# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=264

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

**Page:** 265

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## [Transformation matrix - RAS to LPS](https://discourse.slicer.org/t/transformation-matrix-ras-to-lps/19352)

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**Author:** [@hmaguilera](https://discourse.slicer.org/u/hmaguilera)\
**Replies:** 4\
**Last updated:** [August 26, 2021, 6:16am UTC](https://discourse.slicer.org/t/transformation-matrix-ras-to-lps/19352 "2021-08-26T06:16:38Z")

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Hi, As I read in another thread link and have been observing when I export the coordinates from slicer to .json the coordinates are saved in LPS instead of RAS. I wanted to transform some coordinates by using the trans…

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## [How to set model or segmentation occluded visibility like Markups in 3D view？](https://discourse.slicer.org/t/how-to-set-model-or-segmentation-occluded-visibility-like-markups-in-3d-view/19358)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 3\
**Last updated:** [August 26, 2021, 3:54am UTC](https://discourse.slicer.org/t/how-to-set-model-or-segmentation-occluded-visibility-like-markups-in-3d-view/19358 "2021-08-26T03:54:51Z")

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Slicer 4.11 As is shown in this video . How to set model or segmentation occluded visibility like Markups in 3D view？

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## [Load one patient onto screen](https://discourse.slicer.org/t/load-one-patient-onto-screen/19319)

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**Author:** [@alyssan](https://discourse.slicer.org/u/alyssan)\
**Replies:** 6\
**Last updated:** [August 25, 2021, 4:41pm UTC](https://discourse.slicer.org/t/load-one-patient-onto-screen/19319 "2021-08-25T16:41:32Z")

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Hello, I have a folder of dicom files but would like to automatically load on patient onto the screen every time. I have loaded my dicom files into the DICOM database using this code: dicomDataDir = "c:/my/folder/with/…

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## [Extract systematic volumes, quantify their and export their stl models](https://discourse.slicer.org/t/extract-systematic-volumes-quantify-their-and-export-their-stl-models/19302)

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**Author:** [@qubalee](https://discourse.slicer.org/u/qubalee)\
**Replies:** 12\
**Last updated:** [August 25, 2021, 2:53pm UTC](https://discourse.slicer.org/t/extract-systematic-volumes-quantify-their-and-export-their-stl-models/19302 "2021-08-25T14:53:29Z")

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Hi there! I am currently working on a volume and need to slice it into subvolumes (smaller, i.e., Rubik’s Cube), quantify each subvolume, and export it as a .stl model. I need also to increase/decrease the number of sub…

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## [Image segmentation implementation end to end](https://discourse.slicer.org/t/image-segmentation-implementation-end-to-end/19280)

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**Author:** [@Aamir\_Khan](https://discourse.slicer.org/u/Aamir_Khan)\
**Replies:** 3\
**Last updated:** [August 25, 2021, 11:52am UTC](https://discourse.slicer.org/t/image-segmentation-implementation-end-to-end/19280 "2021-08-25T11:52:13Z")

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Hi. I have been trying to implement a deep learning based automatic segmentation for pelvic bone structure. I have a few questions: Is there some open source pelvic bone structure image segmentation dataset already im…

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## [Average Hausdorff Distance](https://discourse.slicer.org/t/average-hausdorff-distance/19334)

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**Author:** [@11116](https://discourse.slicer.org/u/11116)\
**Replies:** 2\
**Last updated:** [August 25, 2021, 8:05am UTC](https://discourse.slicer.org/t/average-hausdorff-distance/19334 "2021-08-25T08:05:22Z")

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Hi, I want to use the mean Hausdorff Distance as a validaton metric to compare ground truth with predicted segmentation masks. What is the theoretical background that 3D slices use to calculate AHD? Thank you in advanc…

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## [How to use slicer to simulate the effect of blood flow in blood vessels](https://discourse.slicer.org/t/how-to-use-slicer-to-simulate-the-effect-of-blood-flow-in-blood-vessels/19328)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 3\
**Last updated:** [August 25, 2021, 4:42am UTC](https://discourse.slicer.org/t/how-to-use-slicer-to-simulate-the-effect-of-blood-flow-in-blood-vessels/19328 "2021-08-25T04:42:04Z")

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Slicer 4.11 win 64 Hello, friends, I used Slicer to create a blood vessel model, which contains arteries and veins. I want to know how to add blood flow animation to the blood vessels. Any suggestions will be helpfu…

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## [Meaning of negative values in the Deformable Vector Field histogram](https://discourse.slicer.org/t/meaning-of-negative-values-in-the-deformable-vector-field-histogram/19342)

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**Author:** [@toyama](https://discourse.slicer.org/u/toyama)\
**Replies:** 1\
**Last updated:** [August 24, 2021, 10:55pm UTC](https://discourse.slicer.org/t/meaning-of-negative-values-in-the-deformable-vector-field-histogram/19342 "2021-08-24T22:55:16Z")

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We are trying to get the histogram of each contour of the DVF to see how it changes before and after the DIR. So, I created a DVF using the transform module and got the histogram of each countour of its VectorField. Ho…

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## [Craniofacial Voxel Analysis](https://discourse.slicer.org/t/craniofacial-voxel-analysis/19235)

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**Author:** [@Jose\_Tomas\_Ahumada\_S](https://discourse.slicer.org/u/Jose_Tomas_Ahumada_S)\
**Replies:** 5\
**Last updated:** [August 24, 2021, 1:29pm UTC](https://discourse.slicer.org/t/craniofacial-voxel-analysis/19235 "2021-08-24T13:29:59Z")

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Operating system: Windows 10 Slicer version: 4.11.2021 Hello, I’m a relative new user of Slicer and I need to do a Cranio-facial voxel analysis, but I really don’t know how to do it (until the moment I know how to load…

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## [Slicer3d compilation on Ubuntu 20.04 lts](https://discourse.slicer.org/t/slicer3d-compilation-on-ubuntu-20-04-lts/19335)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 1\
**Last updated:** [August 24, 2021, 11:47am UTC](https://discourse.slicer.org/t/slicer3d-compilation-on-ubuntu-20-04-lts/19335 "2021-08-24T11:47:58Z")

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I am trying to build slicer by compiling the source code. When I am building it through cmake command it’s saying that it requires atleast 5.15.1. But when I am using qt-default , it’s not installing the required vers…

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## [ jpg series to Dicom conversion](https://discourse.slicer.org/t/jpg-series-to-dicom-conversion/19324)

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**Author:** [@SogolSadeghi](https://discourse.slicer.org/u/SogolSadeghi)\
**Replies:** 1\
**Last updated:** [August 23, 2021, 9:09pm UTC](https://discourse.slicer.org/t/jpg-series-to-dicom-conversion/19324 "2021-08-23T21:09:56Z")

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Operating system: Windows 7 x64 Slicer version:4.8.1 Expected behavior: Actual behavior:

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## [How to color different parts of a 3d model with different colors according to the pixel value from the ct scans?](https://discourse.slicer.org/t/how-to-color-different-parts-of-a-3d-model-with-different-colors-according-to-the-pixel-value-from-the-ct-scans/19321)

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**Author:** [@akshay\_pillai](https://discourse.slicer.org/u/akshay_pillai)\
**Replies:** 3\
**Last updated:** [August 23, 2021, 8:41pm UTC](https://discourse.slicer.org/t/how-to-color-different-parts-of-a-3d-model-with-different-colors-according-to-the-pixel-value-from-the-ct-scans/19321 "2021-08-23T20:41:23Z")

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I have created a 3d model of a head from ct scans of the head. I would like to know how I can color different parts of the head in different colors using the pixel value in the ct scans. Is there a way to do this? I kno…

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## [Bands appear in the painted area when segmenting brain MRI](https://discourse.slicer.org/t/bands-appear-in-the-painted-area-when-segmenting-brain-mri/19320)

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**Author:** [@H.Khasawneh](https://discourse.slicer.org/u/H.Khasawneh)\
**Replies:** 1\
**Last updated:** [August 23, 2021, 4:05pm UTC](https://discourse.slicer.org/t/bands-appear-in-the-painted-area-when-segmenting-brain-mri/19320 "2021-08-23T16:05:55Z")

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We have been facing some issues when trying to create segmentations on Brain MRI. The draw tool wouldn’t work and when we try to use the paint tool we get lines or band like segmentations instead of the circular shape of…

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## [Horos compatibility](https://discourse.slicer.org/t/horos-compatibility/9147)

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**Author:** [@Melodicpinpon](https://discourse.slicer.org/u/Melodicpinpon)\
**Replies:** 5\
**Last updated:** [August 23, 2021, 12:39pm UTC](https://discourse.slicer.org/t/horos-compatibility/9147 "2021-08-23T12:39:57Z")

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Hi, If I work with 3D Slicer, can I import and export all the data with ‘Horus’ and ‘Osirix’? Thank you

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## [Overlay a segmentation over a grayscale volume](https://discourse.slicer.org/t/overlay-a-segmentation-over-a-grayscale-volume/19314)

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**Author:** [@LHJ](https://discourse.slicer.org/u/LHJ)\
**Replies:** 1\
**Last updated:** [August 23, 2021, 12:09pm UTC](https://discourse.slicer.org/t/overlay-a-segmentation-over-a-grayscale-volume/19314 "2021-08-23T12:09:20Z")

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I want to visualize the ground truth segmentation overlayed on the chest CT volume. Last time I managed to get a clear visible segmentation overlay (shown below). However, when I try again today, I do not get the sam…

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## [Mandibular nerve canal](https://discourse.slicer.org/t/mandibular-nerve-canal/19215)

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**Author:** [@Fatih\_Hamircu](https://discourse.slicer.org/u/Fatih_Hamircu)\
**Replies:** 6\
**Last updated:** [August 23, 2021, 12:43am UTC](https://discourse.slicer.org/t/mandibular-nerve-canal/19215 "2021-08-23T00:43:18Z")

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I have dicom from the entire skull. I segmented the lower jaw from this. What I’m trying to do now: expose the lower jaw nerve canal. How can I do that? I found no video nor Tutorial.

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## [How to adjust the diameter of lines](https://discourse.slicer.org/t/how-to-adjust-the-diameter-of-lines/19299)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [August 22, 2021, 5:46pm UTC](https://discourse.slicer.org/t/how-to-adjust-the-diameter-of-lines/19299 "2021-08-22T17:46:12Z")

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How to adjust the diameter of these three kinds of lines, I want to make them thicker :smiling\_face\_with\_three\_hearts:

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## [4D ultrasound - extract 3D data to use in other applications?](https://discourse.slicer.org/t/4d-ultrasound-extract-3d-data-to-use-in-other-applications/19230)

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**Author:** [@arumiat](https://discourse.slicer.org/u/arumiat)\
**Replies:** 4\
**Last updated:** [August 21, 2021, 3:51am UTC](https://discourse.slicer.org/t/4d-ultrasound-extract-3d-data-to-use-in-other-applications/19230 "2021-08-21T03:51:36Z")

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Hi Slicer community, I’ve been sent a cardiac dataset which appears to be a number of volumes extracted directly from an ultrasound machine (I am attaching a video of all the volumes available). I have never…

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## [Crop Sequence Nodes](https://discourse.slicer.org/t/crop-sequence-nodes/19279)

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**Author:** [@tom.birdsong](https://discourse.slicer.org/u/tom.birdsong)\
**Replies:** 3\
**Last updated:** [August 20, 2021, 6:53pm UTC](https://discourse.slicer.org/t/crop-sequence-nodes/19279 "2021-08-20T18:53:24Z")

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Hi there, I am trying to decrease the size of an example ultrasound sequence dataset and am wondering if there is a way to crop along the time axis with the Sequences module. “Crop volume sequences” seems to be effectiv…

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## [How to open a centerline 3d image in 3dslicer?](https://discourse.slicer.org/t/how-to-open-a-centerline-3d-image-in-3dslicer/18921)

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**Author:** [@parvaneh.a](https://discourse.slicer.org/u/parvaneh.a)\
**Replies:** 12\
**Last updated:** [August 20, 2021, 6:47pm UTC](https://discourse.slicer.org/t/how-to-open-a-centerline-3d-image-in-3dslicer/18921 "2021-08-20T18:47:36Z")

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Operating system: ubuntu 20 Slicer version:4.11.20210226 Expected behavior: open a centerline image as expected Actual behavior: opens the centerline image abnormally Hi, I have extracted the center line of my label…

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## [4D straightened volume rendering](https://discourse.slicer.org/t/4d-straightened-volume-rendering/19269)

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**Author:** [@xiaolin](https://discourse.slicer.org/u/xiaolin)\
**Replies:** 1\
**Last updated:** [August 20, 2021, 6:19pm UTC](https://discourse.slicer.org/t/4d-straightened-volume-rendering/19269 "2021-08-20T18:19:42Z")

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Hi everyone. Warm Greetings. This is Xiaolin Sun, a doctoral student in Berlin. I am writing this message to ask for your kind help with 4D straightened volume rendering. I used the animal cardiac CT to reconstruct t…

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## [Segmentation of Mitral Valve from TEE](https://discourse.slicer.org/t/segmentation-of-mitral-valve-from-tee/19285)

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**Author:** [@HodaJavadi](https://discourse.slicer.org/u/HodaJavadi)\
**Replies:** 1\
**Last updated:** [August 20, 2021, 6:06pm UTC](https://discourse.slicer.org/t/segmentation-of-mitral-valve-from-tee/19285 "2021-08-20T18:06:09Z")

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Operating system: Windows Slicer version: 4.11.20210226 Expected behavior: Show the multi-plane images to be able to segment the Mitral Valve Actual behavior: Doesn’t show the multiplane images properly Super new to …

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## [Load Data into 3D slicer](https://discourse.slicer.org/t/load-data-into-3d-slicer/19288)

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**Author:** [@alyssan](https://discourse.slicer.org/u/alyssan)\
**Replies:** 1\
**Last updated:** [August 20, 2021, 6:02pm UTC](https://discourse.slicer.org/t/load-data-into-3d-slicer/19288 "2021-08-20T18:02:17Z")

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I am new to 3D slicer and would like to load data for segmentation using the python interactor. I have been using this code to load the sample data: import SampleData sampleDataLogic = SampleData.SampleDataLogic() ma…

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## [How to prevent Slicer from getting "Could not load: 997 Dose record as a scalar volume" error and having black screen with white dots?](https://discourse.slicer.org/t/how-to-prevent-slicer-from-getting-could-not-load-997-dose-record-as-a-scalar-volume-error-and-having-black-screen-with-white-dots/19281)

<div class="topic-metadata">

**Author:** [@geonse](https://discourse.slicer.org/u/geonse)\
**Replies:** 3\
**Last updated:** [August 20, 2021, 1:53pm UTC](https://discourse.slicer.org/t/how-to-prevent-slicer-from-getting-could-not-load-997-dose-record-as-a-scalar-volume-error-and-having-black-screen-with-white-dots/19281 "2021-08-20T13:53:40Z")

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Hi everyone, I was trying to get Brain CT images from our hospital server in Slicer preview version to annotate them via Nvidia extension. Until I fetched them everything was fine, however, when I loaded them it pops ou…

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## [Save & load (scalar opacity | Scalar color | gradient opacity) mapping settings from volume rendering?](https://discourse.slicer.org/t/save-load-scalar-opacity-scalar-color-gradient-opacity-mapping-settings-from-volume-rendering/19271)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 3\
**Last updated:** [August 19, 2021, 6:57pm UTC](https://discourse.slicer.org/t/save-load-scalar-opacity-scalar-color-gradient-opacity-mapping-settings-from-volume-rendering/19271 "2021-08-19T18:57:52Z")

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Hey all, Is there a way (python or otherwise) to save and load the “transfer curves”, meaning the scalar opacity mapping, scalar color mapping, and gradient opacity mapping settings to a file for reloading later? I do n…

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## [The image dimension changes after segment editting the segment in 3d slicer](https://discourse.slicer.org/t/the-image-dimension-changes-after-segment-editting-the-segment-in-3d-slicer/19264)

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**Author:** [@parvaneh.a](https://discourse.slicer.org/u/parvaneh.a)\
**Replies:** 1\
**Last updated:** [August 19, 2021, 10:51am UTC](https://discourse.slicer.org/t/the-image-dimension-changes-after-segment-editting-the-segment-in-3d-slicer/19264 "2021-08-19T10:51:19Z")

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Operating system: Slicer version: Expected behavior: saving the edited segment in the same dimension Actual behavior:The image dimension changes after segment editing the segment in 3d slicer I have a nii.gz segment …

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## [Read data file from disk and convert displayable node to vtkActor or vtkProp](https://discourse.slicer.org/t/read-data-file-from-disk-and-convert-displayable-node-to-vtkactor-or-vtkprop/19244)

<div class="topic-metadata">

**Author:** [@xianger-qi](https://discourse.slicer.org/u/xianger-qi)\
**Replies:** 2\
**Last updated:** [August 19, 2021, 10:48am UTC](https://discourse.slicer.org/t/read-data-file-from-disk-and-convert-displayable-node-to-vtkactor-or-vtkprop/19244 "2021-08-19T10:48:35Z")

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I have some Non-DICOM data files. such as \*.nrrd, \*.stl, etc. but how can i read these data files from disk in C++, and convert these to vtkActor or vtkProp class? Thanks for replying!

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## [Linux, visual Studio code, Single Step Debug,](https://discourse.slicer.org/t/linux-visual-studio-code-single-step-debug/19242)

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**Author:** [@xianger-qi](https://discourse.slicer.org/u/xianger-qi)\
**Replies:** 3\
**Last updated:** [August 19, 2021, 5:38am UTC](https://discourse.slicer.org/t/linux-visual-studio-code-single-step-debug/19242 "2021-08-19T05:38:59Z")

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hello every one. I have a question about slicer c++ development. my develop environment is linux os, and use visual studio code to code. how can i perform single step debug in visual studio code and have normal auto comp…

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## [Question about using NRRD files in 3D Slicer for 3D printing](https://discourse.slicer.org/t/question-about-using-nrrd-files-in-3d-slicer-for-3d-printing/19259)

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**Author:** [@DylanR](https://discourse.slicer.org/u/DylanR)\
**Replies:** 2\
**Last updated:** [August 18, 2021, 5:59pm UTC](https://discourse.slicer.org/t/question-about-using-nrrd-files-in-3d-slicer-for-3d-printing/19259 "2021-08-18T17:59:43Z")

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I am interested in using de-identified NRRD files to create STL files for 3D printing in 3D Slicer. I previously used DICOM data (CT) which works great, but want to use de-identified data. Is it correct that I can go dir…

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## [How to project fiducials on the other side of a symmetry plane ?](https://discourse.slicer.org/t/how-to-project-fiducials-on-the-other-side-of-a-symmetry-plane/19254)

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**Author:** [@Saggittaman](https://discourse.slicer.org/u/Saggittaman)\
**Replies:** 1\
**Last updated:** [August 18, 2021, 4:54pm UTC](https://discourse.slicer.org/t/how-to-project-fiducials-on-the-other-side-of-a-symmetry-plane/19254 "2021-08-18T16:54:11Z")

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Hello everyone, I created a model with a symmetry plane and I would like to project a bunch of fiducials from one side to the other side of this plane symmetrically. Do someone know if it’s possible to do this and if ye…

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