# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=185

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

**Page:** 186

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## [Signal intensity of a ROI](https://discourse.slicer.org/t/signal-intensity-of-a-roi/27222)

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**Author:** [@dszimatore](https://discourse.slicer.org/u/dszimatore)\
**Replies:** 0\
**Last updated:** [January 13, 2023, 10:31am UTC](https://discourse.slicer.org/t/signal-intensity-of-a-roi/27222 "2023-01-13T10:31:14Z")

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Hello everybody! can you show me the way passage by passage to calcuate signal intensity of a ROI. I read that is possible using the tool “segment statistics” but i can obtain only info about volumes. Thank you very muc…

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## [Get voxel values as a CSV file](https://discourse.slicer.org/t/get-voxel-values-as-a-csv-file/27216)

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**Author:** [@Mmirzaa1](https://discourse.slicer.org/u/Mmirzaa1)\
**Replies:** 2\
**Last updated:** [January 12, 2023, 5:51pm UTC](https://discourse.slicer.org/t/get-voxel-values-as-a-csv-file/27216 "2023-01-12T17:51:15Z")

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Dear Andras Could you please determine how (using the code above) we can extract the voxel values as a table? or a csv file? thank you very much

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## [Bug: \[5.2.1\] Data is loaded from database but doesn't appear under "Loaded data"](https://discourse.slicer.org/t/bug-5-2-1-data-is-loaded-from-database-but-doesnt-appear-under-loaded-data/27174)

<div class="topic-metadata">

**Author:** [@Gabriel\_WK](https://discourse.slicer.org/u/Gabriel_WK)\
**Replies:** 2\
**Last updated:** [January 12, 2023, 5:42pm UTC](https://discourse.slicer.org/t/bug-5-2-1-data-is-loaded-from-database-but-doesnt-appear-under-loaded-data/27174 "2023-01-12T17:42:13Z")

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Problem report for Slicer 5.2.1 win-amd64: Expected behavior: Loaded data appear under “Loaded data” on the DICOM Module Actual behavior: Nothing appears under “Loaded data” Data still showing normally on the Da…

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## [3D model does not show up](https://discourse.slicer.org/t/3d-model-does-not-show-up/27189)

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**Author:** [@Oleg\_Alexandrov](https://discourse.slicer.org/u/Oleg_Alexandrov)\
**Replies:** 2\
**Last updated:** [January 12, 2023, 5:34pm UTC](https://discourse.slicer.org/t/3d-model-does-not-show-up/27189 "2023-01-12T17:34:52Z")

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Dear Team After segmentation, I click “Show 3D” and nothing happens, I can not see the model, the window is empty. Tried many times, did not work. Is there any solution to this problem?

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## [New segment editor effects: Mask volume and Surface cut](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 17\
**Last updated:** [January 12, 2023, 4:04pm UTC](https://discourse.slicer.org/t/new-segment-editor-effects-mask-volume-and-surface-cut/699 "2023-01-12T16:04:32Z")

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See short demo video of the new "Mask volume" and "Surface cut" Segment editor effects here: These effects were developed by Kyle Macneil (Med-i Lab, Queen's University; SPL, Brigham and Women's Hospital), with help fr…

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## [Opening Downloaded '.mrml' Files](https://discourse.slicer.org/t/opening-downloaded-mrml-files/26351)

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**Author:** [@JacobD](https://discourse.slicer.org/u/JacobD)\
**Replies:** 2\
**Last updated:** [January 11, 2023, 9:51pm UTC](https://discourse.slicer.org/t/opening-downloaded-mrml-files/26351 "2023-01-11T21:51:04Z")

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Regarding ‘.mrml’ files downloaded from a Google Drive folder, when attempting to load them to view completed segmentations, the segmentation does not appear, and only a section of the scanned image appears. When attemp…

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## [Reading probed values for volume elements](https://discourse.slicer.org/t/reading-probed-values-for-volume-elements/27175)

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**Author:** [@ZSoltani](https://discourse.slicer.org/u/ZSoltani)\
**Replies:** 4\
**Last updated:** [January 11, 2023, 6:28pm UTC](https://discourse.slicer.org/t/reading-probed-values-for-volume-elements/27175 "2023-01-11T18:28:30Z")

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HI ALL, After using Probe volume with model, is there any way that I can export the HU values of the elements in a readable format? I need them for FE analysis. p.s. I can see that slicer.util.array() can be used for r…

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## [Convert segmentation to closed curve markup](https://discourse.slicer.org/t/convert-segmentation-to-closed-curve-markup/27182)

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**Author:** [@MayaSF](https://discourse.slicer.org/u/MayaSF)\
**Replies:** 4\
**Last updated:** [January 11, 2023, 6:05pm UTC](https://discourse.slicer.org/t/convert-segmentation-to-closed-curve-markup/27182 "2023-01-11T18:05:23Z")

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Hi there, Is there a way I can convert a Segmentation to a Closed Curve Markup by sampling the outside boundary of the segmented area with a certain number of points? I find it significantly faster to use the Draw tool …

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## [Slicer sample data](https://discourse.slicer.org/t/slicer-sample-data/27184)

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**Author:** [@firatoz](https://discourse.slicer.org/u/firatoz)\
**Replies:** 3\
**Last updated:** [January 11, 2023, 5:49pm UTC](https://discourse.slicer.org/t/slicer-sample-data/27184 "2023-01-11T17:49:00Z")

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I downloaded the CTP cardio sample data in Slicer and converted it from seq.nrrd format to DICOM format. The file works as 4d in seq.nrrd format but becomes 3d in DICOM format. How can I convert this file to 4d in DICOM …

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## [conversion NII to NRRD segmentation](https://discourse.slicer.org/t/conversion-nii-to-nrrd-segmentation/27176)

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**Author:** [@Marianne\_75](https://discourse.slicer.org/u/Marianne_75)\
**Replies:** 3\
**Last updated:** [January 11, 2023, 4:14pm UTC](https://discourse.slicer.org/t/conversion-nii-to-nrrd-segmentation/27176 "2023-01-11T16:14:42Z")

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Hello, I used Slicer 5.0.3 to segment brain lesions on MRIs. After that, I converted the seg.nrrd files into nii.gz files to fit in my coregistration workflow (I have to work on different dates for each patient). Where…

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## [Airway Inspector Wall Area errors](https://discourse.slicer.org/t/airway-inspector-wall-area-errors/27192)

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**Author:** [@mulia159](https://discourse.slicer.org/u/mulia159)\
**Replies:** 0\
**Last updated:** [January 11, 2023, 3:46pm UTC](https://discourse.slicer.org/t/airway-inspector-wall-area-errors/27192 "2023-01-11T15:46:43Z")

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Operating system: Slicer version: 5.2.1 Expected behavior: Wall area computation works correctly identifying the b3 walls Actual behavior:Wall area computation does not work correctly identifying the b3 walls, in whic…

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## [DICOM Information from Scalar Volume Node](https://discourse.slicer.org/t/dicom-information-from-scalar-volume-node/27170)

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**Author:** [@kleingeo](https://discourse.slicer.org/u/kleingeo)\
**Replies:** 2\
**Last updated:** [January 11, 2023, 1:53pm UTC](https://discourse.slicer.org/t/dicom-information-from-scalar-volume-node/27170 "2023-01-11T13:53:51Z")

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I have a vtkMRMLScalarVolumeNode that is imported from a DICOM database. Is there a way to obtain the DICOM information from the scalar volume node? It seems like all DICOM information is lost in the volume itself, but I…

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## [error no attribute 'setParameter' when using segment editor in python interactor](https://discourse.slicer.org/t/error-no-attribute-setparameter-when-using-segment-editor-in-python-interactor/27177)

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**Author:** [@ibowennn](https://discourse.slicer.org/u/ibowennn)\
**Replies:** 1\
**Last updated:** [January 11, 2023, 1:10pm UTC](https://discourse.slicer.org/t/error-no-attribute-setparameter-when-using-segment-editor-in-python-interactor/27177 "2023-01-11T13:10:16Z")

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Hi, I used the segment editor in python interactor for a list of segmentations. However, the codes work for a while and raise Error: ‘NoneType’ object has no attribute ‘setParameter.’ Below is my code: dir\_roi = '/my/s…

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## [Is there a way to convert Markups to Volume?](https://discourse.slicer.org/t/is-there-a-way-to-convert-markups-to-volume/27126)

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**Author:** [@nnzzll](https://discourse.slicer.org/u/nnzzll)\
**Replies:** 3\
**Last updated:** [January 11, 2023, 1:05pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-convert-markups-to-volume/27126 "2023-01-11T13:05:18Z")

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I got a ScalarVolumeNode and a FiducialNode with aboslute glyph size like the screenshot below Is there a way to convert the vtkMRMLMarkupsFiducialNode to a vtkMRMLLabelmapVolumeNode? I suppose that if I can get the…

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## [multiple monitors, drawing tablet](https://discourse.slicer.org/t/multiple-monitors-drawing-tablet/27114)

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**Author:** [@JaredAmudeo](https://discourse.slicer.org/u/JaredAmudeo)\
**Replies:** 1\
**Last updated:** [January 10, 2023, 10:51pm UTC](https://discourse.slicer.org/t/multiple-monitors-drawing-tablet/27114 "2023-01-10T22:51:55Z")

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Hi! is there any way to work with a single layout (e.g. the green) in a drawing tablet (xp-pen artist 12 pro) and let the other like the red, yellow or the 3d view in the main monitor?.

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## [Reading Masks made by a different software](https://discourse.slicer.org/t/reading-masks-made-by-a-different-software/27178)

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**Author:** [@arezoo.movahed](https://discourse.slicer.org/u/arezoo.movahed)\
**Replies:** 0\
**Last updated:** [January 10, 2023, 8:52pm UTC](https://discourse.slicer.org/t/reading-masks-made-by-a-different-software/27178 "2023-01-10T20:52:31Z")

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Hello, I can import open access data, human heart segmentation. I can simply open and see the segmentation, but it is like images, I cannot work on it. What I need is just 3D export of that segmentation, STL format. Th…

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## [Volumetric mesh generation for finite element analysis of spine](https://discourse.slicer.org/t/volumetric-mesh-generation-for-finite-element-analysis-of-spine/26052)

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**Author:** [@Ron](https://discourse.slicer.org/u/Ron)\
**Replies:** 14\
**Last updated:** [November 15, 2022, 5:44pm UTC](https://discourse.slicer.org/t/volumetric-mesh-generation-for-finite-element-analysis-of-spine/26052 "2022-11-15T17:44:22Z")

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Andras hi Dr. Zahra Soltani is working with me on an NIH patient study as part of our MIT collaboration. Previously, we have used Medtool to 1) create tet-based meshes for the vertebrae (it uses CGAL for this purpose) …

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## [Is it possible to use a box/circle for region on interest segmentation on CT-scans?](https://discourse.slicer.org/t/is-it-possible-to-use-a-box-circle-for-region-on-interest-segmentation-on-ct-scans/27167)

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**Author:** [@a.mohseni](https://discourse.slicer.org/u/a.mohseni)\
**Replies:** 3\
**Last updated:** [January 10, 2023, 5:34pm UTC](https://discourse.slicer.org/t/is-it-possible-to-use-a-box-circle-for-region-on-interest-segmentation-on-ct-scans/27167 "2023-01-10T17:34:23Z")

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So basically what I want to do is using a box or region of interest (in 3 different views) to encapsulate a part of the liver/spleen that I want to be segmentated. I tried using the segment editor, but I can’t find the f…

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## [Registering 2D images using Slicer Elastix](https://discourse.slicer.org/t/registering-2d-images-using-slicer-elastix/25379)

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**Author:** [@Krishna\_Nanda](https://discourse.slicer.org/u/Krishna_Nanda)\
**Replies:** 3\
**Last updated:** [January 10, 2023, 5:28pm UTC](https://discourse.slicer.org/t/registering-2d-images-using-slicer-elastix/25379 "2023-01-10T17:28:21Z")

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Operating system: Windows 10 Slicer version: 5.0.3 Expected behavior: Completes successfully Actual behavior: Error during registration Hello, I am trying to register 2 X-ray images using the Slicer Elastix module w…

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## [Mesh generation using Cleaver method](https://discourse.slicer.org/t/mesh-generation-using-cleaver-method/27171)

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**Author:** [@ZSoltani](https://discourse.slicer.org/u/ZSoltani)\
**Replies:** 2\
**Last updated:** [January 10, 2023, 5:19pm UTC](https://discourse.slicer.org/t/mesh-generation-using-cleaver-method/27171 "2023-01-10T17:19:48Z")

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HI ALL, I’m trying to use Cleaver for meshing a vertebra in Segment Mesher. The output contains regions with different mesh resolutions and the volume elements looks bizarre too (below images). I appreciate any comment …

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## [How to control mesh size on the boundary](https://discourse.slicer.org/t/how-to-control-mesh-size-on-the-boundary/27140)

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**Author:** [@ZSoltani](https://discourse.slicer.org/u/ZSoltani)\
**Replies:** 2\
**Last updated:** [January 10, 2023, 3:53pm UTC](https://discourse.slicer.org/t/how-to-control-mesh-size-on-the-boundary/27140 "2023-01-10T15:53:00Z")

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HI ALL, After segmentation and exporting the volume, I need to mesh it using Gmsh. My problem is that in the stl fine, the size of triangles on the outer surface of the volume is so small (even on the flat surfaces). So…

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## [Install Slicer on AWS EC2 instance](https://discourse.slicer.org/t/install-slicer-on-aws-ec2-instance/11659)

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**Author:** [@lennymartinez](https://discourse.slicer.org/u/lennymartinez)\
**Replies:** 10\
**Last updated:** [January 10, 2023, 10:13am UTC](https://discourse.slicer.org/t/install-slicer-on-aws-ec2-instance/11659 "2023-01-10T10:13:03Z")

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Anybody have experience installing Slicer on an AWS EC2 instance? I want to be able to send folders of Dicom images to be processed by a Slicer plugin (already made) in an EC2 instance but I’m not sure what the best way …

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## [Loading image and corresponding mask on Slicer from command line](https://discourse.slicer.org/t/loading-image-and-corresponding-mask-on-slicer-from-command-line/9930)

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**Author:** [@tbillah](https://discourse.slicer.org/u/tbillah)\
**Replies:** 12\
**Last updated:** [January 10, 2023, 7:34am UTC](https://discourse.slicer.org/t/loading-image-and-corresponding-mask-on-slicer-from-command-line/9930 "2023-01-10T07:34:40Z")

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Hi there, Is there a command like: Slicer T1.nii.gz LabelMap=Mask.nii.gz using which I can load an image and its mask (as LabelMap) directly from the command line? Basically, I want to replicate the following GUI l…

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## [Cylinder fit in the superior facies of the trochlea tali for local coordinate system](https://discourse.slicer.org/t/cylinder-fit-in-the-superior-facies-of-the-trochlea-tali-for-local-coordinate-system/27147)

<div class="topic-metadata">

**Author:** [@Daan1](https://discourse.slicer.org/u/Daan1)\
**Replies:** 0\
**Last updated:** [January 9, 2023, 10:49pm UTC](https://discourse.slicer.org/t/cylinder-fit-in-the-superior-facies-of-the-trochlea-tali-for-local-coordinate-system/27147 "2023-01-09T22:49:58Z")

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I want to fit a cylinder in the superior facies of the trochlea tali of the talus, to finally arrive at a local coordinate system. Is there a direct way for this? I can find how to do this with a sphere, but not with a c…

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## [Can one cut a model along a Plane to measure an object's thickness?](https://discourse.slicer.org/t/can-one-cut-a-model-along-a-plane-to-measure-an-objects-thickness/27146)

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**Author:** [@robin](https://discourse.slicer.org/u/robin)\
**Replies:** 0\
**Last updated:** [January 9, 2023, 10:49pm UTC](https://discourse.slicer.org/t/can-one-cut-a-model-along-a-plane-to-measure-an-objects-thickness/27146 "2023-01-09T22:49:54Z")

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Operating system:Windows 10 Slicer version: 5.2.1 Expected behavior: Actual behavior: I need to measure thicknesses of (iliac) bones from obj or STL. I am trying measure them by placing cross and dot glyphs on each s…

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## [Importing multiple json files of semi-landmarks into R for PCA analysis](https://discourse.slicer.org/t/importing-multiple-json-files-of-semi-landmarks-into-r-for-pca-analysis/27145)

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**Author:** [@JitziRose](https://discourse.slicer.org/u/JitziRose)\
**Replies:** 0\
**Last updated:** [January 9, 2023, 10:49pm UTC](https://discourse.slicer.org/t/importing-multiple-json-files-of-semi-landmarks-into-r-for-pca-analysis/27145 "2023-01-09T22:49:47Z")

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I have looked through the tutorial available on Github (Tutorials/parser\_and\_sample\_R\_analysis.md at main · SlicerMorph/Tutorials · GitHub) but am still having trouble with importing my files containing semi-landmarks in…

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## [Question about SlicerDMRI / whitematteranalysis](https://discourse.slicer.org/t/question-about-slicerdmri-whitematteranalysis/27125)

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**Author:** [@Joshuazzzs](https://discourse.slicer.org/u/Joshuazzzs)\
**Replies:** 1\
**Last updated:** [January 9, 2023, 6:26pm UTC](https://discourse.slicer.org/t/question-about-slicerdmri-whitematteranalysis/27125 "2023-01-09T18:26:33Z")

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Hi! The row names in the first column of the final.CSV file represent exactly which part of the brain’s fiber bundle? I don’t know what these abbreviations mean. For example, what does “T\_AF\_Left” mean?

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## [How to set PET SUVmax 40% threshold？](https://discourse.slicer.org/t/how-to-set-pet-suvmax-40-threshold/27124)

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**Author:** [@zhang\_ming](https://discourse.slicer.org/u/zhang_ming)\
**Replies:** 1\
**Last updated:** [January 9, 2023, 3:55pm UTC](https://discourse.slicer.org/t/how-to-set-pet-suvmax-40-threshold/27124 "2023-01-09T15:55:41Z")

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When I watch PET/CT，I need to draw the ROI to quantificat the SUV value of some volum, but how can I set the threshold of PET to appointed value like SUVmax 40% …

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## [Segmentation from curved plane by markup points](https://discourse.slicer.org/t/segmentation-from-curved-plane-by-markup-points/16629)

<div class="topic-metadata">

**Author:** [@hubelef](https://discourse.slicer.org/u/hubelef)\
**Replies:** 14\
**Last updated:** [January 9, 2023, 2:40pm UTC](https://discourse.slicer.org/t/segmentation-from-curved-plane-by-markup-points/16629 "2023-01-09T14:40:07Z")

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Operating system: Mac OS 10.13 Slicer version: 4.11.20200930 Expected behavior: separate segmented volume in two segmented volume by a curved plane (drawn by markup points) Actual behavior: I am nuclear medicine phys…

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## [Accessing a list of a Model's Vertices programmatically?](https://discourse.slicer.org/t/accessing-a-list-of-a-models-vertices-programmatically/27039)

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**Author:** [@stevenagl12](https://discourse.slicer.org/u/stevenagl12)\
**Replies:** 2\
**Last updated:** [January 8, 2023, 10:47pm UTC](https://discourse.slicer.org/t/accessing-a-list-of-a-models-vertices-programmatically/27039 "2023-01-08T22:47:18Z")

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How would you go about accessing a list of a model’s vertices programmatically once a model has been added to the scene?

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