicer.org/u/Swarna_Yerebairapura)\
**Replies:** 1\
**Last updated:** [November 21, 2024, 10:23pm UTC](https://discourse.slicer.org/t/superimposition-of-mandibular-canal-tracings/40322 "2024-11-21T22:23:42Z")

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This pertains to the superimposition of mandibular canal tracings performed in three different CBCT software programs. I aim to import DICOM files with mandibular canal tracings into 3D Slicer. However, in all the CBCT s…

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## [How to perform tumor segmentation on PET and map it onto CT](https://discourse.slicer.org/t/how-to-perform-tumor-segmentation-on-pet-and-map-it-onto-ct/40319)

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**Author:** [@ko\_cindy](https://discourse.slicer.org/u/ko_cindy)\
**Replies:** 0\
**Last updated:** [November 21, 2024, 10:18pm UTC](https://discourse.slicer.org/t/how-to-perform-tumor-segmentation-on-pet-and-map-it-onto-ct/40319 "2024-11-21T22:18:01Z")

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Hi, I am new to slicer. I have PETCT images (nifti). I can segment tumor on PET based on threshold method. But I don’t know how to put it on the CT image and then saved as nifti. Anyone know how to perform it? Kind …

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## [Struggling with SUV quantification in ROI](https://discourse.slicer.org/t/struggling-with-suv-quantification-in-roi/40318)

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**Author:** [@wiaam91](https://discourse.slicer.org/u/wiaam91)\
**Replies:** 0\
**Last updated:** [November 21, 2024, 10:17pm UTC](https://discourse.slicer.org/t/struggling-with-suv-quantification-in-roi/40318 "2024-11-21T22:17:38Z")

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Dear Team , I will be gratful for your help. I am trying to meaure the SUV for 3 ROI in PET MRI scans, Liver, spleen and pancreas. My PET-IndiC is not active , my quanative reporting extension is also not showing any te…

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## [Module PET Tumor Segmentation](https://discourse.slicer.org/t/module-pet-tumor-segmentation/40306)

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**Author:** [@imbeatriz](https://discourse.slicer.org/u/imbeatriz)\
**Replies:** 6\
**Last updated:** [November 21, 2024, 7:16pm UTC](https://discourse.slicer.org/t/module-pet-tumor-segmentation/40306 "2024-11-21T19:16:25Z")

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Hi everyone, I’m working on segmenting a liver lesion using the PET Tumor Segmentation module on a PET image. To assist, I followed a YouTube tutorial (https://www.youtube.com/watch?v=oYlFhqxdptE). However, when I attem…

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## [Merging landmarks and semi-landmarks with SlicerMorph](https://discourse.slicer.org/t/merging-landmarks-and-semi-landmarks-with-slicermorph/39977)

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**Author:** [@Ruiqi-CUB](https://discourse.slicer.org/u/Ruiqi-CUB)\
**Replies:** 9\
**Last updated:** [November 21, 2024, 5:50pm UTC](https://discourse.slicer.org/t/merging-landmarks-and-semi-landmarks-with-slicermorph/39977 "2024-11-21T17:50:48Z")

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I am Slicer 5.6.2. My project use 1) 5 homologous landmarks 2) semilandmarks on a open curve 3) semilandmarks on a closed curve, My goal is to merge them and create a PCA plot in R with merged data. I tried to use Merge…

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## [Shoulder mri segmentation](https://discourse.slicer.org/t/shoulder-mri-segmentation/40303)

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**Author:** [@benedettabottelli](https://discourse.slicer.org/u/benedettabottelli)\
**Replies:** 0\
**Last updated:** [November 21, 2024, 9:47am UTC](https://discourse.slicer.org/t/shoulder-mri-segmentation/40303 "2024-11-21T09:47:20Z")

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If I need to segment a MRI of a shoulder is it possible to use TotalSegmentator? if yes how can I have the license to the MR module?

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## [Monai Label defaulting to CPU only training with segmentation model](https://discourse.slicer.org/t/monai-label-defaulting-to-cpu-only-training-with-segmentation-model/40301)

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**Author:** [@Saim\_ali](https://discourse.slicer.org/u/Saim_ali)\
**Replies:** 0\
**Last updated:** [November 21, 2024, 4:07am UTC](https://discourse.slicer.org/t/monai-label-defaulting-to-cpu-only-training-with-segmentation-model/40301 "2024-11-21T04:07:30Z")

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Hi all, novice in programming so I am learning as I go. I have a set of CT scans with custom labels and I have figured out how to employ Monai Label to customize the segmentation model but I am having some trouble using…

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## [Is there any extension to measure the angle between a line and a planes directly?](https://discourse.slicer.org/t/is-there-any-extension-to-measure-the-angle-between-a-line-and-a-planes-directly/21360)

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**Author:** [@zHOU](https://discourse.slicer.org/u/zHOU)\
**Replies:** 2\
**Last updated:** [November 21, 2024, 2:45am UTC](https://discourse.slicer.org/t/is-there-any-extension-to-measure-the-angle-between-a-line-and-a-planes-directly/21360 "2024-11-21T02:45:10Z")

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Operating system: Mac os Slicer version: 4.11 Expected behavior: I want to measure the angle between a line and a plane in 3D model Actual behavior: I have used similar extensions like “Angle planes” or " Q3DC", but n…

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## [Threshold bug in slicer preview release](https://discourse.slicer.org/t/threshold-bug-in-slicer-preview-release/40214)

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**Author:** [@alientex](https://discourse.slicer.org/u/alientex)\
**Replies:** 8\
**Last updated:** [November 20, 2024, 9:20pm UTC](https://discourse.slicer.org/t/threshold-bug-in-slicer-preview-release/40214 "2024-11-20T21:20:22Z")

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Hello, The threshold preview and apply operations do not work after following the steps below: Open the DICOM module, import, and load a DICOM directory. Go to the Segment Editor and add a segment. Open the threshold …

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## [Voxelized phantom creation on 3D slicer](https://discourse.slicer.org/t/voxelized-phantom-creation-on-3d-slicer/40278)

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**Author:** [@imbeatriz](https://discourse.slicer.org/u/imbeatriz)\
**Replies:** 3\
**Last updated:** [November 20, 2024, 9:16pm UTC](https://discourse.slicer.org/t/voxelized-phantom-creation-on-3d-slicer/40278 "2024-11-20T21:16:43Z")

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Hello everyone, I am currently working on constructing a patient-specific phantom for GATE simulations. I’ve uploaded a CT image and segmented the regions of interest using the TotalSegmentator module. The resulting seg…

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## [Loading GE Ultrasound ](https://discourse.slicer.org/t/loading-ge-ultrasound/40298)

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**Author:** [@ipintos](https://discourse.slicer.org/u/ipintos)\
**Replies:** 1\
**Last updated:** [November 20, 2024, 9:11pm UTC](https://discourse.slicer.org/t/loading-ge-ultrasound/40298 "2024-11-20T21:11:58Z")

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Hi all, I have a set of US data from a couple of patients that were exported from EchoPAC with the idea of working with raw data to train an AI model. The folder structure is: TEST02 ---DICOMDIR ---GEMS\_DB |\_\_\_\_A…

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## [3D prints from ultrasound](https://discourse.slicer.org/t/3d-prints-from-ultrasound/40297)

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**Author:** [@Nadia](https://discourse.slicer.org/u/Nadia)\
**Replies:** 0\
**Last updated:** [November 20, 2024, 9:01pm UTC](https://discourse.slicer.org/t/3d-prints-from-ultrasound/40297 "2024-11-20T21:01:21Z")

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Good afternoon, I perform ultrasounds of babies in my practice. Currently I have a partner who makes 3D prints of my ultrasounds but since I want to invest in a 3D printer I want to be able to print them myself. Only I …

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## [Dynamic segmentation subtraction](https://discourse.slicer.org/t/dynamic-segmentation-subtraction/40296)

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**Author:** [@ava23](https://discourse.slicer.org/u/ava23)\
**Replies:** 1\
**Last updated:** [November 20, 2024, 9:01pm UTC](https://discourse.slicer.org/t/dynamic-segmentation-subtraction/40296 "2024-11-20T21:01:09Z")

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I have a Volume A (a PET scan) with two segmentations: Seg1 and Seg2. A user is making adjustments to Seg2 (adding and removing voxels). I would like to dynamically display all voxels that are in Seg1 but not in Seg2 i…

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## [SlicerMorph MorphologikaLMConverter module- landmark orientation issue](https://discourse.slicer.org/t/slicermorph-morphologikalmconverter-module-landmark-orientation-issue/40256)

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**Author:** [@A\_Auerbach](https://discourse.slicer.org/u/A_Auerbach)\
**Replies:** 3\
**Last updated:** [November 20, 2024, 4:31pm UTC](https://discourse.slicer.org/t/slicermorph-morphologikalmconverter-module-landmark-orientation-issue/40256 "2024-11-20T16:31:11Z")

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Hello all, I’ve used Slicer for segmentation but Checkpoint for landmarking, exporting my landmarks as Morphologika and csv files. However, to create good visualizations of my landmarks on the skull surface for publicat…

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## [How to adjust DVH bin width?](https://discourse.slicer.org/t/how-to-adjust-dvh-bin-width/40088)

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**Author:** [@wilbysl](https://discourse.slicer.org/u/wilbysl)\
**Replies:** 2\
**Last updated:** [November 20, 2024, 2:00pm UTC](https://discourse.slicer.org/t/how-to-adjust-dvh-bin-width/40088 "2024-11-20T14:00:25Z")

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Hello. Can anyone tell me if it’s possible to change the bin width for DVHs in v5.6.2 of Slicer3D please? Many thanks

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## [Resample Modules](https://discourse.slicer.org/t/resample-modules/40280)

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**Author:** [@benedettabottelli](https://discourse.slicer.org/u/benedettabottelli)\
**Replies:** 3\
**Last updated:** [November 20, 2024, 12:53pm UTC](https://discourse.slicer.org/t/resample-modules/40280 "2024-11-20T12:53:03Z")

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Which is the difference between the Resample Scalar volume module and the Resample scalar/vector/DWI volume module? when do I use one rather than the other?

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## [4D Registration: How to output the coordinates of the meshing points?](https://discourse.slicer.org/t/4d-registration-how-to-output-the-coordinates-of-the-meshing-points/22586)

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**Author:** [@Gening\_Dong](https://discourse.slicer.org/u/Gening_Dong)\
**Replies:** 1\
**Last updated:** [November 20, 2024, 11:19am UTC](https://discourse.slicer.org/t/4d-registration-how-to-output-the-coordinates-of-the-meshing-points/22586 "2024-11-20T11:19:08Z")

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Operating system: Windows 11 Slicer version: 4.11 Hi! I used the 4D Elastix plugin (Sequence Registration) to complete the image registration and the module Transform to transform a model generated by the module Segme…

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## [Remove small islands voxel size](https://discourse.slicer.org/t/remove-small-islands-voxel-size/40268)

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**Author:** [@FraP](https://discourse.slicer.org/u/FraP)\
**Replies:** 3\
**Last updated:** [November 20, 2024, 9:25am UTC](https://discourse.slicer.org/t/remove-small-islands-voxel-size/40268 "2024-11-20T09:25:26Z")

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I am using the “Remove Small Islands” function with a voxel size of 10 after segmenting with the threshold function. The information of the volume I’m working with is the following: Could you confirm if I understand…

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## [Error in segment statistics](https://discourse.slicer.org/t/error-in-segment-statistics/40283)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 2\
**Last updated:** [November 20, 2024, 3:39am UTC](https://discourse.slicer.org/t/error-in-segment-statistics/40283 "2024-11-20T03:39:01Z")

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I want to calculate volume of segemented region,but when i use statics tool , i did not see segemted region to apply , i also paste code here \[VTK\] There is more than one file, use the vtkITKArchetypeImageSeriesReade…

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## [Segment Editor module won't present my segment in 3D](https://discourse.slicer.org/t/segment-editor-module-wont-present-my-segment-in-3d/40277)

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**Author:** [@21verbeks](https://discourse.slicer.org/u/21verbeks)\
**Replies:** 1\
**Last updated:** [November 19, 2024, 10:42pm UTC](https://discourse.slicer.org/t/segment-editor-module-wont-present-my-segment-in-3d/40277 "2024-11-19T22:42:20Z")

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Hi! I am having trouble with my segment editor module. I have my segmentations highlighted of my ct data of a primate tooth and can see all of them in the 2D screens. But everytime I press the “show in 3D” button, nothin…

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## [Python command tooltips](https://discourse.slicer.org/t/python-command-tooltips/40279)

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**Author:** [@Aidan](https://discourse.slicer.org/u/Aidan)\
**Replies:** 1\
**Last updated:** [November 19, 2024, 10:36pm UTC](https://discourse.slicer.org/t/python-command-tooltips/40279 "2024-11-19T22:36:35Z")

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The current recommendation for users wishing to learn how to Python script Slicer operations that they are already familiar with in the GUI is rather convoluted and time consuming. It involves searching the Slicer GitHub…

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## [WholeBrain Model in MONAI Auto3D Seg Module](https://discourse.slicer.org/t/wholebrain-model-in-monai-auto3d-seg-module/40276)

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**Author:** [@Bobby\_Zee](https://discourse.slicer.org/u/Bobby_Zee)\
**Replies:** 0\
**Last updated:** [November 19, 2024, 10:10pm UTC](https://discourse.slicer.org/t/wholebrain-model-in-monai-auto3d-seg-module/40276 "2024-11-19T22:10:03Z")

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Hi all, I am trying to use this model “Wholebrainseg large unest segmentation” (from here MONAI Model Zoo) in MONAI Auto3D Seg in Slicer 3D. I put it in the correct path according to Github (GitHub - lassoan/SlicerMONAI…

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