# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=269

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

**Page:** 270

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## [Perform cortical and  trabecular bone segmentation of a Talus bone to generate a 2body STL file](https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950)

<div class="topic-metadata">

**Author:** [@Manav\_Kothari](https://discourse.slicer.org/u/Manav_Kothari)\
**Replies:** 2\
**Last updated:** [July 18, 2021, 3:15am UTC](https://discourse.slicer.org/t/perform-cortical-and-trabecular-bone-segmentation-of-a-talus-bone-to-generate-a-2body-stl-file/17950 "2021-07-18T03:15:22Z")

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I apologise for being extremely naive in the field of biomechanics and radiology but I need to extract a 3D model of Talus bone from a CT scan of a foot. So far I have been successful in segmenting the outer structure of…

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## [Port placement for placing surgical needle on correct entry point and desired angle](https://discourse.slicer.org/t/port-placement-for-placing-surgical-needle-on-correct-entry-point-and-desired-angle/16976)

<div class="topic-metadata">

**Author:** [@abatpool](https://discourse.slicer.org/u/abatpool)\
**Replies:** 5\
**Last updated:** [July 18, 2021, 3:05am UTC](https://discourse.slicer.org/t/port-placement-for-placing-surgical-needle-on-correct-entry-point-and-desired-angle/16976 "2021-07-18T03:05:36Z")

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Hello, I have been reading about port placement in the documentation, but not able find that module in IGT or extension manager. Please let me know where can i find that module, or how to install it.

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## [How to keep continuity when surface smoothing](https://discourse.slicer.org/t/how-to-keep-continuity-when-surface-smoothing/16598)

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**Author:** [@xiang\_luo](https://discourse.slicer.org/u/xiang_luo)\
**Replies:** 7\
**Last updated:** [July 18, 2021, 3:00am UTC](https://discourse.slicer.org/t/how-to-keep-continuity-when-surface-smoothing/16598 "2021-07-18T03:00:48Z")

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When i smooth the pulmonary artery, i find that the vessel continuity had beed destoryed sharply. Like this: Also i find this happend in Mimics when i set the prefer to accuracy, while the default value is continuity,…

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## [Have sequence of steps executed when adding data](https://discourse.slicer.org/t/have-sequence-of-steps-executed-when-adding-data/17682)

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**Author:** [@Jonathan\_Lesage](https://discourse.slicer.org/u/Jonathan_Lesage)\
**Replies:** 6\
**Last updated:** [July 18, 2021, 2:52am UTC](https://discourse.slicer.org/t/have-sequence-of-steps-executed-when-adding-data/17682 "2021-07-18T02:52:28Z")

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Operating system: Windows 10 Slicer version: 4.11.20210226 Expected behavior: Reformatting views in .sliccerrc file remains active when adding a volume Actual behavior: Views reset to Axial, Sagittal, Coronal when add…

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## [Apply nonlinear transform to point in python](https://discourse.slicer.org/t/apply-nonlinear-transform-to-point-in-python/16701)

<div class="topic-metadata">

**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 2\
**Last updated:** [March 23, 2021, 4:51pm UTC](https://discourse.slicer.org/t/apply-nonlinear-transform-to-point-in-python/16701 "2021-03-23T16:51:43Z")

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Hello, I have a nonlinear transform which was generated by the CurvedPlanarReformat module. I would like to programmatically find the corresponding point in the original volume space to a point identified in the straigh…

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## [Radiomic analysis thesis questions](https://discourse.slicer.org/t/radiomic-analysis-thesis-questions/18366)

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**Author:** [@retidani18](https://discourse.slicer.org/u/retidani18)\
**Replies:** 1\
**Last updated:** [July 17, 2021, 11:11pm UTC](https://discourse.slicer.org/t/radiomic-analysis-thesis-questions/18366 "2021-07-17T23:11:49Z")

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Hi! I am new here. I am doing my medical physics masters and my thesis heavily involves 3D Slicer. In short a lung sample was imaged using a special x-ray technique. Than the cells in this sample was dyed. I can use thi…

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## [Ultrasound image difference in Slicer version 4.10 and 4.11](https://discourse.slicer.org/t/ultrasound-image-difference-in-slicer-version-4-10-and-4-11/18428)

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**Author:** [@Marijn\_H](https://discourse.slicer.org/u/Marijn_H)\
**Replies:** 3\
**Last updated:** [July 17, 2021, 11:04pm UTC](https://discourse.slicer.org/t/ultrasound-image-difference-in-slicer-version-4-10-and-4-11/18428 "2021-07-17T23:04:27Z")

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Hi, I am using slicerIGT with plusserver to load tracked ultrasound images into 3D Slicer. We use the BK ultrasound system. On Slicer version 4.10, this worked fine and the ultrasound image is displayed like this: N…

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## [How to build high accuracy SPECT Imaging](https://discourse.slicer.org/t/how-to-build-high-accuracy-spect-imaging/18754)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 9\
**Last updated:** [July 17, 2021, 4:17pm UTC](https://discourse.slicer.org/t/how-to-build-high-accuracy-spect-imaging/18754 "2021-07-17T16:17:35Z")

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Hi All, I did the SPECT image segmentation using the PETTumorSegmentation extension. But there is low accuracy. Let say, my dummy sphere volume phantom is 27 ml, using PETTumorSegmenation I got 44ml. Does anyone know…

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## [Baby 3D ultrasound printing](https://discourse.slicer.org/t/baby-3d-ultrasound-printing/18758)

<div class="topic-metadata">

**Author:** [@bevuly](https://discourse.slicer.org/u/bevuly)\
**Replies:** 1\
**Last updated:** [July 16, 2021, 8:31pm UTC](https://discourse.slicer.org/t/baby-3d-ultrasound-printing/18758 "2021-07-16T20:31:19Z")

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Hello, I’m having trouble to get 3D volume. Have exported DICOM files from the GE Voluson but couldn’t get the 3D volume. In this case what would be the problem? Can anyone please help me? I have attached the image …

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## [PET and MR display issues](https://discourse.slicer.org/t/pet-and-mr-display-issues/18704)

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**Author:** [@dougPorter](https://discourse.slicer.org/u/dougPorter)\
**Replies:** 17\
**Last updated:** [July 16, 2021, 6:25pm UTC](https://discourse.slicer.org/t/pet-and-mr-display-issues/18704 "2021-07-16T18:25:01Z")

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Does anyone have issues displaying PET and MR series in Slicer. Try these and please let me know if you have any ideas on why this happens… (link has been removed until it is confirmed that the images do not contain PHI…

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## [Segmentation Mask not overlayed on top of the original data](https://discourse.slicer.org/t/segmentation-mask-not-overlayed-on-top-of-the-original-data/18733)

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**Author:** [@ZakiaKhatun](https://discourse.slicer.org/u/ZakiaKhatun)\
**Replies:** 8\
**Last updated:** [July 15, 2021, 7:28pm UTC](https://discourse.slicer.org/t/segmentation-mask-not-overlayed-on-top-of-the-original-data/18733 "2021-07-15T19:28:04Z")

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Hello everyone, I have a CT scan of the knee and an STL file (as segmentation mask) separately. When I load the STL file, it does not overlay on top of my CT data. From the image below, you can see that the 3D object in…

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## [Slicer is freezing on macOS when clicking on "Import DICOM files"](https://discourse.slicer.org/t/slicer-is-freezing-on-macos-when-clicking-on-import-dicom-files/18624)

<div class="topic-metadata">

**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 22\
**Last updated:** [July 15, 2021, 7:12pm UTC](https://discourse.slicer.org/t/slicer-is-freezing-on-macos-when-clicking-on-import-dicom-files/18624 "2021-07-15T19:12:29Z")

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version 2021.07.08 on mac M1 once I press load Dicom , slicer freezes and nothing can be done. interestingly, when I try to force turn off, I don’t get ( not responding ) next to the app showing a freeze. older version…

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## [Add signature to segmentation](https://discourse.slicer.org/t/add-signature-to-segmentation/18327)

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**Author:** [@ni5h](https://discourse.slicer.org/u/ni5h)\
**Replies:** 9\
**Last updated:** [July 15, 2021, 3:56pm UTC](https://discourse.slicer.org/t/add-signature-to-segmentation/18327 "2021-07-15T15:56:03Z")

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@lassoan - an unrelated question and I am unsure if you can answer this (it may require our IT); once we have annotated and segmented an area, are we able to configure and add a medical signature on to the annotation wit…

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## [Osteotomy Planner v2.0](https://discourse.slicer.org/t/osteotomy-planner-v2-0/18384)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 15\
**Last updated:** [July 15, 2021, 2:52pm UTC](https://discourse.slicer.org/t/osteotomy-planner-v2-0/18384 "2021-07-15T14:52:32Z")

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Hello, I was testing out the osteotomy planner module but seems like version 2.0 is different from the one shown in this video. I can easily create plane cuts, curve cuts, and perform local transforms, but I am not abl…

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## [how to fill in an existing segment](https://discourse.slicer.org/t/how-to-fill-in-an-existing-segment/18730)

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**Author:** [@art](https://discourse.slicer.org/u/art)\
**Replies:** 2\
**Last updated:** [July 15, 2021, 2:14pm UTC](https://discourse.slicer.org/t/how-to-fill-in-an-existing-segment/18730 "2021-07-15T14:14:52Z")

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Operating system: windows 10 64bit Slicer version: 4.11.2020 Expected behavior: I am trying to segment a liver in non-contrast CT. The steps are as follows: threshold HU 0~100 for masking. paint liver in multiple axi…

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## [Help regarding "Synchronize with Volumes module"](https://discourse.slicer.org/t/help-regarding-synchronize-with-volumes-module/18356)

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**Author:** [@pranaysingh](https://discourse.slicer.org/u/pranaysingh)\
**Replies:** 7\
**Last updated:** [July 15, 2021, 3:48am UTC](https://discourse.slicer.org/t/help-regarding-synchronize-with-volumes-module/18356 "2021-07-15T03:48:43Z")

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Hi, I am trying to do volume rendering of my dicom dataset. I want it to render the object with exact intensity values of the voxels, for this I was suggested “Synchronize with Volumes module” on community, which I did …

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## [Best way to export image and segmentation in same space to view in ParaView?](https://discourse.slicer.org/t/best-way-to-export-image-and-segmentation-in-same-space-to-view-in-paraview/18713)

<div class="topic-metadata">

**Author:** [@tossin](https://discourse.slicer.org/u/tossin)\
**Replies:** 3\
**Last updated:** [July 14, 2021, 11:22pm UTC](https://discourse.slicer.org/t/best-way-to-export-image-and-segmentation-in-same-space-to-view-in-paraview/18713 "2021-07-14T23:22:12Z")

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I’m sure this type of problem pops up a lot, but I couldn’t find an exact answer to my problem. I have an image volume imported from a DICOM sequence which I’ve segmented first with the VMTK Extension (produces a node n…

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## [STL file support](https://discourse.slicer.org/t/stl-file-support/18710)

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**Author:** [@landerson](https://discourse.slicer.org/u/landerson)\
**Replies:** 7\
**Last updated:** [July 14, 2021, 9:44pm UTC](https://discourse.slicer.org/t/stl-file-support/18710 "2021-07-14T21:44:57Z")

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Operating system: Windows Slicer version: 4.11 Expected behavior: Load STL file as a 3D model Actual behavior: No 3D model was produced. The STL file does not seem to be corrupted (I am able to open it on Meshlab)

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## [Export Deformation Field as Dicom](https://discourse.slicer.org/t/export-deformation-field-as-dicom/13657)

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**Author:** [@iTheoch](https://discourse.slicer.org/u/iTheoch)\
**Replies:** 18\
**Last updated:** [July 14, 2021, 8:32pm UTC](https://discourse.slicer.org/t/export-deformation-field-as-dicom/13657 "2021-07-14T20:32:09Z")

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Dear all, I am looking if 3D Slicer is capable of exporting Deformable Registration Objects as DICOM. Of course my first priority was to search your forum and see if anyone else had a similar request. Indeed I found a c…

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## [Create a 3D solid model from CT scans](https://discourse.slicer.org/t/create-a-3d-solid-model-from-ct-scans/18562)

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**Author:** [@Leelhan](https://discourse.slicer.org/u/Leelhan)\
**Replies:** 9\
**Last updated:** [July 14, 2021, 8:14pm UTC](https://discourse.slicer.org/t/create-a-3d-solid-model-from-ct-scans/18562 "2021-07-14T20:14:21Z")

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Hello, I have CT scans of a vertebra and I’m trying to export a 3D solid model from Slicer so I can import in Abaqus. I have already segmented and created the model, but once on Abaqus I realised it was just a surface m…

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## [Deploying slicer in an immutable container (Singularity)](https://discourse.slicer.org/t/deploying-slicer-in-an-immutable-container-singularity/18702)

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**Author:** [@Blake\_Fitch](https://discourse.slicer.org/u/Blake_Fitch)\
**Replies:** 6\
**Last updated:** [July 14, 2021, 12:41pm UTC](https://discourse.slicer.org/t/deploying-slicer-in-an-immutable-container-singularity/18702 "2021-07-14T12:41:19Z")

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Hello Sir, I am deploying slicer in an immutable container (Singularity) and the install directory is not writable. From reading the above posts, it seems like there is a way to tell Slicer to keep all extensions, etc,…

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## [cannot use mpReviewpreprocessor to convert dicom to nrrd in batch mode ](https://discourse.slicer.org/t/cannot-use-mpreviewpreprocessor-to-convert-dicom-to-nrrd-in-batch-mode/18717)

<div class="topic-metadata">

**Author:** [@Vuong\_Thuy\_Tran](https://discourse.slicer.org/u/Vuong_Thuy_Tran)\
**Replies:** 3\
**Last updated:** [July 14, 2021, 3:37am UTC](https://discourse.slicer.org/t/cannot-use-mpreviewpreprocessor-to-convert-dicom-to-nrrd-in-batch-mode/18717 "2021-07-14T03:37:20Z")

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Hi, I am trying to convert dicom series to nrrd in batch mode by using mpReviewpreprocessor module in 3d slicer 4.10.2, but it always shows error like the photo below. How can I handle it? Thank you! This is error me…

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## [Show 3D does not work after editing the segmentation](https://discourse.slicer.org/t/show-3d-does-not-work-after-editing-the-segmentation/18655)

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**Author:** [@bywbilly](https://discourse.slicer.org/u/bywbilly)\
**Replies:** 3\
**Last updated:** [July 13, 2021, 4:31pm UTC](https://discourse.slicer.org/t/show-3d-does-not-work-after-editing-the-segmentation/18655 "2021-07-13T16:31:44Z")

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Hi, I have a CT scan and its segmentation. I can create a 3D view of the segmentation through the show 3D of the segmentation editor module. However, when I create a new label using the threshold method in the segmenta…

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## [TypeError: Function takes 2 positional arguments but 3 were given](https://discourse.slicer.org/t/typeerror-function-takes-2-positional-arguments-but-3-were-given/18647)

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**Author:** [@Ahmet\_Yildiz](https://discourse.slicer.org/u/Ahmet_Yildiz)\
**Replies:** 11\
**Last updated:** [July 13, 2021, 2:03pm UTC](https://discourse.slicer.org/t/typeerror-function-takes-2-positional-arguments-but-3-were-given/18647 "2021-07-13T14:03:05Z")

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I have been modifying a code to measure angle between Markup lines. It worked just fine in Slicer’s Python terminal. However, as soon as i moved on to create a module the following error pops up: TypeError: ShowAngle() …

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## [Get ROI size in pixels](https://discourse.slicer.org/t/get-roi-size-in-pixels/18665)

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**Author:** [@xackey](https://discourse.slicer.org/u/xackey)\
**Replies:** 1\
**Last updated:** [July 13, 2021, 1:58pm UTC](https://discourse.slicer.org/t/get-roi-size-in-pixels/18665 "2021-07-13T13:58:08Z")

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Dear lassoan Could you teach me how to determine the ROI size by number of pixels, not millimeter? My goal is to set both L-R and P-A ranges into 100 pixels, and make a cropped volume with x and y lengths = 100 pixels. …

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## [Using Displacement Map to Deform or Morph a Segment/Model](https://discourse.slicer.org/t/using-displacement-map-to-deform-or-morph-a-segment-model/18552)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 5\
**Last updated:** [July 13, 2021, 1:50pm UTC](https://discourse.slicer.org/t/using-displacement-map-to-deform-or-morph-a-segment-model/18552 "2021-07-13T13:50:47Z")

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Hello, Is it possible to use a displacement map/volume, like the output from the Model to Model Distance module, to deform or morph another segment/volume/model? Even if it just a simple approximation. I am trying to s…

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## [Edit and modify the geometry](https://discourse.slicer.org/t/edit-and-modify-the-geometry/18566)

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**Author:** [@smm9886](https://discourse.slicer.org/u/smm9886)\
**Replies:** 3\
**Last updated:** [July 13, 2021, 1:15pm UTC](https://discourse.slicer.org/t/edit-and-modify-the-geometry/18566 "2021-07-13T13:15:17Z")

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Hi all, I am working with some patient-specific DICOM data files in 3D-Slicer, trying to extract the aorta and coronary arteries, see the attached photo, from a whole thorax and heart model. I need to modify this mod…

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## [Unable to install extensions when Slicer is installed in system location](https://discourse.slicer.org/t/unable-to-install-extensions-when-slicer-is-installed-in-system-location/16588)

<div class="topic-metadata">

**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 1\
**Last updated:** [March 17, 2021, 4:27am UTC](https://discourse.slicer.org/t/unable-to-install-extensions-when-slicer-is-installed-in-system-location/16588 "2021-03-17T04:27:39Z")

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I have packaged and installed Slicer 4.13.0-2021-03-16 (from a local build) into a system location for all users at “C:/Program Files/Slicer 4.13.0-2021-03-16”, however I’m unable to install extensions. The following me…

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## [Defining ROI dimensions and position](https://discourse.slicer.org/t/defining-roi-dimensions-and-position/3279)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 1\
**Last updated:** [June 25, 2018, 4:30pm UTC](https://discourse.slicer.org/t/defining-roi-dimensions-and-position/3279 "2018-06-25T16:30:23Z")

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Hi, I was wondering if there is a way to define the dimensions and position of an ROI exactly either programmatically or through a given module? I am trying to do it more efficiently than dropping the ROI points and manu…

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## [Create axis trough cylinder model](https://discourse.slicer.org/t/create-axis-trough-cylinder-model/18543)

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**Author:** [@sfglio](https://discourse.slicer.org/u/sfglio)\
**Replies:** 3\
**Last updated:** [July 13, 2021, 3:06am UTC](https://discourse.slicer.org/t/create-axis-trough-cylinder-model/18543 "2021-07-13T03:06:40Z")

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I would like to create (by calculation) an axis in the middle of a cylinder (as seen in the attached file). Is this something which could be achieved in Slicer? I thought of performing hole filling in advance and ma…

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