# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=310

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

**Page:** 311

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## [Isolated muscle segmentation from MRI](https://discourse.slicer.org/t/isolated-muscle-segmentation-from-mri/14628)

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**Author:** [@Sz368](https://discourse.slicer.org/u/Sz368)\
**Replies:** 6\
**Last updated:** [November 20, 2020, 3:05pm UTC](https://discourse.slicer.org/t/isolated-muscle-segmentation-from-mri/14628 "2020-11-20T15:05:13Z")

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Hello everybody I am creating a 3D foot from a MRI for medical education. I see Materialise/Mimic say they have a ‘gradient’ application where you can trace muscle to the boundary of the most contrast tissue difference …

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## [Radiomics Image normalization](https://discourse.slicer.org/t/radiomics-image-normalization/14710)

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**Author:** [@sarvpriya1985](https://discourse.slicer.org/u/sarvpriya1985)\
**Replies:** 0\
**Last updated:** [November 20, 2020, 2:30pm UTC](https://discourse.slicer.org/t/radiomics-image-normalization/14710 "2020-11-20T14:30:19Z")

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Hi everyone, I would like to ask about process of doing image normalization for radionics. I have multi sequence MRI brain images. I would like your opinion on should I first normalize the entire image or I should first…

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## [Use python to run toolbar function](https://discourse.slicer.org/t/use-python-to-run-toolbar-function/14708)

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**Author:** [@Changing](https://discourse.slicer.org/u/Changing)\
**Replies:** 0\
**Last updated:** [November 20, 2020, 11:49am UTC](https://discourse.slicer.org/t/use-python-to-run-toolbar-function/14708 "2020-11-20T11:49:26Z")

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Hello,I want to know how can I use python python to run toolbar function in the 3D slicer.For example,I want to use python to run the next frame function automactically.I refer to the ScriptRepository examples and I try …

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## [NIFTI data batch pcocessing](https://discourse.slicer.org/t/nifti-data-batch-pcocessing/14698)

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**Author:** [@Legendsevl](https://discourse.slicer.org/u/Legendsevl)\
**Replies:** 4\
**Last updated:** [November 20, 2020, 7:22am UTC](https://discourse.slicer.org/t/nifti-data-batch-pcocessing/14698 "2020-11-20T07:22:41Z")

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3D slicer uses Slicer Radiology and NVIDIA AIAA extension to achieve good results in image feature extraction, image segmentation and other fields. However, these extensions usually deal with a single medical image ( nii…

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## [binary label map layers](https://discourse.slicer.org/t/binary-label-map-layers/14701)

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**Author:** [@dzf](https://discourse.slicer.org/u/dzf)\
**Replies:** 0\
**Last updated:** [November 20, 2020, 4:40am UTC](https://discourse.slicer.org/t/binary-label-map-layers/14701 "2020-11-20T04:40:50Z")

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Operating system: windows10 Slicer version: 4.11.20200930 Expected behavior: every segment in different layers after saving Actual behavior: all segments are automatically collapse 1 layer after saving. how can i sol…

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## [Exporting data from DSIstudio to 3DSlicer](https://discourse.slicer.org/t/exporting-data-from-dsistudio-to-3dslicer/14690)

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**Author:** [@SteveJJ](https://discourse.slicer.org/u/SteveJJ)\
**Replies:** 0\
**Last updated:** [November 19, 2020, 2:53pm UTC](https://discourse.slicer.org/t/exporting-data-from-dsistudio-to-3dslicer/14690 "2020-11-19T14:53:40Z")

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Hello I have some data in DSI studio which I would like to visualise in slicer using the standard diffusion MRI tools. Does anyone know how to do this? Thanks Steve

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## [Landmark Detection/Registration difficulties](https://discourse.slicer.org/t/landmark-detection-registration-difficulties/14689)

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**Author:** [@Cesar\_Puga](https://discourse.slicer.org/u/Cesar_Puga)\
**Replies:** 0\
**Last updated:** [November 19, 2020, 2:32pm UTC](https://discourse.slicer.org/t/landmark-detection-registration-difficulties/14689 "2020-11-19T14:32:09Z")

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Dear Slicer Community, During the last months i have been trying to solve a problem that i cant find a solution to, therefore i would like to kindly ask your support with ideas on how to approach it, I’m trying to dete…

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## [Image definition spontaneous problem! ](https://discourse.slicer.org/t/image-definition-spontaneous-problem/14662)

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**Author:** [@hernandez42](https://discourse.slicer.org/u/hernandez42)\
**Replies:** 6\
**Last updated:** [November 19, 2020, 1:04pm UTC](https://discourse.slicer.org/t/image-definition-spontaneous-problem/14662 "2020-11-19T13:04:35Z")

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Hi everybody! This problem happened spontaneously, I did not change any setting of 3D Slicer so I can not get around why I am having this issue! So, any help will be more than welcome! I am working with .nii.gz files (…

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## [Connect to a running Slicer session](https://discourse.slicer.org/t/connect-to-a-running-slicer-session/14685)

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**Author:** [@pll\_llq](https://discourse.slicer.org/u/pll_llq)\
**Replies:** 1\
**Last updated:** [November 19, 2020, 12:48pm UTC](https://discourse.slicer.org/t/connect-to-a-running-slicer-session/14685 "2020-11-19T12:48:54Z")

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Is there a way to connect to a running Slicer session from a standalone script? Given I have Slicer open And I have an image open in Slicer And I have a python script resting on my desktop When I execute the python scri…

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## [How to get the RAS coordinates of the pixel in a slice view by using python code](https://discourse.slicer.org/t/how-to-get-the-ras-coordinates-of-the-pixel-in-a-slice-view-by-using-python-code/14668)

<div class="topic-metadata">

**Author:** [@Changing](https://discourse.slicer.org/u/Changing)\
**Replies:** 5\
**Last updated:** [November 19, 2020, 8:56am UTC](https://discourse.slicer.org/t/how-to-get-the-ras-coordinates-of-the-pixel-in-a-slice-view-by-using-python-code/14668 "2020-11-19T08:56:12Z")

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Hello,I am using the SlicerHeart module.There is a valve view function there.It can rotate the slice view(‘red’,‘green’,‘yellow’) to any angle. My goal is as followed:I want to add fiducial in the rotating slice view in…

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## [AI segmentation extension with GPU](https://discourse.slicer.org/t/ai-segmentation-extension-with-gpu/14681)

<div class="topic-metadata">

**Author:** [@Legendsevl](https://discourse.slicer.org/u/Legendsevl)\
**Replies:** 4\
**Last updated:** [November 19, 2020, 7:05am UTC](https://discourse.slicer.org/t/ai-segmentation-extension-with-gpu/14681 "2020-11-19T07:05:44Z")

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Operating system:Win10 Slicer version:4.11 Expected behavior:local GPU accelerate Actual behavior:I know that volume rendering can accelerate GPU, but in other extensions, such as NVIDIA’s segmentation model, data is …

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## [Minimum Distance Between Segmentations](https://discourse.slicer.org/t/minimum-distance-between-segmentations/14646)

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**Author:** [@ahopf](https://discourse.slicer.org/u/ahopf)\
**Replies:** 3\
**Last updated:** [November 19, 2020, 3:14am UTC](https://discourse.slicer.org/t/minimum-distance-between-segmentations/14646 "2020-11-19T03:14:04Z")

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I am trying to calculate the minimum Hausdorff distance between two segmentations. I am new to coding and wondering if someone can tell me if the code (from the Support discussion thread “Distance between two segments”) …

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## [Viewport brightness/contrast adjustments broken in Big Sur?](https://discourse.slicer.org/t/viewport-brightness-contrast-adjustments-broken-in-big-sur/14678)

<div class="topic-metadata">

**Author:** [@pll\_llq](https://discourse.slicer.org/u/pll_llq)\
**Replies:** 4\
**Last updated:** [November 18, 2020, 9:12pm UTC](https://discourse.slicer.org/t/viewport-brightness-contrast-adjustments-broken-in-big-sur/14678 "2020-11-18T21:12:36Z")

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Hi there, After the Big Sur update on my Mac I noticed that clicking and dragging over viewport windows with slices does not change the image brightness/contrast as it used to. Is this a bug or did I miss a migration o…

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## [Volume rendering - staircase artifacts](https://discourse.slicer.org/t/volume-rendering-staircase-artifacts/14666)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 7\
**Last updated:** [November 18, 2020, 7:13pm UTC](https://discourse.slicer.org/t/volume-rendering-staircase-artifacts/14666 "2020-11-18T19:13:36Z")

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We have been discussing this tweet that compares volume rendering in Slicer to the commercial VG Studio software. The question of staircase artifacts came up and thought that the discussion could be of general interest. …

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## [How does the aortic diameter in cross-section analysis calculated?](https://discourse.slicer.org/t/how-does-the-aortic-diameter-in-cross-section-analysis-calculated/14653)

<div class="topic-metadata">

**Author:** [@chendong9416](https://discourse.slicer.org/u/chendong9416)\
**Replies:** 9\
**Last updated:** [November 18, 2020, 12:05pm UTC](https://discourse.slicer.org/t/how-does-the-aortic-diameter-in-cross-section-analysis-calculated/14653 "2020-11-18T12:05:13Z")

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Hi, i just want to know how the aortic diameter shown in cross-section analysis (after extract centerline) is calculated, thanks.

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## [TextNode changes not saved with scene](https://discourse.slicer.org/t/textnode-changes-not-saved-with-scene/14664)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 3\
**Last updated:** [November 18, 2020, 12:26am UTC](https://discourse.slicer.org/t/textnode-changes-not-saved-with-scene/14664 "2020-11-18T00:26:42Z")

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Hi, I am using vtkMRMLTextNodes, but am having problems with modifications to them being saved when I save the scene. Basically, changes to text nodes never seem to trigger that the scene has been changed or that they h…

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## [Converting a STL file to nifti](https://discourse.slicer.org/t/converting-a-stl-file-to-nifti/14638)

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**Author:** [@ycaspi](https://discourse.slicer.org/u/ycaspi)\
**Replies:** 7\
**Last updated:** [November 17, 2020, 4:19pm UTC](https://discourse.slicer.org/t/converting-a-stl-file-to-nifti/14638 "2020-11-17T16:19:49Z")

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Hello Guys, I am trying to convert an stl file to nifti using Dicer. I found the following: Conversation: https://discourse.slicer.org/t/converting-stl-files-to-binary-label-maps-in-nii-format-using-python/13038/6 I h…

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## [Requesting DICOM Data from a Hospital](https://discourse.slicer.org/t/requesting-dicom-data-from-a-hospital/14661)

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**Author:** [@Brandon\_Holt](https://discourse.slicer.org/u/Brandon_Holt)\
**Replies:** 6\
**Last updated:** [November 17, 2020, 1:48pm UTC](https://discourse.slicer.org/t/requesting-dicom-data-from-a-hospital/14661 "2020-11-17T13:48:58Z")

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Hello everyone, I am no Radiologist so I am constantly learning new vocabulary in the field of DICOM. I need help understanding the correct way to request DICOM data from a Hospital. I don’t need help writing the email,…

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## [Volume rendering a masked area](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637)

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**Author:** [@Jason\_C](https://discourse.slicer.org/u/Jason_C)\
**Replies:** 5\
**Last updated:** [November 17, 2020, 6:48am UTC](https://discourse.slicer.org/t/volume-rendering-a-masked-area/14637 "2020-11-17T06:48:50Z")

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I’d like to use the volume renderer to render a portion of an MRI, but I only want to render the area covered by (a) specific segmentation(s). I’m just learning slicer so this might be a rtfm case, but how can I do this…

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## [can't rename markup line](https://discourse.slicer.org/t/cant-rename-markup-line/14656)

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**Author:** [@chendong9416](https://discourse.slicer.org/u/chendong9416)\
**Replies:** 4\
**Last updated:** [November 17, 2020, 6:30am UTC](https://discourse.slicer.org/t/cant-rename-markup-line/14656 "2020-11-17T06:30:47Z")

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Hi, i want to chang the markupsline/markupsline\_1 to other name, but after i did this, nothing changed in the image of cross-section analysis, how can I do it ?

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## [Export annotations as vector paths / svgs](https://discourse.slicer.org/t/export-annotations-as-vector-paths-svgs/14602)

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**Author:** [@noisyneuron](https://discourse.slicer.org/u/noisyneuron)\
**Replies:** 5\
**Last updated:** [November 17, 2020, 2:35am UTC](https://discourse.slicer.org/t/export-annotations-as-vector-paths-svgs/14602 "2020-11-17T02:35:01Z")

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Hi, I was wondering if it would be possible to export the annotated areas on an image as vector paths / svgs?

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## [In Segment Editor module some parts can not be marked](https://discourse.slicer.org/t/in-segment-editor-module-some-parts-can-not-be-marked/14624)

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**Author:** [@Aitekk](https://discourse.slicer.org/u/Aitekk)\
**Replies:** 2\
**Last updated:** [November 17, 2020, 2:21am UTC](https://discourse.slicer.org/t/in-segment-editor-module-some-parts-can-not-be-marked/14624 "2020-11-17T02:21:33Z")

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In Segment Editor module, the editable area of the volume is smaller than the whole volume, which makes some parts can not be marked Operating system:Windows 10 Slicer version:4.11 Expected behavior:The whole volume s…

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## [Export segmentation (or label maps) outlines as vector paths (svgs)](https://discourse.slicer.org/t/export-segmentation-or-label-maps-outlines-as-vector-paths-svgs/14650)

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**Author:** [@noisyneuron](https://discourse.slicer.org/u/noisyneuron)\
**Replies:** 0\
**Last updated:** [November 17, 2020, 12:11am UTC](https://discourse.slicer.org/t/export-segmentation-or-label-maps-outlines-as-vector-paths-svgs/14650 "2020-11-17T00:11:33Z")

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Operating system: OS X Slicer version: 4.11.0 I building a website in which I render segmentations I generated in 3D slicer, and want to manipulate them with html/css (for eg. change the color of a specific segment). …

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## [From the hollow back to the lumen](https://discourse.slicer.org/t/from-the-hollow-back-to-the-lumen/14648)

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**Author:** [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Replies:** 1\
**Last updated:** [November 16, 2020, 11:21pm UTC](https://discourse.slicer.org/t/from-the-hollow-back-to-the-lumen/14648 "2020-11-16T23:21:23Z")

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Hello everyone, I have a completely segmented vessel model and wanted to ask whether I can remove the vessel walls again in order to only see the lumen? So I could measure the internal dimensions of the segmented vesse…

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## [Calculate perimeter and area of Head CT from DICOM](https://discourse.slicer.org/t/calculate-perimeter-and-area-of-head-ct-from-dicom/14612)

<div class="topic-metadata">

**Author:** [@med\_student](https://discourse.slicer.org/u/med_student)\
**Replies:** 3\
**Last updated:** [November 16, 2020, 7:15pm UTC](https://discourse.slicer.org/t/calculate-perimeter-and-area-of-head-ct-from-dicom/14612 "2020-11-16T19:15:45Z")

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I’m trying to calculate the perimeter and area of the outer lining of the skull from head computed tomography scans. I assume this involves edge detection.

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## [How to convert STL files to DICOM file](https://discourse.slicer.org/t/how-to-convert-stl-files-to-dicom-file/7026)

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**Author:** [@Emma\_Gibney](https://discourse.slicer.org/u/Emma_Gibney)\
**Replies:** 1\
**Last updated:** [March 10, 2020, 1:18pm UTC](https://discourse.slicer.org/t/how-to-convert-stl-files-to-dicom-file/7026 "2020-03-10T13:18:34Z")

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Hello, I am new to this software. I have 10 stl files exported from an FEA model over the time frame of the simulation. I want to convert these files into a DICOM file. Is this possible with this software? Any tips woul…

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## [How to hide empty black regions of the slice in 3D view](https://discourse.slicer.org/t/how-to-hide-empty-black-regions-of-the-slice-in-3d-view/14639)

<div class="topic-metadata">

**Author:** [@SteveJJ](https://discourse.slicer.org/u/SteveJJ)\
**Replies:** 2\
**Last updated:** [November 16, 2020, 4:26pm UTC](https://discourse.slicer.org/t/how-to-hide-empty-black-regions-of-the-slice-in-3d-view/14639 "2020-11-16T16:26:53Z")

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Thanks I wonder if you know a way to remove the black regions visible on the slices in the 3D view? I would like the view to look like the head was being sliced, but without the black areas. Thanks again in advance fo…

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## [Progress bars on long operations](https://discourse.slicer.org/t/progress-bars-on-long-operations/14636)

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**Author:** [@Jason\_C](https://discourse.slicer.org/u/Jason_C)\
**Replies:** 0\
**Last updated:** [November 16, 2020, 4:19pm UTC](https://discourse.slicer.org/t/progress-bars-on-long-operations/14636 "2020-11-16T16:19:49Z")

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I’d really like to see progress bars on long operations; examples include: Loading a scene and its volumes Long segmentation operations e.g. grow from seeds Long operations in extensions (e.g. algorithms that take a wh…

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## [Accurate positioning of CT slices](https://discourse.slicer.org/t/accurate-positioning-of-ct-slices/14629)

<div class="topic-metadata">

**Author:** [@1119](https://discourse.slicer.org/u/1119)\
**Replies:** 0\
**Last updated:** [November 16, 2020, 8:14am UTC](https://discourse.slicer.org/t/accurate-positioning-of-ct-slices/14629 "2020-11-16T08:14:39Z")

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For a given CT slice, can we arbitrarily rotate to a set angle? The show reformat widget can rotate the slices, but this kind of rotation cannot accurately locate the angle I need. , Is there any way to achieve this. Fo…

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## [Segmentation changes when applying Treshold](https://discourse.slicer.org/t/segmentation-changes-when-applying-treshold/14603)

<div class="topic-metadata">

**Author:** [@Papis](https://discourse.slicer.org/u/Papis)\
**Replies:** 1\
**Last updated:** [November 15, 2020, 8:54am UTC](https://discourse.slicer.org/t/segmentation-changes-when-applying-treshold/14603 "2020-11-15T08:54:53Z")

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Operating system: MacOS Mojave 10.14.6 Slicer version: 4.11.20200930 Expected behavior: Save segmented area within chosen threshold Actual behavior: Cuts off majority of segmented area when applying threshold leaving …

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