# Support **URL:** https://discourse.slicer.org/c/support/11.md?page=114 [Latest](https://discourse.slicer.org/latest.md) · [Categories](https://discourse.slicer.org/categories.md) · [Tags](https://discourse.slicer.org/tags.md) **Page:** 115 --- ## [Segmentation masks disappears from 2d views after histogram thresholding (but not 3d)](https://discourse.slicer.org/t/segmentation-masks-disappears-from-2d-views-after-histogram-thresholding-but-not-3d/34199)
**Author:** [@bbkonk](https://discourse.slicer.org/u/bbkonk)\ **Replies:** 2\ **Last updated:** [February 11, 2024, 11:50am UTC](https://discourse.slicer.org/t/segmentation-masks-disappears-from-2d-views-after-histogram-thresholding-but-not-3d/34199 "2024-02-11T11:50:05Z")
Not sure if this is a Slicer issue or a MONAI issue, but I’ve only hit the issue so far using the MONAILabel and MONAILabel Reviewer plugins. When I use threshold an image and see, for example Editable area = Inside segm… --- ## [DVH segmentation](https://discourse.slicer.org/t/dvh-segmentation/34218)
**Author:** [@Mouadh\_Ben\_Nasr](https://discourse.slicer.org/u/Mouadh_Ben_Nasr)\ **Replies:** 9\ **Last updated:** [February 11, 2024, 11:48am UTC](https://discourse.slicer.org/t/dvh-segmentation/34218 "2024-02-11T11:48:33Z")
Hey everyone, I am conducting a study about selective intraarterial radiation therapy (SIRT) in HCC. I used Simplicity software (Boston) for segmenting Liver, tumor, perfused volume and normal liver tissue. The isodose… --- ## [cant find LungCTanalyzer in module finder](https://discourse.slicer.org/t/cant-find-lungctanalyzer-in-module-finder/34241)
**Author:** [@evas](https://discourse.slicer.org/u/evas)\ **Replies:** 1\ **Last updated:** [February 11, 2024, 11:14am UTC](https://discourse.slicer.org/t/cant-find-lungctanalyzer-in-module-finder/34241 "2024-02-11T11:14:32Z")
Hello, I have 3D Slicer 5.6.1 and I want LungCTAnalyzer extension. I downloaded it in the Extensisons manager with the PyTorch. So I may have this after the restart in the menu. But I cant find it even in the modules and… --- ## [Are shadows enabled by default for Volume Rendering in new previews](https://discourse.slicer.org/t/are-shadows-enabled-by-default-for-volume-rendering-in-new-previews/34219)
**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\ **Replies:** 2\ **Last updated:** [February 10, 2024, 6:00pm UTC](https://discourse.slicer.org/t/are-shadows-enabled-by-default-for-volume-rendering-in-new-previews/34219 "2024-02-10T18:00:33Z")
This is the default volume rendering of MRHead in 5.6.1 by simply dragging and dropping to 3D viewer. No adjustment. This is the same thing from the preview I just installed (r32708). It seems darker with shadows. So… --- ## [Exporting several labelmaps](https://discourse.slicer.org/t/exporting-several-labelmaps/34237)
**Author:** [@Mouadh\_Ben\_Nasr](https://discourse.slicer.org/u/Mouadh_Ben_Nasr)\ **Replies:** 2\ **Last updated:** [February 10, 2024, 5:07pm UTC](https://discourse.slicer.org/t/exporting-several-labelmaps/34237 "2024-02-10T17:07:20Z")
I am conducting a research about liver SIRT. I segmented the liver, tumor and radiation sectors on Simplicity (Boston Scientific) console and exported the structures into RTStructure file. I imported the RTStructure fi… --- ## [Can not load any DICOM file in SLicer 3D on notebook with](https://discourse.slicer.org/t/can-not-load-any-dicom-file-in-slicer-3d-on-notebook-with/34201)
**Author:** [@alexpos1989](https://discourse.slicer.org/u/alexpos1989)\ **Replies:** 2\ **Last updated:** [February 10, 2024, 5:06pm UTC](https://discourse.slicer.org/t/can-not-load-any-dicom-file-in-slicer-3d-on-notebook-with/34201 "2024-02-10T17:06:22Z")
\[ERROR\]\[VTK\] 08.02.2024 02:53:28 \[vtkXMLDataParser (0000025E65826F80)\] (vtkXMLParser.cxx:380) - Error parsing XML in stream at line 1, column 0, byte index 0: not well-formed (invalid token) \[ERROR\]\[VTK\] 08.02.2024 02:53… --- ## [Design bone flap for skull](https://discourse.slicer.org/t/design-bone-flap-for-skull/15864)
**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\ **Replies:** 19\ **Last updated:** [February 10, 2024, 5:00pm UTC](https://discourse.slicer.org/t/design-bone-flap-for-skull/15864 "2024-02-10T17:00:26Z")
Dear teachers, as you can see, I made a bone flap, but there is a little bulge. Is there any tool to change the curvature of the model so that it will be perfect?Or is there a way to reshape the model like an iron wire, … --- ## [Extension for deep learning project in Slicer](https://discourse.slicer.org/t/extension-for-deep-learning-project-in-slicer/20205)
**Author:** [@AMK](https://discourse.slicer.org/u/AMK)\ **Replies:** 5\ **Last updated:** [February 10, 2024, 5:44am UTC](https://discourse.slicer.org/t/extension-for-deep-learning-project-in-slicer/20205 "2024-02-10T05:44:57Z")
Hi, I am trying to develop a deep learning based module, whereby a few clicks would allow to segment the CT volume. I am using the nnUNET for my implementation, which is basically a UNET with fixed hyperparameter and th… --- ## [How to instal old version of extension from file](https://discourse.slicer.org/t/how-to-instal-old-version-of-extension-from-file/34212)
**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\ **Replies:** 9\ **Last updated:** [February 9, 2024, 7:01pm UTC](https://discourse.slicer.org/t/how-to-instal-old-version-of-extension-from-file/34212 "2024-02-09T19:01:59Z")
Hello, I want to install the version of total segmentator of 3DSlicer 5.4 to have access to the “liver vessel” task I found a branch on the github repository named 5.4 and downloaded the code I then opened the extensi… --- ## [ALPACA TPS warped model not showing](https://discourse.slicer.org/t/alpaca-tps-warped-model-not-showing/34196)
**Author:** [@ThomasVanParys](https://discourse.slicer.org/u/ThomasVanParys)\ **Replies:** 13\ **Last updated:** [February 9, 2024, 4:10pm UTC](https://discourse.slicer.org/t/alpaca-tps-warped-model-not-showing/34196 "2024-02-09T16:10:13Z")
Hello, I am looking to analyse shape variation of different human lungs. For this, I have generated a template lung with adequate surface landmark coverage which can be used for the ALPACA function. However, when I run … --- ## [Connecting NDI aurora tracking system to 3D slicer](https://discourse.slicer.org/t/connecting-ndi-aurora-tracking-system-to-3d-slicer/34226)
**Author:** [@angelinabarsoum](https://discourse.slicer.org/u/angelinabarsoum)\ **Replies:** 1\ **Last updated:** [February 9, 2024, 4:07pm UTC](https://discourse.slicer.org/t/connecting-ndi-aurora-tracking-system-to-3d-slicer/34226 "2024-02-09T16:07:49Z")
Hi! I have been trying to do some research online to find out how to connect the NDI aurora EM tracking system into 3D slicer to show a live feed of the sensors but I haven’t had much luck. I have downloaded the Plus to… --- ## [Convert 3D dose distribution to DICOM RT dose](https://discourse.slicer.org/t/convert-3d-dose-distribution-to-dicom-rt-dose/6930)
**Author:** [@ToufikDZ](https://discourse.slicer.org/u/ToufikDZ)\ **Replies:** 35\ **Last updated:** [February 9, 2024, 11:30am UTC](https://discourse.slicer.org/t/convert-3d-dose-distribution-to-dicom-rt-dose/6930 "2024-02-09T11:30:13Z")
Operating system: windows 7 64bit Slicer version: 4.8.0 Expected behavior: DICOM dose distribution Actual behavior: Hello, I got 3D dose distribution from Monte Carlo simulation. I want to know if 3D slicer can conv… --- ## [Failed to fetch models from remote server](https://discourse.slicer.org/t/failed-to-fetch-models-from-remote-server/34221)
**Author:** [@keyurradia](https://discourse.slicer.org/u/keyurradia)\ **Replies:** 0\ **Last updated:** [February 9, 2024, 7:54am UTC](https://discourse.slicer.org/t/failed-to-fetch-models-from-remote-server/34221 "2024-02-09T07:54:03Z")
Hi, I am trying to use Nvidia AIAA for liver segmentation. I am not able to fetch the model from the remote server. Earlier it was working properly. Is there a new server address? I have tried the following one and … --- ## [3D connected components ](https://discourse.slicer.org/t/3d-connected-components/34209)
**Author:** [@rkraaijveld](https://discourse.slicer.org/u/rkraaijveld)\ **Replies:** 1\ **Last updated:** [February 8, 2024, 2:35pm UTC](https://discourse.slicer.org/t/3d-connected-components/34209 "2024-02-08T14:35:44Z")
Hi! I would like to extract the 3D connected components from my binary mask in 3D slicer. Is there any way to do that? --- ## [Hausdorff and Dice calculation principle](https://discourse.slicer.org/t/hausdorff-and-dice-calculation-principle/34172)
**Author:** [@LukasKnybel](https://discourse.slicer.org/u/LukasKnybel)\ **Replies:** 2\ **Last updated:** [February 8, 2024, 12:24pm UTC](https://discourse.slicer.org/t/hausdorff-and-dice-calculation-principle/34172 "2024-02-08T12:24:46Z")
Dear Slicer Users, sorry if this question is stupid but I realize I am not sure about the principle of DICE coef or Hausdorff distance calculation (even I know the equations). The question: I am comparing 2 objects, 1 … --- ## [FreeSurfer volumetric analysis](https://discourse.slicer.org/t/freesurfer-volumetric-analysis/34197)
**Author:** [@Nicolas\_Fuentes](https://discourse.slicer.org/u/Nicolas_Fuentes)\ **Replies:** 1\ **Last updated:** [February 7, 2024, 11:43pm UTC](https://discourse.slicer.org/t/freesurfer-volumetric-analysis/34197 "2024-02-07T23:43:10Z")
Hi everyone, I’m new to Slicer and I have some questions about the software’s capabilities for volumetric analysis. I work with neuroimages and I have patients processed with FreeSurfer. With that said, what I want to do… --- ## [Generating surface area from a 3D region](https://discourse.slicer.org/t/generating-surface-area-from-a-3d-region/34131)
**Author:** [@Logan\_Moore](https://discourse.slicer.org/u/Logan_Moore)\ **Replies:** 3\ **Last updated:** [February 7, 2024, 10:55pm UTC](https://discourse.slicer.org/t/generating-surface-area-from-a-3d-region/34131 "2024-02-07T22:55:08Z")
Operating system: Windows 11 Slicer version: 5.6.1 Hi all! I am currently working on a set of human crania, and I am trying to quantify the 3D surface area of the region in the closed curve. I see that it generates an… --- ## [Cortical vessel segmentation](https://discourse.slicer.org/t/cortical-vessel-segmentation/34152)
**Author:** [@anja\_pantovic](https://discourse.slicer.org/u/anja_pantovic)\ **Replies:** 3\ **Last updated:** [February 7, 2024, 5:37pm UTC](https://discourse.slicer.org/t/cortical-vessel-segmentation/34152 "2024-02-07T17:37:48Z")
Hello, I am trying to segment cortical vessels fro gadolinium enhanced t1 MRI images. I tried using local thresholding as well as vessleness filtering, however, scalp and even white matter interfere with the segmentatio… --- ## [How to export Markups point coordinates as another coordinate system](https://discourse.slicer.org/t/how-to-export-markups-point-coordinates-as-another-coordinate-system/34188)
**Author:** [@quddngud0598](https://discourse.slicer.org/u/quddngud0598)\ **Replies:** 1\ **Last updated:** [February 7, 2024, 4:03pm UTC](https://discourse.slicer.org/t/how-to-export-markups-point-coordinates-as-another-coordinate-system/34188 "2024-02-07T16:03:19Z")
When I use the Markup function in the Slicer to label a point and export the coordinates as json, the red box and coordinate value are saved. I found that the coordinates are in the LPS coordinate system. However, I … --- ## [Extract RAS coordinates by clicking](https://discourse.slicer.org/t/extract-ras-coordinates-by-clicking/33531)
**Author:** [@SANTIAGO\_PENDON\_MING](https://discourse.slicer.org/u/SANTIAGO_PENDON_MING)\ **Replies:** 2\ **Last updated:** [February 7, 2024, 11:53am UTC](https://discourse.slicer.org/t/extract-ras-coordinates-by-clicking/33531 "2024-02-07T11:53:26Z")
Hi to everyone :slight\_smile: Today I want to extract RAS coordinates to 3d markups/curves to click. My goal is interact with 3d view (if is not possible, interact with 2d views would great too). Processing the click I… --- ## [Create PDF from a jupyter notebook](https://discourse.slicer.org/t/create-pdf-from-a-jupyter-notebook/34183)
**Author:** [@Katya\_Stansfield](https://discourse.slicer.org/u/Katya_Stansfield)\ **Replies:** 0\ **Last updated:** [February 7, 2024, 8:56am UTC](https://discourse.slicer.org/t/create-pdf-from-a-jupyter-notebook/34183 "2024-02-07T08:56:34Z")
Hello – is it possible to export a Jupyter Notebook that works on Slicer 5.6 python kernel to a .pdf? I struggle to do so directly in ‘jupyter notebook’ and in VScode. VScode error is Error: Loading C:/Users/EKATAR~1/A… --- ## [The dependency "DicomRtImportExport" failed to be loaded - SlicerRT Issue](https://discourse.slicer.org/t/the-dependency-dicomrtimportexport-failed-to-be-loaded-slicerrt-issue/32073)
**Author:** [@Soumen\_Mohanty](https://discourse.slicer.org/u/Soumen_Mohanty)\ **Replies:** 5\ **Last updated:** [February 7, 2024, 5:42am UTC](https://discourse.slicer.org/t/the-dependency-dicomrtimportexport-failed-to-be-loaded-slicerrt-issue/32073 "2024-02-07T05:42:19Z")
Hello, I recently updated slicer and reinstalled the extensions I was using. For some reason, I’m unable to use SlicerRT and get the following errors. I have tried reinstalling and using different versions, but I’m unab… --- ## [Registration of MRI to CT](https://discourse.slicer.org/t/registration-of-mri-to-ct/34170)
**Author:** [@robsfill](https://discourse.slicer.org/u/robsfill)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 4:37pm UTC](https://discourse.slicer.org/t/registration-of-mri-to-ct/34170 "2024-02-06T16:37:21Z")
Hi everyone! I have a problem with my thesis project. I segmented images of 5 vertebrae from CT and the corresponding 4 discs but from MRI. I have to transport the MRI discs in the same reference system. How can I do th… --- ## [Export DICOM in Colors](https://discourse.slicer.org/t/export-dicom-in-colors/19301)
**Author:** [@zlwei](https://discourse.slicer.org/u/zlwei)\ **Replies:** 11\ **Last updated:** [February 6, 2024, 4:30pm UTC](https://discourse.slicer.org/t/export-dicom-in-colors/19301 "2024-02-06T16:30:19Z")
Dear all, I imported a set of DICOM files to Slicer. These DICOMs are for 3D echo doppler so they are colorful. Then, I export them in “Data” → “Export to DICOM” in the right-click menu. The exported files are grayscale… --- ## [Probe position and IJK\_RAS coordinates](https://discourse.slicer.org/t/probe-position-and-ijk-ras-coordinates/34169)
**Author:** [@alessandro\_um](https://discourse.slicer.org/u/alessandro_um)\ **Replies:** 1\ **Last updated:** [February 6, 2024, 4:21pm UTC](https://discourse.slicer.org/t/probe-position-and-ijk-ras-coordinates/34169 "2024-02-06T16:21:17Z")
Hello, I am learning the ropes with orienting dicoms, so I am using some well known softwares as a ground of truth, among them I’m using Slicer. Through math formulas I obtained the same data found under Volume Informa… --- ## [Slicer, evaluation of cursor origin on slice](https://discourse.slicer.org/t/slicer-evaluation-of-cursor-origin-on-slice/34173)
**Author:** [@alessandro\_um](https://discourse.slicer.org/u/alessandro_um)\ **Replies:** 0\ **Last updated:** [February 6, 2024, 3:24pm UTC](https://discourse.slicer.org/t/slicer-evaluation-of-cursor-origin-on-slice/34173 "2024-02-06T15:24:01Z")
Hello, I am learning the ropes with orienting dicoms, so I am using some well known softwares as a ground of truth, among them I’m using Slicer. Through math formulas I obtained the same data found under Volume Informa… --- ## [Labelmap combine issue](https://discourse.slicer.org/t/labelmap-combine-issue/34171)
**Author:** [@Hobart10](https://discourse.slicer.org/u/Hobart10)\ **Replies:** 0\ **Last updated:** [February 6, 2024, 3:23pm UTC](https://discourse.slicer.org/t/labelmap-combine-issue/34171 "2024-02-06T15:23:55Z")
Hi, there are two labelmap volumes from same source brain atlas that I would like to combine to one for further registration, but they are both having sequential digital labels and I hope to not overwrite in ‘Image label… --- ## [How the tensor is stored in NRRD](https://discourse.slicer.org/t/how-the-tensor-is-stored-in-nrrd/34084)
**Author:** [@Yixun\_Liu](https://discourse.slicer.org/u/Yixun_Liu)\ **Replies:** 2\ **Last updated:** [February 6, 2024, 4:30am UTC](https://discourse.slicer.org/t/how-the-tensor-is-stored-in-nrrd/34084 "2024-02-06T04:30:45Z")
Hi, I use the 3DSlicer Diffusion module to load DWI, estimate its tensor and then store the tensor image into NRRD. I want to know how the tensor is stored in NRRD? Is it stored as 6 upper triangle elements of the 3x3 … --- ## [Segment Statistics Module](https://discourse.slicer.org/t/segment-statistics-module/34014)
**Author:** [@Tati](https://discourse.slicer.org/u/Tati)\ **Replies:** 9\ **Last updated:** [February 5, 2024, 11:09pm UTC](https://discourse.slicer.org/t/segment-statistics-module/34014 "2024-02-05T23:09:10Z")
Hello all, I have installed the 5.6.1 version of 3D slicer. My problem is related to the segment statistic module; it does not show the Input and Output fields. Could you please guide me on this matter? --- ## [Superimpose multiple MRIs](https://discourse.slicer.org/t/superimpose-multiple-mris/34158)
**Author:** [@Vittorio](https://discourse.slicer.org/u/Vittorio)\ **Replies:** 1\ **Last updated:** [February 5, 2024, 10:41pm UTC](https://discourse.slicer.org/t/superimpose-multiple-mris/34158 "2024-02-05T22:41:24Z")
I have a problem because I can’t superimpose multiple MRIs. I’m trying to reconstruct a 3D model of my brain but I have a problem. I have selected 3 scans with the best resolution but I have to merge them because, for … [Previous page](https://discourse.slicer.org/c/support/11.md?page=113) [Next page](https://discourse.slicer.org/c/support/11.md?page=115)