# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=128

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

**Page:** 129

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## [How to export a lung segmentation neoplasm primary to separately image files](https://discourse.slicer.org/t/how-to-export-a-lung-segmentation-neoplasm-primary-to-separately-image-files/32955)

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**Author:** [@Felix\_Mauricio\_Varga](https://discourse.slicer.org/u/Felix_Mauricio_Varga)\
**Replies:** 1\
**Last updated:** [November 22, 2023, 12:28pm UTC](https://discourse.slicer.org/t/how-to-export-a-lung-segmentation-neoplasm-primary-to-separately-image-files/32955 "2023-11-22T12:28:44Z")

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Hi, I need to view-export only lung tumor slides to images, so how to export a neoplasm lung segmentation to separately image files for example png. Thanks

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## [Direction of tool tip](https://discourse.slicer.org/t/direction-of-tool-tip/32925)

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**Author:** [@saeedeh\_lavasany](https://discourse.slicer.org/u/saeedeh_lavasany)\
**Replies:** 4\
**Last updated:** [November 22, 2023, 8:00am UTC](https://discourse.slicer.org/t/direction-of-tool-tip/32925 "2023-11-22T08:00:05Z")

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Hello, I tracked a tool using the EMT system and restored transformation matrices. I have obtained the position of the tool in a 3D space, which I’ve derived from CT/SPECT images in MATLAB. Now, I aim to represent the t…

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## [How to set matrix to slice node?](https://discourse.slicer.org/t/how-to-set-matrix-to-slice-node/32944)

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**Author:** [@derekcbr](https://discourse.slicer.org/u/derekcbr)\
**Replies:** 0\
**Last updated:** [November 22, 2023, 5:34am UTC](https://discourse.slicer.org/t/how-to-set-matrix-to-slice-node/32944 "2023-11-22T05:34:48Z")

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matrix\_transform = np.array(\[ \[1, 0, 0, 0.2\], \[0, 1, 0, 0.3\], \[0, 0, 1, 0.4\], \[0, 0, 0, 1\] \]) viewNode = ‘Green’ sliceNode = slicer.app.layoutManager().sliceWidget(viewNode).mrmlSliceNode() sliceNode.SetSliceTORA…

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## [Linking slice views to cropped volume rendering](https://discourse.slicer.org/t/linking-slice-views-to-cropped-volume-rendering/32931)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [November 21, 2023, 7:00pm UTC](https://discourse.slicer.org/t/linking-slice-views-to-cropped-volume-rendering/32931 "2023-11-21T19:00:54Z")

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I am playing with this excellent zebrafish embryo dataset Dryad | Data – Computational 3D histological phenotyping of whole zebrafish by X-ray histotomography (datadryad.org) I can do nice surface visualization with vol…

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## [Slicer 5.4.0 Sequence Loading Breaks](https://discourse.slicer.org/t/slicer-5-4-0-sequence-loading-breaks/32927)

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**Author:** [@Liam\_S](https://discourse.slicer.org/u/Liam_S)\
**Replies:** 1\
**Last updated:** [November 21, 2023, 3:17pm UTC](https://discourse.slicer.org/t/slicer-5-4-0-sequence-loading-breaks/32927 "2023-11-21T15:17:31Z")

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Hi there I have a 4D CT dataset, already saved as an NRRD sequence. I load it into slicer, save the case (incl. mrml file but excluding rewriting any image files) in the same working directory as the image and close sli…

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## [Save 3D Reconstruction](https://discourse.slicer.org/t/save-3d-reconstruction/32929)

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**Author:** [@FelixP](https://discourse.slicer.org/u/FelixP)\
**Replies:** 1\
**Last updated:** [November 21, 2023, 3:13pm UTC](https://discourse.slicer.org/t/save-3d-reconstruction/32929 "2023-11-21T15:13:59Z")

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Hey, I would appreciate, if someone could tell me how I can save my 3D Reconstruction on my Mac, so that I can later open it again and edit/measure it again? Because I first want to reconstruct my bones structure of my…

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## [Slicer Crashes During ALPACA/FastModelAlign](https://discourse.slicer.org/t/slicer-crashes-during-alpaca-fastmodelalign/32912)

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**Author:** [@AaronHardgrave](https://discourse.slicer.org/u/AaronHardgrave)\
**Replies:** 6\
**Last updated:** [November 21, 2023, 2:05pm UTC](https://discourse.slicer.org/t/slicer-crashes-during-alpaca-fastmodelalign/32912 "2023-11-21T14:05:52Z")

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Hello, I am using ALPACA to landmark vertebrae and there are certain models that will cause Slicer to crash. I have gotten most of my dataset landmarked but these select few are causing me trouble. I am trying to figure…

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## [Error occured while loading selected files](https://discourse.slicer.org/t/error-occured-while-loading-selected-files/32926)

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**Author:** [@applyints4](https://discourse.slicer.org/u/applyints4)\
**Replies:** 0\
**Last updated:** [November 21, 2023, 12:03pm UTC](https://discourse.slicer.org/t/error-occured-while-loading-selected-files/32926 "2023-11-21T12:03:29Z")

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I would like to ask for the error that occured in loading files. I worked with the 5.4.0 version and processed Dicom files. After processing, i tried to load the files at another computer with the 5.4.0 version. But e…

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## [How to use "split volume" (SegmentEditorExtraEffects Effect)](https://discourse.slicer.org/t/how-to-use-split-volume-segmenteditorextraeffects-effect/32874)

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**Author:** [@Lara](https://discourse.slicer.org/u/Lara)\
**Replies:** 5\
**Last updated:** [November 21, 2023, 11:55am UTC](https://discourse.slicer.org/t/how-to-use-split-volume-segmenteditorextraeffects-effect/32874 "2023-11-21T11:55:40Z")

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I am a biomedical engineering student and I’m doing a project using 3D Slicer. I downloaded the extension SegmentEditorExtraEffects and I need to use the tool “split volume” to isolate the jaw from the rest of the skull,…

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## [When running Slicer with Chinese parameters in CMD, how can I correctly pass and retrieve the Chinese parameters?](https://discourse.slicer.org/t/when-running-slicer-with-chinese-parameters-in-cmd-how-can-i-correctly-pass-and-retrieve-the-chinese-parameters/32920)

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**Author:** [@yulaomao](https://discourse.slicer.org/u/yulaomao)\
**Replies:** 2\
**Last updated:** [November 21, 2023, 6:49am UTC](https://discourse.slicer.org/t/when-running-slicer-with-chinese-parameters-in-cmd-how-can-i-correctly-pass-and-retrieve-the-chinese-parameters/32920 "2023-11-21T06:49:36Z")

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Hi, everyone. I would like to pass some Chinese parameters when launching Slicer, such as ‘Slicer.exe -f “你好！”’ so that I can read these parameters within Slicer. Currently, I have managed to read the parameters using ap…

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## [Segment Mesher through Jupyter notebook](https://discourse.slicer.org/t/segment-mesher-through-jupyter-notebook/32919)

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**Author:** [@ElaniaDiBart](https://discourse.slicer.org/u/ElaniaDiBart)\
**Replies:** 0\
**Last updated:** [November 21, 2023, 6:12am UTC](https://discourse.slicer.org/t/segment-mesher-through-jupyter-notebook/32919 "2023-11-21T06:12:42Z")

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Hi! I’m using Jupyter notebook to work with Slicer. I want to create a volumetric mesh of the bone that I’ve already segmented. Can anyone help me with the code? Thank you

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## [Novice Guidance for Using MONAI Label to Create an Automatic Segmentation App](https://discourse.slicer.org/t/novice-guidance-for-using-monai-label-to-create-an-automatic-segmentation-app/27504)

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**Author:** [@JacobD](https://discourse.slicer.org/u/JacobD)\
**Replies:** 20\
**Last updated:** [November 21, 2023, 5:49am UTC](https://discourse.slicer.org/t/novice-guidance-for-using-monai-label-to-create-an-automatic-segmentation-app/27504 "2023-11-21T05:49:32Z")

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I attended the recent MONAI Label Workshop, and with a background of sports medicine/orthopaedics research, I am new to this concept and do not have a strong background in computer programming. I am familiar with 3D Slic…

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## [Remove Unwanted Areas - Hip and Knee Joint Model](https://discourse.slicer.org/t/remove-unwanted-areas-hip-and-knee-joint-model/32916)

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**Author:** [@hd00561](https://discourse.slicer.org/u/hd00561)\
**Replies:** 1\
**Last updated:** [November 21, 2023, 3:35am UTC](https://discourse.slicer.org/t/remove-unwanted-areas-hip-and-knee-joint-model/32916 "2023-11-21T03:35:06Z")

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Hi there, I am required to create a 3D model of the hip and knee joint with the bones as different segments. I have used a threshold range of 99 to 242 but it includes unwanted areas of soft tissue (arteries and ca…

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## [Coral USB accelerator](https://discourse.slicer.org/t/coral-usb-accelerator/32109)

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**Author:** [@Cris](https://discourse.slicer.org/u/Cris)\
**Replies:** 5\
**Last updated:** [November 20, 2023, 12:55pm UTC](https://discourse.slicer.org/t/coral-usb-accelerator/32109 "2023-11-20T12:55:11Z")

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Can I use the Coral usb accelerator from Google for the 3d slicer?

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## [Converting .dcm to .nii.gz](https://discourse.slicer.org/t/converting-dcm-to-nii-gz/32905)

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**Author:** [@nguess19](https://discourse.slicer.org/u/nguess19)\
**Replies:** 1\
**Last updated:** [November 20, 2023, 12:39am UTC](https://discourse.slicer.org/t/converting-dcm-to-nii-gz/32905 "2023-11-20T00:39:36Z")

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Howdy, I am new to Slicer and am trying to convert dicom to nifti files for my project. The only method I have found is SlicerBatchAnonymize. At least one extension I will be using has problems reported with dicom files…

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## [Exporting DICOM files in different orientation.](https://discourse.slicer.org/t/exporting-dicom-files-in-different-orientation/32906)

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**Author:** [@Burak\_Kula](https://discourse.slicer.org/u/Burak_Kula)\
**Replies:** 1\
**Last updated:** [November 19, 2023, 9:30pm UTC](https://discourse.slicer.org/t/exporting-dicom-files-in-different-orientation/32906 "2023-11-19T21:30:41Z")

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Hello everyone, I am an MSc student and for my thesis, I have PET images in the transverse plane but for my data analysis, ı need images in the coronal plane. Is it possible to import a data set in the transverse plane …

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## [Split 4D CT scan into separate time frame series](https://discourse.slicer.org/t/split-4d-ct-scan-into-separate-time-frame-series/32740)

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**Author:** [@LindaV](https://discourse.slicer.org/u/LindaV)\
**Replies:** 6\
**Last updated:** [November 19, 2023, 10:42am UTC](https://discourse.slicer.org/t/split-4d-ct-scan-into-separate-time-frame-series/32740 "2023-11-19T10:42:05Z")

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Hello, First I would like to say that I am very impressed with all the functionalities of 3D Slicer. I am new to Slicer, so I hope I get the terminology right. For my project I am working with a 4D CT scan. Slicer can r…

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## [Problems installing pyradiomics via pip install](https://discourse.slicer.org/t/problems-installing-pyradiomics-via-pip-install/32879)

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**Author:** [@Magnus](https://discourse.slicer.org/u/Magnus)\
**Replies:** 4\
**Last updated:** [November 18, 2023, 7:23pm UTC](https://discourse.slicer.org/t/problems-installing-pyradiomics-via-pip-install/32879 "2023-11-18T19:23:53Z")

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Hello, I want to batch process a number radiomic extractions. Since I believe there is no way to do that through 3D Slicer, I tried to install pyradiomics. I’ve tried with the suggested python-versions as well as newer,…

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## [Need help for a script of saving screenshot for many times](https://discourse.slicer.org/t/need-help-for-a-script-of-saving-screenshot-for-many-times/32877)

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**Author:** [@jp\_jp\_jp](https://discourse.slicer.org/u/jp_jp_jp)\
**Replies:** 3\
**Last updated:** [November 18, 2023, 9:35am UTC](https://discourse.slicer.org/t/need-help-for-a-script-of-saving-screenshot-for-many-times/32877 "2023-11-18T09:35:07Z")

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Hi, I am working on this red slice The range is from -500mm to 500mm, and all I know is I can save it by clicking Annotation Screenshot, and choosing Red Slice View It would be great if someone could provide a Pyt…

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## [N4ITKBiasFieldCorrection using nipype error](https://discourse.slicer.org/t/n4itkbiasfieldcorrection-using-nipype-error/32880)

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**Author:** [@georgek](https://discourse.slicer.org/u/georgek)\
**Replies:** 0\
**Last updated:** [November 17, 2023, 4:09pm UTC](https://discourse.slicer.org/t/n4itkbiasfieldcorrection-using-nipype-error/32880 "2023-11-17T16:09:57Z")

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Hi all, I am just getting started with nipype and trying to perform N4 bias field correction on MR images. Here is the relevant code: import nipype import nipype.interfaces.slicer as Slicer BFC=Slicer.N4ITKBiasFieldC…

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## [Internal Structure of STL](https://discourse.slicer.org/t/internal-structure-of-stl/32812)

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**Author:** [@WillSteger](https://discourse.slicer.org/u/WillSteger)\
**Replies:** 3\
**Last updated:** [November 17, 2023, 12:00pm UTC](https://discourse.slicer.org/t/internal-structure-of-stl/32812 "2023-11-17T12:00:25Z")

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Hi, I’m a new 3D Slicer user attempting to use it for dental research purposes. Specifically, I have been sent a series of STL models built from microCT scans and have been asked to isolate the enamel-dentine junction (…

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## [How to get the CT value (HU) of ROI; and area of ROI using markup closed curve? ](https://discourse.slicer.org/t/how-to-get-the-ct-value-hu-of-roi-and-area-of-roi-using-markup-closed-curve/32873)

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**Author:** [@SUSZHF](https://discourse.slicer.org/u/SUSZHF)\
**Replies:** 0\
**Last updated:** [November 17, 2023, 11:55am UTC](https://discourse.slicer.org/t/how-to-get-the-ct-value-hu-of-roi-and-area-of-roi-using-markup-closed-curve/32873 "2023-11-17T11:55:02Z")

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How to get the CT value (unit:Hu) of ROI for muscle and vetebra using 3D Slicer? In addition, i don’t ensure whether the value of area of ROI is correct using the method “markup-closed curve-Quantification-segment statis…

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## [TotalSegmentator](https://discourse.slicer.org/t/totalsegmentator/32687)

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**Author:** [@yuanw](https://discourse.slicer.org/u/yuanw)\
**Replies:** 4\
**Last updated:** [November 17, 2023, 1:57am UTC](https://discourse.slicer.org/t/totalsegmentator/32687 "2023-11-17T01:57:07Z")

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When I use the Total Segmentator module for total segmentation, if I select full resolution, the following error will appear, but if I select fast, the following error will not appear. Failed to compute results. Comman…

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## [Scaling Segmentation in 3D space](https://discourse.slicer.org/t/scaling-segmentation-in-3d-space/32784)

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**Author:** [@lena\_b](https://discourse.slicer.org/u/lena_b)\
**Replies:** 7\
**Last updated:** [November 16, 2023, 10:23pm UTC](https://discourse.slicer.org/t/scaling-segmentation-in-3d-space/32784 "2023-11-16T22:23:20Z")

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Hello, Is there a feature where you can scale a segmentation? I have used the Warping Tool in the Fiducial Registration Wizard, but for certain objects it requires too many points. Are there x, y, z sliders (for example)…

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## [How to "slice through" the model, like when browsing a series of images?](https://discourse.slicer.org/t/how-to-slice-through-the-model-like-when-browsing-a-series-of-images/32861)

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**Author:** [@Blizna](https://discourse.slicer.org/u/Blizna)\
**Replies:** 6\
**Last updated:** [November 16, 2023, 8:50pm UTC](https://discourse.slicer.org/t/how-to-slice-through-the-model-like-when-browsing-a-series-of-images/32861 "2023-11-16T20:50:57Z")

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Hello! I’m a new user, neuroscientist, and I’m just exploring this amazing tool. I viewed a few tutorials and I managed to import a DICOM series of a brain MRI into the tool, and get it shown in 3D. However - and this i…

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## [Exported meshes have incorrect colors](https://discourse.slicer.org/t/exported-meshes-have-incorrect-colors/32811)

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**Author:** [@jaimigray](https://discourse.slicer.org/u/jaimigray)\
**Replies:** 21\
**Last updated:** [November 16, 2023, 7:19pm UTC](https://discourse.slicer.org/t/exported-meshes-have-incorrect-colors/32811 "2023-11-16T19:19:57Z")

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I’m exporting multiple models for my skull anatomy models. I cannot get Slicer to export my models with their colors. Anyone know how to get the models exported with their colors? I have tried exporting them in several d…

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## [BoneTexture extension Attribute error](https://discourse.slicer.org/t/bonetexture-extension-attribute-error/32863)

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**Author:** [@thangngoc89](https://discourse.slicer.org/u/thangngoc89)\
**Replies:** 2\
**Last updated:** [November 16, 2023, 7:18pm UTC](https://discourse.slicer.org/t/bonetexture-extension-attribute-error/32863 "2023-11-16T19:18:30Z")

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I encountered an error with BoneTexture module, it’s probably because it wasn’t updated with the latest code changes from 3D Slicer. As soon as I load the BoneTexture module, an error was thrown in the console and none …

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## [Trying to save edits to a DICOM file](https://discourse.slicer.org/t/trying-to-save-edits-to-a-dicom-file/32860)

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**Author:** [@John\_Wilcox](https://discourse.slicer.org/u/John_Wilcox)\
**Replies:** 1\
**Last updated:** [November 16, 2023, 6:56pm UTC](https://discourse.slicer.org/t/trying-to-save-edits-to-a-dicom-file/32860 "2023-11-16T18:56:21Z")

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Operating system: macOS Slicer version: 5.4.0 First time using Slicer, and I have uploaded and edited a DICOM file. I have made simple volume renderings to it and I am trying to save this to re-access it at a later dat…

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## [Segment Editor Causes Freeze](https://discourse.slicer.org/t/segment-editor-causes-freeze/32821)

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**Author:** [@KiraKiralina](https://discourse.slicer.org/u/KiraKiralina)\
**Replies:** 2\
**Last updated:** [November 16, 2023, 5:06pm UTC](https://discourse.slicer.org/t/segment-editor-causes-freeze/32821 "2023-11-16T17:06:50Z")

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Hi all, 3D Slicer keeps throwing this error when I load it up. Once it does, it acts normally until I try to edit a segment, and then it freezes on me. I’ve tried everything I can think of to fix this and can’t. The on…

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## [Connect 3D Slicer with Oculus Quest 2](https://discourse.slicer.org/t/connect-3d-slicer-with-oculus-quest-2/32800)

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**Author:** [@antonella\_siso](https://discourse.slicer.org/u/antonella_siso)\
**Replies:** 1\
**Last updated:** [November 16, 2023, 3:52pm UTC](https://discourse.slicer.org/t/connect-3d-slicer-with-oculus-quest-2/32800 "2023-11-16T15:52:51Z")

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Hello, I have tried to connect the Oculus Quest 2 through the VR slicer and I have not been able to. If you could advise me on how to connect it to the 3D slicer, I would appreciate it.

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