# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=142

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

**Page:** 143

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## [Displaying Brain Aneurysm in 3D from Mask](https://discourse.slicer.org/t/displaying-brain-aneurysm-in-3d-from-mask/31496)

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**Author:** [@Vineet\_Saravanan](https://discourse.slicer.org/u/Vineet_Saravanan)\
**Replies:** 2\
**Last updated:** [September 3, 2023, 7:55pm UTC](https://discourse.slicer.org/t/displaying-brain-aneurysm-in-3d-from-mask/31496 "2023-09-03T19:55:48Z")

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Hello, I have some aneurysm masks I want to visualize in 3D. I have imported them into the 3D slicer and first tried to use the thresholding tool, but I only see green when the threshold is less than 1, and then the whol…

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## [Monailabel and slicer segmentation label number](https://discourse.slicer.org/t/monailabel-and-slicer-segmentation-label-number/31502)

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**Author:** [@Ylim](https://discourse.slicer.org/u/Ylim)\
**Replies:** 2\
**Last updated:** [September 2, 2023, 12:28pm UTC](https://discourse.slicer.org/t/monailabel-and-slicer-segmentation-label-number/31502 "2023-09-02T12:28:06Z")

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Hi all, sorry if this is a rather trivial question. I have slicer and monailabel. Found the label number to be very confusing. Within \\monilabel\\apps\\radiology\\main.py Within slicer’s segmentation I have the imp…

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## [How can I manually segmentat retinal images (2D-image)?](https://discourse.slicer.org/t/how-can-i-manually-segmentat-retinal-images-2d-image/31517)

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**Author:** [@Atena](https://discourse.slicer.org/u/Atena)\
**Replies:** 0\
**Last updated:** [September 2, 2023, 11:16am UTC](https://discourse.slicer.org/t/how-can-i-manually-segmentat-retinal-images-2d-image/31517 "2023-09-02T11:16:15Z")

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Hi I work to the version of 5-4 3D slicer. I want the manual segmentation of vessels in retinal images. but I don’t know which module is useful for this?

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## [Do we need to create an isotropic image in radiomics study?](https://discourse.slicer.org/t/do-we-need-to-create-an-isotropic-image-in-radiomics-study/1779)

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**Author:** [@MimiPoon](https://discourse.slicer.org/u/MimiPoon)\
**Replies:** 4\
**Last updated:** [September 2, 2023, 11:15am UTC](https://discourse.slicer.org/t/do-we-need-to-create-an-isotropic-image-in-radiomics-study/1779 "2023-09-02T11:15:45Z")

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Hi, As medical images are usually anisotropic images, do we need to convert images to isotropic ones for the purpose of texture analysis? Does Radiomics module take care of it? If it is needed to convert the images, wh…

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## [IA-FEMesh extension for Abaqus](https://discourse.slicer.org/t/ia-femesh-extension-for-abaqus/13317)

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**Author:** [@nithin](https://discourse.slicer.org/u/nithin)\
**Replies:** 14\
**Last updated:** [September 1, 2023, 9:13pm UTC](https://discourse.slicer.org/t/ia-femesh-extension-for-abaqus/13317 "2023-09-01T21:13:59Z")

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Dear all, I am trying to apply material mapping to the vertebral model and analyze in Abaqus. I exported image data and surface model (.stl) from the 3D slicer, but when the same are imported IA-FEMesh, there is no over…

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## [How to export only the area within the segmentation?](https://discourse.slicer.org/t/how-to-export-only-the-area-within-the-segmentation/31494)

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**Author:** [@Kelly\_Lee](https://discourse.slicer.org/u/Kelly_Lee)\
**Replies:** 2\
**Last updated:** [September 1, 2023, 3:13am UTC](https://discourse.slicer.org/t/how-to-export-only-the-area-within-the-segmentation/31494 "2023-09-01T03:13:39Z")

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I have a completed segmented 2D image, and this is its volume image. Could I export only the area within the segmentation (excluding the area outside of the segmentation)? Here is the saved scene view.

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## [MRI image segmentation and export](https://discourse.slicer.org/t/mri-image-segmentation-and-export/31460)

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**Author:** [@Kelly\_Lee](https://discourse.slicer.org/u/Kelly_Lee)\
**Replies:** 2\
**Last updated:** [September 1, 2023, 1:32am UTC](https://discourse.slicer.org/t/mri-image-segmentation-and-export/31460 "2023-09-01T01:32:00Z")

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I have an image, and I’ve already used the segment editor to outline the ROI. How can I remove the image outside the ROI and export the MRI image within the ROI (in JPG, DICOM, or JSON format)?

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## [Undo button for mistakes in segmentation](https://discourse.slicer.org/t/undo-button-for-mistakes-in-segmentation/31486)

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**Author:** [@SOFIA\_R](https://discourse.slicer.org/u/SOFIA_R)\
**Replies:** 1\
**Last updated:** [September 1, 2023, 12:09am UTC](https://discourse.slicer.org/t/undo-button-for-mistakes-in-segmentation/31486 "2023-09-01T00:09:41Z")

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Hello, I’m doing a manual segmentation in 3D slicer and I made a mistake with the brush tool, how can i undo this action? There’s a yellow button in the segmentation module that seems to be an “undo option” but it doesn’…

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## [Segmentation With "fill between slices" Error](https://discourse.slicer.org/t/segmentation-with-fill-between-slices-error/31487)

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**Author:** [@fazilent](https://discourse.slicer.org/u/fazilent)\
**Replies:** 0\
**Last updated:** [August 31, 2023, 10:43pm UTC](https://discourse.slicer.org/t/segmentation-with-fill-between-slices-error/31487 "2023-08-31T22:43:14Z")

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Hello everyone. I’m trying to segment nasal masses with 3d Slicer. I tried many tools through the segment editor. I want to manipulate the segmentation I created using the “fill between slices” tool. but when I try to de…

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## [slicer interactions \[can't find in 5.2.2 ver. in 3DSlicer\]](https://discourse.slicer.org/t/slicer-interactions-cant-find-in-5-2-2-ver-in-3dslicer/31485)

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**Author:** [@JayZhi](https://discourse.slicer.org/u/JayZhi)\
**Replies:** 0\
**Last updated:** [August 31, 2023, 10:42pm UTC](https://discourse.slicer.org/t/slicer-interactions-cant-find-in-5-2-2-ver-in-3dslicer/31485 "2023-08-31T22:42:55Z")

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Operating system: win11 Slicer version: 5.2.2 Expected behavior: The video I watched had slicer interactions under the Toggle crosshair visibility category. He had 3D slicer ver. 4.13.0 Actual behavior: I don’t find t…

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## [How to save dicom image or segmentation mask to a .py file or .nii file?](https://discourse.slicer.org/t/how-to-save-dicom-image-or-segmentation-mask-to-a-py-file-or-nii-file/12108)

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**Author:** [@SummerZ2020](https://discourse.slicer.org/u/SummerZ2020)\
**Replies:** 5\
**Last updated:** [August 31, 2023, 5:51pm UTC](https://discourse.slicer.org/t/how-to-save-dicom-image-or-segmentation-mask-to-a-py-file-or-nii-file/12108 "2023-08-31T17:51:07Z")

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I used the “segment editor” to get the bone tissue just now. and then I need save the segmentation mask to a .py file. I did not find how to do it in GUI, so I tried to do it with python script.I tried to get the data fr…

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## [Markups curve in 2D](https://discourse.slicer.org/t/markups-curve-in-2d/31444)

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**Author:** [@M111](https://discourse.slicer.org/u/M111)\
**Replies:** 2\
**Last updated:** [August 31, 2023, 5:40pm UTC](https://discourse.slicer.org/t/markups-curve-in-2d/31444 "2023-08-31T17:40:21Z")

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Hello everyone. I am trying to draw a Markups curve in 2D ( a plane curve). Is it possible to constrain Slicer 3D to draw the curve in 2D instead of 3D? Thanks.

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## [Simple Undo button](https://discourse.slicer.org/t/simple-undo-button/10995)

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**Author:** [@mimi](https://discourse.slicer.org/u/mimi)\
**Replies:** 7\
**Last updated:** [August 31, 2023, 5:13pm UTC](https://discourse.slicer.org/t/simple-undo-button/10995 "2023-08-31T17:13:35Z")

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Is there a simple undo button in case I make mistakes in registration or segmentation? Closing and reopening the study from the latest saved version is quite cumbersome. Thank you

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## [Need help in Uniform remesh in Surface Toolbox](https://discourse.slicer.org/t/need-help-in-uniform-remesh-in-surface-toolbox/31440)

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**Author:** [@telomere](https://discourse.slicer.org/u/telomere)\
**Replies:** 8\
**Last updated:** [August 31, 2023, 5:01pm UTC](https://discourse.slicer.org/t/need-help-in-uniform-remesh-in-surface-toolbox/31440 "2023-08-31T17:01:53Z")

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Hi. When applying undercut remove or making a base of dental model, the side walls consist of too long voxels. So I want to remesh uniformly. The first image above is the dental model where undercut remove and base …

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## [Extension to execute python function](https://discourse.slicer.org/t/extension-to-execute-python-function/31478)

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**Author:** [@Deep\_Learning](https://discourse.slicer.org/u/Deep_Learning)\
**Replies:** 1\
**Last updated:** [August 31, 2023, 3:44pm UTC](https://discourse.slicer.org/t/extension-to-execute-python-function/31478 "2023-08-31T15:44:12Z")

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Is there a simple extension available to execute python code. Would be a great way to customize 3DSlicer and allow execution of custom code with a button. I find my self using code such as this and it would be great to…

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## [Cross section of segmentation in oblique angle](https://discourse.slicer.org/t/cross-section-of-segmentation-in-oblique-angle/31433)

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**Author:** [@lukasvanderstricht](https://discourse.slicer.org/u/lukasvanderstricht)\
**Replies:** 7\
**Last updated:** [August 31, 2023, 2:40pm UTC](https://discourse.slicer.org/t/cross-section-of-segmentation-in-oblique-angle/31433 "2023-08-31T14:40:35Z")

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Hello everyone! I am interested in calculating cross section areas of my segmentations. I have a segmentation with 1 label (except for the background label) and I want to calculate the area of the cross section of my se…

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## [Segments not showing in 3d](https://discourse.slicer.org/t/segments-not-showing-in-3d/31330)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 13\
**Last updated:** [August 31, 2023, 12:02pm UTC](https://discourse.slicer.org/t/segments-not-showing-in-3d/31330 "2023-08-31T12:02:49Z")

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I have this file where suddenly segments disappear from 3D and can’t be shown.

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## [Recommended VR headset](https://discourse.slicer.org/t/recommended-vr-headset/25504)

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**Author:** [@dhcortes](https://discourse.slicer.org/u/dhcortes)\
**Replies:** 7\
**Last updated:** [August 31, 2023, 8:58am UTC](https://discourse.slicer.org/t/recommended-vr-headset/25504 "2023-08-31T08:58:12Z")

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Hi there, I am planning on using the VR and AR extensions of 3D slicer. Is there a headset brand/model recommended for this? Thanks

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## [Transform processor module](https://discourse.slicer.org/t/transform-processor-module/12925)

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**Author:** [@Selva](https://discourse.slicer.org/u/Selva)\
**Replies:** 4\
**Last updated:** [August 29, 2023, 6:24pm UTC](https://discourse.slicer.org/t/transform-processor-module/12925 "2023-08-29T18:24:28Z")

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Hi, I am trying to decompose a linear transformation into rotation and translation components. What could be the easiest way to do this please. I have tried the transform processor module, but I am not sure what are t…

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## [Totalsegmentator works in fast but not in non-fast](https://discourse.slicer.org/t/totalsegmentator-works-in-fast-but-not-in-non-fast/31417)

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**Author:** [@Ylim](https://discourse.slicer.org/u/Ylim)\
**Replies:** 1\
**Last updated:** [August 31, 2023, 7:55am UTC](https://discourse.slicer.org/t/totalsegmentator-works-in-fast-but-not-in-non-fast/31417 "2023-08-31T07:55:32Z")

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if fast is not selected - Slicer/\_\_SlicerTemp\_\_2023-08-29\_16+39+14.764/segmentation’, ‘–ml’, ‘–task’, ‘total’\]’ returned non-zero exit status 120. under apply button .totalsegmentator\\nnunet\\results\\nnUNet\\3d\_fullres\\…

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## [Extracting 2D axial slice from 3D volume using current slice view](https://discourse.slicer.org/t/extracting-2d-axial-slice-from-3d-volume-using-current-slice-view/31390)

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**Author:** [@calici](https://discourse.slicer.org/u/calici)\
**Replies:** 3\
**Last updated:** [August 31, 2023, 3:54am UTC](https://discourse.slicer.org/t/extracting-2d-axial-slice-from-3d-volume-using-current-slice-view/31390 "2023-08-31T03:54:06Z")

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Hi! Currently I am working on developing a custom extension. One of the functionalities that I want to implement is a user can scroll in axial view and select the axial slice as the slice-of-interest. Then I want to us…

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## [MultiVolume Explorer and Segment Editor Error](https://discourse.slicer.org/t/multivolume-explorer-and-segment-editor-error/3732)

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**Author:** [@aginn](https://discourse.slicer.org/u/aginn)\
**Replies:** 22\
**Last updated:** [August 31, 2023, 2:04am UTC](https://discourse.slicer.org/t/multivolume-explorer-and-segment-editor-error/3732 "2023-08-31T02:04:23Z")

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Hi all - I am trying to load a cine-MRI (link to data is below). I was able to import it through the DICOM import, but the results look off. Furthermore, when I go to “volume rendering,” there is no volume generated, bu…

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## [Exporting and saving mrbs without error](https://discourse.slicer.org/t/exporting-and-saving-mrbs-without-error/31454)

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**Author:** [@trish](https://discourse.slicer.org/u/trish)\
**Replies:** 2\
**Last updated:** [August 30, 2023, 10:57pm UTC](https://discourse.slicer.org/t/exporting-and-saving-mrbs-without-error/31454 "2023-08-30T22:57:05Z")

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Hi there, I am running a Slicer 5.2 kernel in Jupyter notebook and looking to create Medical Reality Bundles (.mrbs) for radiotherapy patients for which I have their CTs, RTStructs, and RTDose files. Slicer is able to b…

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## [Install extensions from the command line using Slicer 5.2.2](https://discourse.slicer.org/t/install-extensions-from-the-command-line-using-slicer-5-2-2/31439)

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**Author:** [@jhlegarreta](https://discourse.slicer.org/u/jhlegarreta)\
**Replies:** 10\
**Last updated:** [August 30, 2023, 2:59pm UTC](https://discourse.slicer.org/t/install-extensions-from-the-command-line-using-slicer-5-2-2/31439 "2023-08-30T14:59:10Z")

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Hi, can Slicer extensions be installed from the command line? If yes, where can I find the related documentation? Thanks.

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## [Draw line that is fit to segmented voxels using SVD](https://discourse.slicer.org/t/draw-line-that-is-fit-to-segmented-voxels-using-svd/31312)

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**Author:** [@Annabel\_W](https://discourse.slicer.org/u/Annabel_W)\
**Replies:** 2\
**Last updated:** [August 23, 2023, 11:34am UTC](https://discourse.slicer.org/t/draw-line-that-is-fit-to-segmented-voxels-using-svd/31312 "2023-08-23T11:34:27Z")

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Hi there, I am attempting to localise the end of intracranial electrodes within a CT scan. I have isolated an electrode in a binarised label map and am now trying to run SVD analysis. I have been running this code; im…

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## [Dice score calculation of 3D binary masks using Segment Comparison module](https://discourse.slicer.org/t/dice-score-calculation-of-3d-binary-masks-using-segment-comparison-module/30124)

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**Author:** [@thanuja](https://discourse.slicer.org/u/thanuja)\
**Replies:** 3\
**Last updated:** [August 29, 2023, 7:59pm UTC](https://discourse.slicer.org/t/dice-score-calculation-of-3d-binary-masks-using-segment-comparison-module/30124 "2023-08-29T19:59:46Z")

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Hi All, Could you please point out where can I find the source code for Segment Comparison module (Slicer version 5.2.2). I’m getting different values of dice score for 3D binary nifti masks when using 3D Slicer and the…

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## [Import VDB File into 3D Slicer](https://discourse.slicer.org/t/import-vdb-file-into-3d-slicer/30823)

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**Author:** [@domdow](https://discourse.slicer.org/u/domdow)\
**Replies:** 7\
**Last updated:** [August 29, 2023, 1:37pm UTC](https://discourse.slicer.org/t/import-vdb-file-into-3d-slicer/30823 "2023-08-29T13:37:27Z")

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Hello, I am looking to import a .VDB file into 3D Slicer. When I try importing I receive a error notification: " Error occurred while loading the selected files. Click ‘Show details’ button and check the application lo…

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## [Segmenting vasculature from two-photon imaging](https://discourse.slicer.org/t/segmenting-vasculature-from-two-photon-imaging/8476)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 14\
**Last updated:** [August 29, 2023, 12:43pm UTC](https://discourse.slicer.org/t/segmenting-vasculature-from-two-photon-imaging/8476 "2023-08-29T12:43:59Z")

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This is on behalf of a colleague who is interested in using 3D Slicer to visualize and segment vasculature from mouse brains using two-photon imaging. Specifically, they are interested in volume rendering of the data an…

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## [Slicer-5.0.x stable downloads](https://discourse.slicer.org/t/slicer-5-0-x-stable-downloads/24278)

<div class="topic-metadata">

**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 12\
**Last updated:** [August 29, 2023, 7:54am UTC](https://discourse.slicer.org/t/slicer-5-0-x-stable-downloads/24278 "2023-08-29T07:54:37Z")

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When I click on the stable Mac download on https://download.slicer.org/ I’m getting the following error: { "message": "Invalid item id (62cc52d2aa08d161a31c1af4).", "type": "rest" }

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## [Change default threshold while masking](https://discourse.slicer.org/t/change-default-threshold-while-masking/31416)

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**Author:** [@V11](https://discourse.slicer.org/u/V11)\
**Replies:** 0\
**Last updated:** [August 29, 2023, 6:38am UTC](https://discourse.slicer.org/t/change-default-threshold-while-masking/31416 "2023-08-29T06:38:43Z")

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Operating system: Windows Slicer version: 5.0.3 I have multiple labels to be annotated in a CT volume. I use the Threshold tool followed by “Use for Masking” to paint the region of interest (ROI) . I want to know if t…

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