# Support

**URL:** https://discourse.slicer.org/c/support/11.md?no_subcategories=false&page=65

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

**Page:** 66

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## [Segment Editor module won't present my segment in 3D](https://discourse.slicer.org/t/segment-editor-module-wont-present-my-segment-in-3d/40277)

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**Author:** [@21verbeks](https://discourse.slicer.org/u/21verbeks)\
**Replies:** 1\
**Last updated:** [November 19, 2024, 10:42pm UTC](https://discourse.slicer.org/t/segment-editor-module-wont-present-my-segment-in-3d/40277 "2024-11-19T22:42:20Z")

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Hi! I am having trouble with my segment editor module. I have my segmentations highlighted of my ct data of a primate tooth and can see all of them in the 2D screens. But everytime I press the “show in 3D” button, nothin…

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## [Python command tooltips](https://discourse.slicer.org/t/python-command-tooltips/40279)

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**Author:** [@Aidan](https://discourse.slicer.org/u/Aidan)\
**Replies:** 1\
**Last updated:** [November 19, 2024, 10:36pm UTC](https://discourse.slicer.org/t/python-command-tooltips/40279 "2024-11-19T22:36:35Z")

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The current recommendation for users wishing to learn how to Python script Slicer operations that they are already familiar with in the GUI is rather convoluted and time consuming. It involves searching the Slicer GitHub…

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## [WholeBrain Model in MONAI Auto3D Seg Module](https://discourse.slicer.org/t/wholebrain-model-in-monai-auto3d-seg-module/40276)

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**Author:** [@Bobby\_Zee](https://discourse.slicer.org/u/Bobby_Zee)\
**Replies:** 0\
**Last updated:** [November 19, 2024, 10:10pm UTC](https://discourse.slicer.org/t/wholebrain-model-in-monai-auto3d-seg-module/40276 "2024-11-19T22:10:03Z")

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Hi all, I am trying to use this model “Wholebrainseg large unest segmentation” (from here MONAI Model Zoo) in MONAI Auto3D Seg in Slicer 3D. I put it in the correct path according to Github (GitHub - lassoan/SlicerMONAI…

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## [Slices in 3D views are blended with the slice view colour on one side](https://discourse.slicer.org/t/slices-in-3d-views-are-blended-with-the-slice-view-colour-on-one-side/40260)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 3\
**Last updated:** [November 19, 2024, 7:21pm UTC](https://discourse.slicer.org/t/slices-in-3d-views-are-blended-with-the-slice-view-colour-on-one-side/40260 "2024-11-19T19:21:23Z")

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Hello, I just noticed this curious display. If we show the red slice view in 3D, it looks as expected when looking from below, but is red tainted when looking from the top. That’s true for the other default slice views…

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## [Exporting NRRD files as TIFF image stack](https://discourse.slicer.org/t/exporting-nrrd-files-as-tiff-image-stack/40221)

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**Author:** [@jaimigray](https://discourse.slicer.org/u/jaimigray)\
**Replies:** 10\
**Last updated:** [November 19, 2024, 6:19pm UTC](https://discourse.slicer.org/t/exporting-nrrd-files-as-tiff-image-stack/40221 "2024-11-19T18:19:35Z")

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Is there a way we can convert and export our NRRD files as a TIFF stack without exporting to imageJ/IrfanView afterwards to convert the format from DICOM to a TIFF image series? If not, this seems like something we shoul…

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## [Can I speed up ALPACA?](https://discourse.slicer.org/t/can-i-speed-up-alpaca/39914)

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**Author:** [@Chuan](https://discourse.slicer.org/u/Chuan)\
**Replies:** 5\
**Last updated:** [November 19, 2024, 1:01pm UTC](https://discourse.slicer.org/t/can-i-speed-up-alpaca/39914 "2024-11-19T13:01:36Z")

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Hi, I have around 7500 landmarks, and now I would like to use ALPACA to get other subjects’ landmarks. I have in total of 50 subjects, but the current problem is the processing is very slow and takes so long time for ev…

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## [Sample data information](https://discourse.slicer.org/t/sample-data-information/40245)

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**Author:** [@Caterina](https://discourse.slicer.org/u/Caterina)\
**Replies:** 1\
**Last updated:** [November 18, 2024, 6:49pm UTC](https://discourse.slicer.org/t/sample-data-information/40245 "2024-11-18T18:49:18Z")

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Dear support, can i have information about CTA cardio images from sample data database? Is it possibile to have clinical report? Thanks

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## [Conversion of .jpg files into DICOM in MRI images](https://discourse.slicer.org/t/conversion-of-jpg-files-into-dicom-in-mri-images/40153)

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**Author:** [@benedettabottelli](https://discourse.slicer.org/u/benedettabottelli)\
**Replies:** 3\
**Last updated:** [November 18, 2024, 4:05pm UTC](https://discourse.slicer.org/t/conversion-of-jpg-files-into-dicom-in-mri-images/40153 "2024-11-18T16:05:18Z")

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I have three different folders containing .jpg images of three different views of a shoulder MRI (axial, coronal, sagittal). How can I convert them into DICOM format? Additionally, if I upload the sequences as they are, …

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## [How to export data from Slicer to LifeX?](https://discourse.slicer.org/t/how-to-export-data-from-slicer-to-lifex/40210)

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**Author:** [@Ann\_Jacob](https://discourse.slicer.org/u/Ann_Jacob)\
**Replies:** 3\
**Last updated:** [November 18, 2024, 3:19pm UTC](https://discourse.slicer.org/t/how-to-export-data-from-slicer-to-lifex/40210 "2024-11-18T15:19:19Z")

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Hello, I need to export brain ROIs from Slicer and then use them in LifeX. However, something goes wrong and LifeX doesn’t display the ROIs, on top of flashing the “Inconsistent ROI size” warning. Both images (patient …

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## [3D Slicer and rek. file](https://discourse.slicer.org/t/3d-slicer-and-rek-file/40232)

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**Author:** [@Kajper](https://discourse.slicer.org/u/Kajper)\
**Replies:** 0\
**Last updated:** [November 17, 2024, 1:53pm UTC](https://discourse.slicer.org/t/3d-slicer-and-rek-file/40232 "2024-11-17T13:53:04Z")

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Dear all, I got a CT scan in the form of a single rek. file. I am unable to open in the Slicer. Is there any way to open/convert this data so I would be able to work on this scan in the Slicer? Presumably this file typ…

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## [Run ALPACA nogui from python script](https://discourse.slicer.org/t/run-alpaca-nogui-from-python-script/40223)

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**Author:** [@atha\_morph](https://discourse.slicer.org/u/atha_morph)\
**Replies:** 3\
**Last updated:** [November 16, 2024, 11:26pm UTC](https://discourse.slicer.org/t/run-alpaca-nogui-from-python-script/40223 "2024-11-16T23:26:36Z")

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Hello all, I would like to run ALPACA lib or the initial python library, in my python script. Any Idea how can I do it? I would like to give as input Source model, Source landmarks and Target model and the final retur…

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## [Frankfurt Horizontal Plane alignment of one model, angle measurements](https://discourse.slicer.org/t/frankfurt-horizontal-plane-alignment-of-one-model-angle-measurements/28639)

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**Author:** [@esomjai](https://discourse.slicer.org/u/esomjai)\
**Replies:** 7\
**Last updated:** [November 16, 2024, 9:14am UTC](https://discourse.slicer.org/t/frankfurt-horizontal-plane-alignment-of-one-model-angle-measurements/28639 "2024-11-16T09:14:23Z")

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Hi there, I am currently starting a masters project in facial approximation with a landmark-heavy plan. I apologise if my questions are answered elsewhere, I truly am new to 3D Slicer. I would like to establish the …

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## [Why did the segment created by threshold masking contain voxels beyond the threshold?](https://discourse.slicer.org/t/why-did-the-segment-created-by-threshold-masking-contain-voxels-beyond-the-threshold/40123)

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**Author:** [@qmsyylsel](https://discourse.slicer.org/u/qmsyylsel)\
**Replies:** 4\
**Last updated:** [November 15, 2024, 2:32pm UTC](https://discourse.slicer.org/t/why-did-the-segment-created-by-threshold-masking-contain-voxels-beyond-the-threshold/40123 "2024-11-15T14:32:33Z")

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As the pictures shows, in Segment Editor, I painted my segment under the masking with a threshold of \>130. But in Segment Statistics, the minimum value of that segment was 85, which was lower than 130, the threshold I se…

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## [Facial muscle segmentation using MONAI Auto3DSeg](https://discourse.slicer.org/t/facial-muscle-segmentation-using-monai-auto3dseg/35734)

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**Author:** [@philippepellerin](https://discourse.slicer.org/u/philippepellerin)\
**Replies:** 27\
**Last updated:** [November 15, 2024, 9:54am UTC](https://discourse.slicer.org/t/facial-muscle-segmentation-using-monai-auto3dseg/35734 "2024-11-15T09:54:51Z")

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Greetings. Much congratulations! As a professional in the field of medical imaging and segmentation, your work on the thorax, abdomen, and brain is undoubtedly significant. However, I believe that your expertise could a…

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## [How does 3dslicer smooth the 3d display of the tag image](https://discourse.slicer.org/t/how-does-3dslicer-smooth-the-3d-display-of-the-tag-image/40211)

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**Author:** [@2570596257hm](https://discourse.slicer.org/u/2570596257hm)\
**Replies:** 0\
**Last updated:** [November 15, 2024, 6:05am UTC](https://discourse.slicer.org/t/how-does-3dslicer-smooth-the-3d-display-of-the-tag-image/40211 "2024-11-15T06:05:28Z")

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I would like to know how to smooth the image to eliminate this jagged feeling, and what specific processing is done to the image.

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## [Extension for 2D-3D registration (2D image to 3D model)](https://discourse.slicer.org/t/extension-for-2d-3d-registration-2d-image-to-3d-model/40206)

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**Author:** [@andy97](https://discourse.slicer.org/u/andy97)\
**Replies:** 0\
**Last updated:** [November 15, 2024, 2:54am UTC](https://discourse.slicer.org/t/extension-for-2d-3d-registration-2d-image-to-3d-model/40206 "2024-11-15T02:54:42Z")

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Hello, I would like to apply a 2D-3D registration and was wondering if there is any extensions within 3D Slicer that can do this? Our case is to register a 2D image (e.g. 2D cerebral angiograms to a 3D model) to a 3D mo…

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## [Volume compressed into ROI](https://discourse.slicer.org/t/volume-compressed-into-roi/40085)

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**Author:** [@OwenProulx](https://discourse.slicer.org/u/OwenProulx)\
**Replies:** 12\
**Last updated:** [November 14, 2024, 9:48pm UTC](https://discourse.slicer.org/t/volume-compressed-into-roi/40085 "2024-11-14T21:48:27Z")

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Hi, I’ve been having this issue for a while. I’ve been trying to create an ROI for one of my specimens, and when I load the ROI at full resolution, it instead compresses the whole volume into it, instead of cropping the …

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## [Slicer vr + htc vive focus 3](https://discourse.slicer.org/t/slicer-vr-htc-vive-focus-3/38495)

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**Author:** [@sebstax](https://discourse.slicer.org/u/sebstax)\
**Replies:** 5\
**Last updated:** [November 14, 2024, 8:50pm UTC](https://discourse.slicer.org/t/slicer-vr-htc-vive-focus-3/38495 "2024-11-14T20:50:48Z")

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Hello @jcfr @LucasGandel I checked if SLICER VR was compatible with an HTC VIVE FOCUS 3 (connected by USB-C to a desktop using VIVE BUSINESS STREAMING software and STEAM VR), but it is not mentionned on GITHUB. By an…

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## [Rugged 3D Segmentation - GPU ( RTX 2080 Ti) not recognized](https://discourse.slicer.org/t/rugged-3d-segmentation-gpu-rtx-2080-ti-not-recognized/40195)

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**Author:** [@bkasmai](https://discourse.slicer.org/u/bkasmai)\
**Replies:** 1\
**Last updated:** [November 14, 2024, 8:18pm UTC](https://discourse.slicer.org/t/rugged-3d-segmentation-gpu-rtx-2080-ti-not-recognized/40195 "2024-11-14T20:18:39Z")

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I have an Nvidia GeForce RTX 2080 Ti card with 11.0 GB of dedicated GPU memory and 32 GB of shared GPU memory. The card is recognized by all of my applications except TotalSegmentator. This is not a big issue as I am hap…

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## [Validation\_set\_Accuracy in MONAILabel](https://discourse.slicer.org/t/validation-set-accuracy-in-monailabel/31027)

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**Author:** [@Spiros\_Karkavitsas](https://discourse.slicer.org/u/Spiros_Karkavitsas)\
**Replies:** 10\
**Last updated:** [November 14, 2024, 5:15pm UTC](https://discourse.slicer.org/t/validation-set-accuracy-in-monailabel/31027 "2024-11-14T17:15:07Z")

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Hello I am currently using MONAILabel extension with Slicer and I would like to ask how I can define which data is assigned for the calculation of the validation Dice similarity metric. I know I can adjust the percentag…

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## [How does create closed surface representation work ?](https://discourse.slicer.org/t/how-does-create-closed-surface-representation-work/40185)

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**Author:** [@Fleur\_Gaudfernau](https://discourse.slicer.org/u/Fleur_Gaudfernau)\
**Replies:** 3\
**Last updated:** [November 14, 2024, 1:53pm UTC](https://discourse.slicer.org/t/how-does-create-closed-surface-representation-work/40185 "2024-11-14T13:53:28Z")

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Hello, I could not find any answer to this rather simple question online. I’m trying different methods for extracting meshes from brain segmentations. I’ve tried several times the Marching Cube algorithm and the resul…

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## [Why does 3D model flip from other views? ](https://discourse.slicer.org/t/why-does-3d-model-flip-from-other-views/28615)

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**Author:** [@Jed](https://discourse.slicer.org/u/Jed)\
**Replies:** 12\
**Last updated:** [November 14, 2024, 12:45pm UTC](https://discourse.slicer.org/t/why-does-3d-model-flip-from-other-views/28615 "2024-11-14T12:45:46Z")

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while using 4 up views, the 3D view is opposite. The 3D view has to be flipped to match. looking at axial. item is on the left, in 3D it’s on the right. The only way I got it to look right was to flip the picture. I hav…

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## [Scale Factor not loading image correctly when trying to save a volume rendering photograph](https://discourse.slicer.org/t/scale-factor-not-loading-image-correctly-when-trying-to-save-a-volume-rendering-photograph/40184)

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**Author:** [@Tatiana\_Egbert](https://discourse.slicer.org/u/Tatiana_Egbert)\
**Replies:** 1\
**Last updated:** [November 13, 2024, 10:22pm UTC](https://discourse.slicer.org/t/scale-factor-not-loading-image-correctly-when-trying-to-save-a-volume-rendering-photograph/40184 "2024-11-13T22:22:47Z")

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When trying to increase the scale factor to obtain a higher resolution volume rendering photograph, any scale factor above 1.0 will alter the image itself and overlap my volume rendering image onto itself and save incorr…

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## [Create DRR of a STL file](https://discourse.slicer.org/t/create-drr-of-a-stl-file/40186)

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**Author:** [@phantom\_gen](https://discourse.slicer.org/u/phantom_gen)\
**Replies:** 0\
**Last updated:** [November 13, 2024, 9:55pm UTC](https://discourse.slicer.org/t/create-drr-of-a-stl-file/40186 "2024-11-13T21:55:44Z")

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Hi guys! I have a STL Design, which I voxelized with a python script into a .nrrd, and assigned density +attenuation coefficients to filled and non filled voxels. How can I use this now to create a DRR like projection? …

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## [Generated stl file on sample ct are all 1k in size and cannot be opened using any 3d viewer applications. No error is generated while saving the stl files.Stl](https://discourse.slicer.org/t/generated-stl-file-on-sample-ct-are-all-1k-in-size-and-cannot-be-opened-using-any-3d-viewer-applications-no-error-is-generated-while-saving-the-stl-files-stl/40180)

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**Author:** [@bkasmai](https://discourse.slicer.org/u/bkasmai)\
**Replies:** 0\
**Last updated:** [November 13, 2024, 7:07pm UTC](https://discourse.slicer.org/t/generated-stl-file-on-sample-ct-are-all-1k-in-size-and-cannot-be-opened-using-any-3d-viewer-applications-no-error-is-generated-while-saving-the-stl-files-stl/40180 "2024-11-13T19:07:15Z")

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I eventually managed to get AutoSegmentator working with 3D Slicer using the sample CT dataset. No error is generated after segmentation and I can view 3d and each of the 22 segments. Using Segmentation module I tried to…

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## [Scale factor on images taken from a scene not working](https://discourse.slicer.org/t/scale-factor-on-images-taken-from-a-scene-not-working/40178)

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**Author:** [@OwenProulx](https://discourse.slicer.org/u/OwenProulx)\
**Replies:** 3\
**Last updated:** [November 13, 2024, 6:34pm UTC](https://discourse.slicer.org/t/scale-factor-on-images-taken-from-a-scene-not-working/40178 "2024-11-13T18:34:09Z")

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Whenever I try to increase the scale factor of an image I’m taking of a scene, the resolution doesn’t increase and the image is split into many identical images.

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## [Unable to open my saved work](https://discourse.slicer.org/t/unable-to-open-my-saved-work/40174)

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**Author:** [@zeyangzhang.de12](https://discourse.slicer.org/u/zeyangzhang.de12)\
**Replies:** 0\
**Last updated:** [November 13, 2024, 2:10pm UTC](https://discourse.slicer.org/t/unable-to-open-my-saved-work/40174 "2024-11-13T14:10:28Z")

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Hi today when i was using 3d slicer and I’m not sure what i clicked and it crashed. then i tried to open my previously saved scene and it popped up with a message saying that "adding data failed. Please help me, i ha…

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## [From 2d image fringe light projection to 3d shape](https://discourse.slicer.org/t/from-2d-image-fringe-light-projection-to-3d-shape/40151)

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**Author:** [@Silvan](https://discourse.slicer.org/u/Silvan)\
**Replies:** 1\
**Last updated:** [November 13, 2024, 10:27am UTC](https://discourse.slicer.org/t/from-2d-image-fringe-light-projection-to-3d-shape/40151 "2024-11-13T10:27:55Z")

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Hi everyone, this is a 2D image obtained by projecting a black and white fringe light. Is it possible with some 3d Slicer function to estimate the 3d shape of the object from this information? thanks in advance!

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## [How to calculate BMD](https://discourse.slicer.org/t/how-to-calculate-bmd/15333)

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**Author:** [@Farhan](https://discourse.slicer.org/u/Farhan)\
**Replies:** 5\
**Last updated:** [November 13, 2024, 10:05am UTC](https://discourse.slicer.org/t/how-to-calculate-bmd/15333 "2024-11-13T10:05:45Z")

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Sir, how to calculate BMD of bone in 3d slicer. Sir, I am working on upper cervical spine and I have to find Young’s modules of elasticity(E) and Poisson’s ratio(u) of different parts of c1, c2 spine. What is the relat…

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## [Shoulder MRI segmentation extension](https://discourse.slicer.org/t/shoulder-mri-segmentation-extension/40152)

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**Author:** [@benedettabottelli](https://discourse.slicer.org/u/benedettabottelli)\
**Replies:** 0\
**Last updated:** [November 12, 2024, 5:09pm UTC](https://discourse.slicer.org/t/shoulder-mri-segmentation-extension/40152 "2024-11-12T17:09:52Z")

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I need an extension to segment bones, muscles, tendons and ligaments in a shoulder MRI, does it exist?

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