# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=250

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

**Page:** 251

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## [AVI to DICOM to single usuable DICOM file](https://discourse.slicer.org/t/avi-to-dicom-to-single-usuable-dicom-file/20628)

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**Author:** [@Chuns\_SS](https://discourse.slicer.org/u/Chuns_SS)\
**Replies:** 2\
**Last updated:** [November 17, 2021, 1:03am UTC](https://discourse.slicer.org/t/avi-to-dicom-to-single-usuable-dicom-file/20628 "2021-11-17T01:03:43Z")

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HI I received 3 AVI files of a CT scan, one axial and one coronal etc. I am able to convert the AVI files to crude DICOM files but is there anyway to combine them to a single DICOM file.

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## [Modelling the Anterior Muscle Compartment](https://discourse.slicer.org/t/modelling-the-anterior-muscle-compartment/20554)

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**Author:** [@ejdr33s](https://discourse.slicer.org/u/ejdr33s)\
**Replies:** 7\
**Last updated:** [November 16, 2021, 10:47pm UTC](https://discourse.slicer.org/t/modelling-the-anterior-muscle-compartment/20554 "2021-11-16T22:47:34Z")

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Hi there. I’m completely new to 3D slicer, let me preface that. My objective is to create a model of the anterior muscle compartment of the leg. I have found an MRI scan of the lower leg, shown in the attached image. My…

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## [Info EMSegmenter ](https://discourse.slicer.org/t/info-emsegmenter/20647)

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**Author:** [@19lollo95](https://discourse.slicer.org/u/19lollo95)\
**Replies:** 1\
**Last updated:** [November 16, 2021, 9:50pm UTC](https://discourse.slicer.org/t/info-emsegmenter/20647 "2021-11-16T21:50:34Z")

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Hi, I’m going to use 3D-Slicer for the first time. Where I can find in the last versions (I installed Slicer-4.11.20210226) the equivalent of EMSegmenter that I can find it in version 3.6.3? Thanks

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## [Deformable registration between two CTs](https://discourse.slicer.org/t/deformable-registration-between-two-cts/20564)

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**Author:** [@alan6690](https://discourse.slicer.org/u/alan6690)\
**Replies:** 8\
**Last updated:** [November 16, 2021, 3:32pm UTC](https://discourse.slicer.org/t/deformable-registration-between-two-cts/20564 "2021-11-16T15:32:13Z")

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Hello. I am a new user of 3D slicer. I am trying to deformably register a set of CBCT with regular CT. However, the CBCT has a much smaller FOV so that there is a large dark region outside the FOV, in which regular CT d…

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## [New feature: configurable volume display presets in right-click menu and Volumes module](https://discourse.slicer.org/t/new-feature-configurable-volume-display-presets-in-right-click-menu-and-volumes-module/20640)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 0\
**Last updated:** [November 16, 2021, 9:22am UTC](https://discourse.slicer.org/t/new-feature-configurable-volume-display-presets-in-right-click-menu-and-volumes-module/20640 "2021-11-16T09:22:57Z")

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Volume display preset selections have been added to the slice view right-click menu (view context menu). It offers setting volume display (window width and level and colormap) from: Window/level presets stored in the v…

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## [CT / MRI Registration on pelvis](https://discourse.slicer.org/t/ct-mri-registration-on-pelvis/20623)

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**Author:** [@Vincebisca](https://discourse.slicer.org/u/Vincebisca)\
**Replies:** 6\
**Last updated:** [November 16, 2021, 8:38am UTC](https://discourse.slicer.org/t/ct-mri-registration-on-pelvis/20623 "2021-11-16T08:38:26Z")

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Hello, I am seeking some help on the available features for automatic image registration involving CT + MRI images. I am searching a way on 3D Slicer to align 2 stacks of images, one being a CT, the other a T2-weighted …

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## [Problem with SlicerRT in Slicer version 4.11.20210226 r29738 / 7a593c8](https://discourse.slicer.org/t/problem-with-slicerrt-in-slicer-version-4-11-20210226-r29738-7a593c8/20510)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 13\
**Last updated:** [November 16, 2021, 6:36am UTC](https://discourse.slicer.org/t/problem-with-slicerrt-in-slicer-version-4-11-20210226-r29738-7a593c8/20510 "2021-11-16T06:36:49Z")

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Hello Dear Developers and Users I can load Structure (RTStructure), Plan (RTPlan) and CT images in dicom format with SlicerRT in Slicer version: 4.10.2 r28257 completely. At now, I want to load these data in SlicerRT w…

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## [Not being able to reconstruct 3D ultrasound images](https://discourse.slicer.org/t/not-being-able-to-reconstruct-3d-ultrasound-images/20636)

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**Author:** [@CompSci101](https://discourse.slicer.org/u/CompSci101)\
**Replies:** 1\
**Last updated:** [November 16, 2021, 6:18am UTC](https://discourse.slicer.org/t/not-being-able-to-reconstruct-3d-ultrasound-images/20636 "2021-11-16T06:18:05Z")

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Operating system: macOS Big Sur Slicer version:4.11.20210226 Expected behavior:For the reconstruction of the 3D ultrasound to display a 3D image similar to the tutorial with the dataset of the TorsoCT. Actual behavior…

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## [Volume rendering appearance changes if ROI box is shown](https://discourse.slicer.org/t/volume-rendering-appearance-changes-if-roi-box-is-shown/20575)

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**Author:** [@DIV](https://discourse.slicer.org/u/DIV)\
**Replies:** 13\
**Last updated:** [November 16, 2021, 5:39am UTC](https://discourse.slicer.org/t/volume-rendering-appearance-changes-if-roi-box-is-shown/20575 "2021-11-16T05:39:02Z")

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Hello, all. I’m not sure whether this is related, but I am seeing an odd dependence of the 3D rendering when toggling the ROI visibility (specifically the ROI that is always enabled to crop the displayed 3D rendering). …

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## [How do access the source filepath(s) of a DICOM image given a \`vtkMRMLScalarVolumeNode\`](https://discourse.slicer.org/t/how-do-access-the-source-filepath-s-of-a-dicom-image-given-a-vtkmrmlscalarvolumenode/20619)

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**Author:** [@aarashy](https://discourse.slicer.org/u/aarashy)\
**Replies:** 2\
**Last updated:** [November 16, 2021, 3:58am UTC](https://discourse.slicer.org/t/how-do-access-the-source-filepath-s-of-a-dicom-image-given-a-vtkmrmlscalarvolumenode/20619 "2021-11-16T03:58:07Z")

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Hello! I’m making my first Slicer plugin, and my goal is to use the pydicom package to read a DICOM file, i.e. pydicom.read\_file(\< Path to the .dcm file, whether it was copied or linked during import \>) I am having tro…

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## [Exporting DICOM with Markups](https://discourse.slicer.org/t/exporting-dicom-with-markups/20609)

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**Author:** [@neuralnet](https://discourse.slicer.org/u/neuralnet)\
**Replies:** 10\
**Last updated:** [November 16, 2021, 3:43am UTC](https://discourse.slicer.org/t/exporting-dicom-with-markups/20609 "2021-11-16T03:43:33Z")

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Hi all, I have a volume that I have marked up with several fiducial points that are clinically useful. I hope to export this back out to DICOM, including the markups (ideally these markups would be visible even in anoth…

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## [Unable to download extensions from the extensions manager](https://discourse.slicer.org/t/unable-to-download-extensions-from-the-extensions-manager/20618)

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**Author:** [@nforwood](https://discourse.slicer.org/u/nforwood)\
**Replies:** 2\
**Last updated:** [November 15, 2021, 11:22pm UTC](https://discourse.slicer.org/t/unable-to-download-extensions-from-the-extensions-manager/20618 "2021-11-15T23:22:40Z")

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Operating system: Windows 10 Slicer version:4.11.20210226 Expected behavior: Download works Actual behavior: Get an error “Error retrieving extension metadata: 60ae226cae4540bf6a89da9d ({303b7c63-e615-43d7-9232-688ef5…

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## [DICOM Browser Layout](https://discourse.slicer.org/t/dicom-browser-layout/8148)

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**Author:** [@Sunderlandkyl](https://discourse.slicer.org/u/Sunderlandkyl)\
**Replies:** 9\
**Last updated:** [November 15, 2021, 9:47pm UTC](https://discourse.slicer.org/t/dicom-browser-layout/8148 "2021-11-15T21:47:25Z")

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The latest nightly builds on all platforms include an updated DICOM browser that is embedded within a layout, rather than as a popup window. To show the dicom browser within a module: slicer.app.layoutManager().set…

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## [OpenIGTLink Fiducial Marker Transfer seems to max out at 2^16 bytes](https://discourse.slicer.org/t/openigtlink-fiducial-marker-transfer-seems-to-max-out-at-2-16-bytes/20587)

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**Author:** [@afhall](https://discourse.slicer.org/u/afhall)\
**Replies:** 7\
**Last updated:** [November 15, 2021, 7:21pm UTC](https://discourse.slicer.org/t/openigtlink-fiducial-marker-transfer-seems-to-max-out-at-2-16-bytes/20587 "2021-11-15T19:21:27Z")

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Operating system: Windows 10 Slicer version: 4.11 Expected behavior: OpenIGTLink - Fiducial marker transfer of all points Actual behavior: OpenIGTLink seems to max out at 2^16 bytes regardless of number of fiducials t…

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## [Zoom factor quantification](https://discourse.slicer.org/t/zoom-factor-quantification/20603)

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**Author:** [@CETUS](https://discourse.slicer.org/u/CETUS)\
**Replies:** 1\
**Last updated:** [November 15, 2021, 7:13am UTC](https://discourse.slicer.org/t/zoom-factor-quantification/20603 "2021-11-15T07:13:28Z")

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Hi, I was curious to ask, is there a specific module or window in 3D slicer that displays the zoom factor changed by the mouse as a percentage, or allows it to be set to a specific percentage? (for example, I have 3 scan…

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## [Colour Gradient Based on Pixel Density of Overlaid Segmentations?](https://discourse.slicer.org/t/colour-gradient-based-on-pixel-density-of-overlaid-segmentations/20294)

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**Author:** [@Greg](https://discourse.slicer.org/u/Greg)\
**Replies:** 11\
**Last updated:** [November 14, 2021, 4:53pm UTC](https://discourse.slicer.org/t/colour-gradient-based-on-pixel-density-of-overlaid-segmentations/20294 "2021-11-14T16:53:41Z")

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Hello, I am new to 3D slicer, but I have a series of MRIs which I have overlaid and segmented. I would like to now take those segmentations and apply a filter to visualize their overlap. I have seen this done with two s…

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## [Exporting 2 volumes as a stack of image files (PNG).](https://discourse.slicer.org/t/exporting-2-volumes-as-a-stack-of-image-files-png/20187)

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**Author:** [@neuralnet](https://discourse.slicer.org/u/neuralnet)\
**Replies:** 2\
**Last updated:** [November 12, 2021, 10:25pm UTC](https://discourse.slicer.org/t/exporting-2-volumes-as-a-stack-of-image-files-png/20187 "2021-11-12T22:25:15Z")

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Operating system: Windows 10 Slicer version: 4.10.2 Expected behavior: N/A Actual behavior: N/A Hi all, I am very new to slicer and to medical imaging in general, so I apologize if this question is very obvious. I …

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## [Tutorial For Making 3D MODEL of Cranial Defect Using 3D SLICERV](https://discourse.slicer.org/t/tutorial-for-making-3d-model-of-cranial-defect-using-3d-slicerv/20599)

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**Author:** [@Pinslahore](https://discourse.slicer.org/u/Pinslahore)\
**Replies:** 1\
**Last updated:** [November 12, 2021, 1:05pm UTC](https://discourse.slicer.org/t/tutorial-for-making-3d-model-of-cranial-defect-using-3d-slicerv/20599 "2021-11-12T13:05:41Z")

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Is their tutorial availabel for making 3d model of cranial defect and i want to know how i can get an STL file of the model for 3D printing .

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## [Checkerboard for registered MRI and CT of hip bone](https://discourse.slicer.org/t/checkerboard-for-registered-mri-and-ct-of-hip-bone/18768)

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**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 12\
**Last updated:** [November 12, 2021, 6:25am UTC](https://discourse.slicer.org/t/checkerboard-for-registered-mri-and-ct-of-hip-bone/18768 "2021-11-12T06:25:20Z")

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Hi everyone, I would like to make a checkerboard image of my registered CT and MRI. This is what I get when the CT image is input volume 1: and this is when I have MRI as the input volume 1: How can I optimize t…

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## [Wacom Tablet Slows Down Slicer During Segmentation](https://discourse.slicer.org/t/wacom-tablet-slows-down-slicer-during-segmentation/20589)

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**Author:** [@DeeMos](https://discourse.slicer.org/u/DeeMos)\
**Replies:** 1\
**Last updated:** [November 11, 2021, 10:47pm UTC](https://discourse.slicer.org/t/wacom-tablet-slows-down-slicer-during-segmentation/20589 "2021-11-11T22:47:21Z")

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Hello. I’ve recently purchased a Wacom Intuos Pro tablet (small size) in the hopes that it would help me speed up my segmentations. However, I’ve noticed that 3D Slicer actually slows down significantly whenever I try t…

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## [FileFormatError when loading PET CT](https://discourse.slicer.org/t/fileformaterror-when-loading-pet-ct/20579)

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**Author:** [@rbumm](https://discourse.slicer.org/u/rbumm)\
**Replies:** 3\
**Last updated:** [November 11, 2021, 5:46pm UTC](https://discourse.slicer.org/t/fileformaterror-when-loading-pet-ct/20579 "2021-11-11T17:46:23Z")

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Hi, I would like to load PET CT images into Slicer 3.13, DICOM import works, but clicking the axial 512x512 PET image series results in: Could not read scalar volume using GDCM approach. Error is: FileFormatError Loadi…

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## [Standard way of running modules from the command line](https://discourse.slicer.org/t/standard-way-of-running-modules-from-the-command-line/20552)

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**Author:** [@Connor-Bowley](https://discourse.slicer.org/u/Connor-Bowley)\
**Replies:** 2\
**Last updated:** [November 11, 2021, 1:57pm UTC](https://discourse.slicer.org/t/standard-way-of-running-modules-from-the-command-line/20552 "2021-11-11T13:57:00Z")

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It would be nice to be able to run some modules from the command line, especially in cases of long running/computationally intensive modules that would be convenient to run on a server. My understanding is that there is …

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## [Scoliosis Module](https://discourse.slicer.org/t/scoliosis-module/20569)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 2\
**Last updated:** [November 11, 2021, 1:03pm UTC](https://discourse.slicer.org/t/scoliosis-module/20569 "2021-11-11T13:03:56Z")

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I have been going through my downloaded extensions and modifying the scripts that apparently have minor issues, probably from using different systems or different python versions, such as print statements that do not hav…

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## [Realization of neuronavigation](https://discourse.slicer.org/t/realization-of-neuronavigation/17523)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 8\
**Last updated:** [November 11, 2021, 5:55am UTC](https://discourse.slicer.org/t/realization-of-neuronavigation/17523 "2021-11-11T05:55:30Z")

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I would love to try the navigation function of this camera, but how should I operate it and which app should I download?Where can I get a more detailed tutorial

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## [VTK file visualization and surface/volume mesh extraction](https://discourse.slicer.org/t/vtk-file-visualization-and-surface-volume-mesh-extraction/20573)

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**Author:** [@EMIL\_fluidM](https://discourse.slicer.org/u/EMIL_fluidM)\
**Replies:** 1\
**Last updated:** [November 11, 2021, 2:47am UTC](https://discourse.slicer.org/t/vtk-file-visualization-and-surface-volume-mesh-extraction/20573 "2021-11-11T02:47:22Z")

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I have a output vtk file from a program that i need to use to create a surface mesh. Some, issues i am having is loading the file in slicer shows strands of surface instead of a clean/connected surface. Changing the view…

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## [DCM Images are blurry and poorly defined](https://discourse.slicer.org/t/dcm-images-are-blurry-and-poorly-defined/20549)

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**Author:** [@Maria\_Lopes](https://discourse.slicer.org/u/Maria_Lopes)\
**Replies:** 1\
**Last updated:** [November 10, 2021, 9:09pm UTC](https://discourse.slicer.org/t/dcm-images-are-blurry-and-poorly-defined/20549 "2021-11-10T21:09:45Z")

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Hi. I’m doing my master’s thesis and I´m getting desperat… When I load the magnetic ressonance images in format dcm, only one plan (coronal, sagittal, axial) is defined. The images from the other plans are blurry and p…

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## [Nvidia AI Assisted Annotation with CT images](https://discourse.slicer.org/t/nvidia-ai-assisted-annotation-with-ct-images/20556)

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**Author:** [@TaraGh](https://discourse.slicer.org/u/TaraGh)\
**Replies:** 4\
**Last updated:** [November 10, 2021, 8:56pm UTC](https://discourse.slicer.org/t/nvidia-ai-assisted-annotation-with-ct-images/20556 "2021-11-10T20:56:32Z")

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Hello, I have a problem in using Nvidia AI-Assisted Annotation for CT images of the head and neck. I want to segment organs at risk with this extension but if I run, I get errors like this images: (I’ have installed the…

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## [Unable to find specific revision of 3DSlicer](https://discourse.slicer.org/t/unable-to-find-specific-revision-of-3dslicer/20568)

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**Author:** [@DeepaKrishnaswamy](https://discourse.slicer.org/u/DeepaKrishnaswamy)\
**Replies:** 5\
**Last updated:** [November 10, 2021, 5:07pm UTC](https://discourse.slicer.org/t/unable-to-find-specific-revision-of-3dslicer/20568 "2021-11-10T17:07:35Z")

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Hi, I am trying to use the module mpReview ( Documentation · SlicerProstate/mpReview Wiki · GitHub) which requires the use of these 3DSlicer versions as listed in the link: macOS: http://download.slicer.org/download?os…

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## [The user-tutorial cannot be readed in China](https://discourse.slicer.org/t/the-user-tutorial-cannot-be-readed-in-china/20536)

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**Author:** [@fanyifeng](https://discourse.slicer.org/u/fanyifeng)\
**Replies:** 7\
**Last updated:** [November 9, 2021, 10:42pm UTC](https://discourse.slicer.org/t/the-user-tutorial-cannot-be-readed-in-china/20536 "2021-11-09T22:42:05Z")

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The user-tutorial(User tutorial | SlicerIGT) cannot be readed in China.

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## [Sequences module GUI does not update when modified](https://discourse.slicer.org/t/sequences-module-gui-does-not-update-when-modified/20551)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 2\
**Last updated:** [November 9, 2021, 8:21pm UTC](https://discourse.slicer.org/t/sequences-module-gui-does-not-update-when-modified/20551 "2021-11-09T20:21:29Z")

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I used the Crop Volume Sequence module to create a new cropped version of a volume sequence. This worked fine, but the resulting sequence is not listed in the Sequences module, despite it clearly having been added to th…

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