**Author:** [@kjg](https://discourse.slicer.org/u/kjg)\
**Replies:** 2\
**Last updated:** [April 5, 2023, 11:37pm UTC](https://discourse.slicer.org/t/how-can-i-get-the-coordinates-of-markups/22167 "2023-04-05T23:37:03Z")
Hi, I’m new to 3dSlicer and am trying to understand how to work with the markup function. My goal is to get the coordinates of three points that I marked up using the “angle” function, so that I can work with them to d…
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## [Using python to save into .mrb file, got a warning message](https://discourse.slicer.org/t/using-python-to-save-into-mrb-file-got-a-warning-message/28735)
**Author:** [@derekcbr](https://discourse.slicer.org/u/derekcbr)\
**Replies:** 4\
**Last updated:** [April 5, 2023, 11:13pm UTC](https://discourse.slicer.org/t/using-python-to-save-into-mrb-file-got-a-warning-message/28735 "2023-04-05T23:13:51Z")
output\_file = os.path.join(file\_dir, “test.mrb”) licer.util.saveScene(output\_file) I got the warnings from Slicer:\[Qt\] class QList\ \_\_cdecl qSlicerCoreIOManagerPrivate::writers(const class QSt…
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## [Convert TotalSegmentator results to RT structure set](https://discourse.slicer.org/t/convert-totalsegmentator-results-to-rt-structure-set/28767)
**Author:** [@LipTeck\_Chew](https://discourse.slicer.org/u/LipTeck_Chew)\
**Replies:** 2\
**Last updated:** [January 18, 2023, 2:20am UTC](https://discourse.slicer.org/t/convert-totalsegmentator-results-to-rt-structure-set/28767 "2023-01-18T02:20:15Z")
Hi Lassoan, After the segmentation by the totalsegmentator is completed, how do we convert it to dicom RT structure set for a dicom rt send to another computer? FYI, we have tested a dicom send and it is working. Thank…
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## [TotalSegmentator indicates that GTX 1060 GPU has not enough memory](https://discourse.slicer.org/t/totalsegmentator-indicates-that-gtx-1060-gpu-has-not-enough-memory/28766)
**Author:** [@kopachini](https://discourse.slicer.org/u/kopachini)\
**Replies:** 1\
**Last updated:** [February 22, 2023, 5:30pm UTC](https://discourse.slicer.org/t/totalsegmentator-indicates-that-gtx-1060-gpu-has-not-enough-memory/28766 "2023-02-22T17:30:03Z")
Hello everyone, first of all I must say that Total Segmentor is a game changer with it’s fast segmentation. GREAT JOB!!! Second, I have a question… I have NVidia GTX 1060 graphic card with GPU memory 13.9 GB as in the …
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## [Can TotalSegmentator capture deformities such as Can TotalSegmentator heterotopic ossification?](https://discourse.slicer.org/t/can-totalsegmentator-capture-deformities-such-as-can-totalsegmentator-heterotopic-ossification/28765)
**Author:** [@William\_Kuo](https://discourse.slicer.org/u/William_Kuo)\
**Replies:** 2\
**Last updated:** [April 5, 2023, 7:57pm UTC](https://discourse.slicer.org/t/can-totalsegmentator-capture-deformities-such-as-can-totalsegmentator-heterotopic-ossification/28765 "2023-04-05T19:57:23Z")
Would this extension be able to capture deformities such as heterotopic ossification?
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## [Hollow Nrrd File Upon Export](https://discourse.slicer.org/t/hollow-nrrd-file-upon-export/28679)
**Author:** [@kristinbindas](https://discourse.slicer.org/u/kristinbindas)\
**Replies:** 20\
**Last updated:** [April 5, 2023, 6:59pm UTC](https://discourse.slicer.org/t/hollow-nrrd-file-upon-export/28679 "2023-04-05T18:59:44Z")
Hi everyone. I have been playing around with my MicroCT DCM files and exporting them as NRRD files. I need them to eventually use in shapeworks. Before using the smoothing filters, the full bone shape showed up fine on …
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## [Draw on a 3D Surface](https://discourse.slicer.org/t/draw-on-a-3d-surface/28431)
**Author:** [@Shovon\_Ahmed](https://discourse.slicer.org/u/Shovon_Ahmed)\
**Replies:** 2\
**Last updated:** [April 5, 2023, 2:36pm UTC](https://discourse.slicer.org/t/draw-on-a-3d-surface/28431 "2023-04-05T14:36:55Z")
Hi, I am currently building an application in VR that should allow drawing on a 3D surface (e.g. Skull model). I have used the "Draw on a Surface Feature’ in Slicer. I would like to know how it is precisely done. If you…
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## [Show displacement matrix and log file during image registration](https://discourse.slicer.org/t/show-displacement-matrix-and-log-file-during-image-registration/28675)
**Author:** [@Laura.K](https://discourse.slicer.org/u/Laura.K)\
**Replies:** 3\
**Last updated:** [April 5, 2023, 2:05pm UTC](https://discourse.slicer.org/t/show-displacement-matrix-and-log-file-during-image-registration/28675 "2023-04-05T14:05:46Z")
Hi everyone, I created a BSpline-transformation with the module General Registration (BRAINS) with a CT-image as fixed volume and an MR-image as moving volume. Visualization of the BSpline coefficients and conversion to…
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## [Clarification re RTSTRUCT display](https://discourse.slicer.org/t/clarification-re-rtstruct-display/15973)
**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 7\
**Last updated:** [April 5, 2023, 4:08am UTC](https://discourse.slicer.org/t/clarification-re-rtstruct-display/15973 "2023-04-05T04:08:07Z")
When I load RTSTRUCT, I see the following: I would like to clarify: do I see the original RTSTRUCT-defined contours in the slice viewers, or those are interpolated contours? is it possible to show the original RTST…
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## [Wrong PET SUV with Philips machine](https://discourse.slicer.org/t/wrong-pet-suv-with-philips-machine/23324)
**Author:** [@tristan421](https://discourse.slicer.org/u/tristan421)\
**Replies:** 10\
**Last updated:** [April 4, 2023, 9:50pm UTC](https://discourse.slicer.org/t/wrong-pet-suv-with-philips-machine/23324 "2023-04-04T21:50:50Z")
Hello. There seems to be an issus with the way PETDICOM module operate on PET images taken from a a phillips machine. The computed SUV are way too low. By looking into the hood, it seems the right way to compute SUV va…
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## [Creating ear model from image](https://discourse.slicer.org/t/creating-ear-model-from-image/28599)
**Author:** [@Mohan\_R\_ed21d021](https://discourse.slicer.org/u/Mohan_R_ed21d021)\
**Replies:** 6\
**Last updated:** [April 4, 2023, 5:36pm UTC](https://discourse.slicer.org/t/creating-ear-model-from-image/28599 "2023-04-04T17:36:04Z")
i want to segment a ear model in the 3D Slicer. could anyone give some ideas to get the accurate ear model?
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## [OutOfMemoryError: CUDA out of memory TotalSegmentator](https://discourse.slicer.org/t/outofmemoryerror-cuda-out-of-memory-totalsegmentator/28697)
**Author:** [@NicoV](https://discourse.slicer.org/u/NicoV)\
**Replies:** 7\
**Last updated:** [April 4, 2023, 4:16pm UTC](https://discourse.slicer.org/t/outofmemoryerror-cuda-out-of-memory-totalsegmentator/28697 "2023-04-04T16:16:58Z")
Operating system: Windows 10 Slicer version: 5.2.2 Expected behavior: TotalSegmentator full resolution segmentation with GPU 8Gb (NVIDIA) Actual behavior: semgmentation fails due to “OutOfMemoryError: CUDA out of memo…
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## [importing a segment from another 3d slicer with the same image](https://discourse.slicer.org/t/importing-a-segment-from-another-3d-slicer-with-the-same-image/28722)
**Author:** [@Frank\_Nyamweya](https://discourse.slicer.org/u/Frank_Nyamweya)\
**Replies:** 1\
**Last updated:** [April 4, 2023, 1:57pm UTC](https://discourse.slicer.org/t/importing-a-segment-from-another-3d-slicer-with-the-same-image/28722 "2023-04-04T13:57:21Z")
Hi, I accidentally saved a file that I had overwritten its original segment. I have the original file and the file in which I made my segment. Is it possible to merge the two by importing the segmentation from the origin…
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## [Code of ROS/ROS2 in the OpenIGTLink](https://discourse.slicer.org/t/code-of-ros-ros2-in-the-openigtlink/28743)
**Author:** [@Wilson\_HO](https://discourse.slicer.org/u/Wilson_HO)\
**Replies:** 0\
**Last updated:** [April 4, 2023, 10:47am UTC](https://discourse.slicer.org/t/code-of-ros-ros2-in-the-openigtlink/28743 "2023-04-04T10:47:07Z")
Hi all, I am a new user in the 3D Slicer, I want to write the code in the socket to connect my real UR5 and 3D Slicer without the ROS/ROS2. Where can find the code of ROS/ROS2 in the OpenIGTLink? I can imitate it in my…
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## [How to run python .py file from windows terminal](https://discourse.slicer.org/t/how-to-run-python-py-file-from-windows-terminal/28740)
**Author:** [@mukund\_shah](https://discourse.slicer.org/u/mukund_shah)\
**Replies:** 4\
**Last updated:** [April 4, 2023, 8:46am UTC](https://discourse.slicer.org/t/how-to-run-python-py-file-from-windows-terminal/28740 "2023-04-04T08:46:27Z")
Slicer.exe --python-script “/full/path/to/myscript.py” --no-splash --no-main-window i am using this command in windows terminal but its showing error The command Slicer.exe was not found, but does exist in the current l…
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## [Totalsegmentator install fails due to certificate issue](https://discourse.slicer.org/t/totalsegmentator-install-fails-due-to-certificate-issue/28564)
**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 11\
**Last updated:** [April 3, 2023, 9:52pm UTC](https://discourse.slicer.org/t/totalsegmentator-install-fails-due-to-certificate-issue/28564 "2023-04-03T21:52:55Z")
This is mostly an issue on our end. I managed to download the zip archive from our end. Is there a way to manually install this? @rbumm Collecting https://github.com/wasserth/TotalSegmentator/archive/b38eb449ad8652a987…
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## [Embedding specimen metadata into the 3D volume](https://discourse.slicer.org/t/embedding-specimen-metadata-into-the-3d-volume/3014)
**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 6\
**Last updated:** [April 3, 2023, 3:22pm UTC](https://discourse.slicer.org/t/embedding-specimen-metadata-into-the-3d-volume/3014 "2023-04-03T15:22:13Z")
Dear all, As part of a project we will be converting large number of 3D high-resolution scans of biological specimens into volumetric format. Currently most of them are in DICOM or some sort of a image sequence, and we …
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## [Interpretation of Lung CT Analyzer results](https://discourse.slicer.org/t/interpretation-of-lung-ct-analyzer-results/28729)
**Author:** [@duan](https://discourse.slicer.org/u/duan)\
**Replies:** 1\
**Last updated:** [April 3, 2023, 2:57pm UTC](https://discourse.slicer.org/t/interpretation-of-lung-ct-analyzer-results/28729 "2023-04-03T14:57:00Z")
Excuse me,I have explained the relevant indicators in the lung segment analyzer,and would like you to see if my explanation is correct.As shown below “Total lungs” is all lungs volume that includes the volume of healthy…
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## [RMSE in Landmarks Registration](https://discourse.slicer.org/t/rmse-in-landmarks-registration/25969)
**Author:** [@domP](https://discourse.slicer.org/u/domP)\
**Replies:** 6\
**Last updated:** [April 3, 2023, 2:33pm UTC](https://discourse.slicer.org/t/rmse-in-landmarks-registration/25969 "2023-04-03T14:33:27Z")
Hello everyone, I’m trying to register two volumes using “Fiducial Registration Wizard” module. My goal is to find the minimum number of fiducial points that give me best result in the alignment. What I observe when I …
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## [Joint Smoothing for only Selected segments](https://discourse.slicer.org/t/joint-smoothing-for-only-selected-segments/28714)
**Author:** [@KSL](https://discourse.slicer.org/u/KSL)\
**Replies:** 4\
**Last updated:** [April 3, 2023, 9:53am UTC](https://discourse.slicer.org/t/joint-smoothing-for-only-selected-segments/28714 "2023-04-03T09:53:53Z")
Hello dear friends, Is it possible to conduct “Joint smoothing” for only “selected segments” e.g. spleen only, from the Total Segmentator module?
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## [Measuring muscle and fat volumes in abdominal CT scans](https://discourse.slicer.org/t/measuring-muscle-and-fat-volumes-in-abdominal-ct-scans/16513)
**Author:** [@dantechao](https://discourse.slicer.org/u/dantechao)\
**Replies:** 3\
**Last updated:** [April 3, 2023, 9:47am UTC](https://discourse.slicer.org/t/measuring-muscle-and-fat-volumes-in-abdominal-ct-scans/16513 "2023-04-03T09:47:27Z")
Operating system: Windows Slicer version: 4.11 Does anyone have any tutorials on how to calculate visceral mass, muscle mass, and visceral adipose tissue volume on abdominal CT scans? I am asking as a new user who has…
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## [How to calculate the muscle and fat volume after muscle segmentation and export it from 3d Slicer to excel sheet](https://discourse.slicer.org/t/how-to-calculate-the-muscle-and-fat-volume-after-muscle-segmentation-and-export-it-from-3d-slicer-to-excel-sheet/28723)
**Author:** [@Hasm201](https://discourse.slicer.org/u/Hasm201)\
**Replies:** 1\
**Last updated:** [April 3, 2023, 9:42am UTC](https://discourse.slicer.org/t/how-to-calculate-the-muscle-and-fat-volume-after-muscle-segmentation-and-export-it-from-3d-slicer-to-excel-sheet/28723 "2023-04-03T09:42:42Z")
s there a tool to get the fat volume and separate it from the muscle volume? I have seen most of questions in the forum does not specify one tool. For example in my project I am planning to segment rotator cuff muscles a…
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## [Total segmentator issue](https://discourse.slicer.org/t/total-segmentator-issue/28695)
**Author:** [@KSL](https://discourse.slicer.org/u/KSL)\
**Replies:** 5\
**Last updated:** [April 3, 2023, 9:20am UTC](https://discourse.slicer.org/t/total-segmentator-issue/28695 "2023-04-03T09:20:30Z")
Hello dear Slicer users, I am posting this query in continuation with my previous post relating to the Total Segmentator module. I am currently using Slicer 5.2.1. I am able to install Pytorch, but the total Segmentator…
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## [Whether the colors in the Rainbow were related to radiomics features](https://discourse.slicer.org/t/whether-the-colors-in-the-rainbow-were-related-to-radiomics-features/28720)
**Author:** [@Liu](https://discourse.slicer.org/u/Liu)\
**Replies:** 0\
**Last updated:** [April 3, 2023, 3:09am UTC](https://discourse.slicer.org/t/whether-the-colors-in-the-rainbow-were-related-to-radiomics-features/28720 "2023-04-03T03:09:01Z")
Operating system:windows Slicer version:4.10.2 We used rainbow in volumes,and found differences between two groups,so we want to know whether the colors in the Rainbow were related to radiomics features.What does thei…
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## [Can watermark be incorporated to 3D viewer?](https://discourse.slicer.org/t/can-watermark-be-incorporated-to-3d-viewer/28703)
**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [March 31, 2023, 7:40pm UTC](https://discourse.slicer.org/t/can-watermark-be-incorporated-to-3d-viewer/28703 "2023-03-31T19:40:02Z")
Currently, I am using the ScreenCapture module to include a watermark in 3D rendering. However, when I do four up screenshots (with a screen snapshot tool), that watermark is not visible. Is it possible to have the water…
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## [Markup shortkeys and model interaction](https://discourse.slicer.org/t/markup-shortkeys-and-model-interaction/28616)
**Author:** [@philippe](https://discourse.slicer.org/u/philippe)\
**Replies:** 6\
**Last updated:** [March 31, 2023, 4:29pm UTC](https://discourse.slicer.org/t/markup-shortkeys-and-model-interaction/28616 "2023-03-31T16:29:16Z")
Hello, I apologize in advance if the answer is clearly stated somewhere but I cannot find a definite answer to my questions below. I found bits and pieces of informations but I may not be using the right keywords. Some…
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## [How to do DSC MRI analysis?](https://discourse.slicer.org/t/how-to-do-dsc-mri-analysis/5296)
**Author:** [@Imen\_Choukari](https://discourse.slicer.org/u/Imen_Choukari)\
**Replies:** 2\
**Last updated:** [March 31, 2023, 1:57pm UTC](https://discourse.slicer.org/t/how-to-do-dsc-mri-analysis/5296 "2023-03-31T13:57:05Z")
I do not know how to use DSC MRI ANALYSIS. There is a tutorial for that extension? Also, there is a database of images which I could use for practice?
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## [How can I calculate an area on a CT image. I can calculate volumes (mm^3) but not areas (mm^2)](https://discourse.slicer.org/t/how-can-i-calculate-an-area-on-a-ct-image-i-can-calculate-volumes-mm-3-but-not-areas-mm-2/1549)
**Author:** [@Ert0](https://discourse.slicer.org/u/Ert0)\
**Replies:** 27\
**Last updated:** [March 31, 2023, 1:51pm UTC](https://discourse.slicer.org/t/how-can-i-calculate-an-area-on-a-ct-image-i-can-calculate-volumes-mm-3-but-not-areas-mm-2/1549 "2023-03-31T13:51:16Z")
Operating system: Slicer version: Expected behavior: Actual behavior:
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## [Watershed feature not available in 5.2.2?](https://discourse.slicer.org/t/watershed-feature-not-available-in-5-2-2/28686)
**Author:** [@swilm](https://discourse.slicer.org/u/swilm)\
**Replies:** 1\
**Last updated:** [March 30, 2023, 7:07pm UTC](https://discourse.slicer.org/t/watershed-feature-not-available-in-5-2-2/28686 "2023-03-30T19:07:15Z")
Hi, I just downloaded the updated slicer version 5.2.2 and I don’t see the watershed function, as well as some other functions, in the segment editor module. Is this a bug or were they taken out for some reason? Thanks…
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## [How to apply a segmented tumor to other imaging](https://discourse.slicer.org/t/how-to-apply-a-segmented-tumor-to-other-imaging/28687)
**Author:** [@curtis\_sohn](https://discourse.slicer.org/u/curtis_sohn)\
**Replies:** 1\
**Last updated:** [March 30, 2023, 6:56pm UTC](https://discourse.slicer.org/t/how-to-apply-a-segmented-tumor-to-other-imaging/28687 "2023-03-30T18:56:23Z")
Hi, everyone. I finished a tumor segmentation from T2-flair imaging and created the output as .nrrd file. Since segmenting all images is time consuming, I want to apply the nrrd file to also other image modalities. How…
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