# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=236

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

**Page:** 237

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## [Missing module: Hausdorff distances, Dice similarity metrics](https://discourse.slicer.org/t/missing-module-hausdorff-distances-dice-similarity-metrics/22159)

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**Author:** [@Young\_Wang](https://discourse.slicer.org/u/Young_Wang)\
**Replies:** 4\
**Last updated:** [February 25, 2022, 8:23pm UTC](https://discourse.slicer.org/t/missing-module-hausdorff-distances-dice-similarity-metrics/22159 "2022-02-25T20:23:43Z")

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Hi there, I’m tyring to calculate the Hausdorff distances, Dice similarity metrics to quantify registration results. However I noticed that SegmentComparison module here is missing. I wonder is there an alternative or re…

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## [Slicer needs to be restarted for extension manager catalogue to be updated](https://discourse.slicer.org/t/slicer-needs-to-be-restarted-for-extension-manager-catalogue-to-be-updated/22184)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [February 25, 2022, 8:06pm UTC](https://discourse.slicer.org/t/slicer-needs-to-be-restarted-for-extension-manager-catalogue-to-be-updated/22184 "2022-02-25T20:06:57Z")

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I am not sure if it is a big deal, but there is corner case. Today, I was tying to install a new extension on today’s preview on linux. It showed only 20 extension. I thought maybe the extensions are still building, and …

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## [How to get a ROI to fit volume in the Volume Rendering module with python?](https://discourse.slicer.org/t/how-to-get-a-roi-to-fit-volume-in-the-volume-rendering-module-with-python/18793)

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**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 11\
**Last updated:** [February 25, 2022, 6:05pm UTC](https://discourse.slicer.org/t/how-to-get-a-roi-to-fit-volume-in-the-volume-rendering-module-with-python/18793 "2022-02-25T18:05:02Z")

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@jamesobutler @jcfr @lassoan @pieper How to get a ROI to fit volume in the Volume Rendering module with python?

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## [How to find radius with vmtk module](https://discourse.slicer.org/t/how-to-find-radius-with-vmtk-module/22183)

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**Author:** [@alyssan](https://discourse.slicer.org/u/alyssan)\
**Replies:** 1\
**Last updated:** [February 25, 2022, 5:52pm UTC](https://discourse.slicer.org/t/how-to-find-radius-with-vmtk-module/22183 "2022-02-25T17:52:55Z")

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Hello I am trying to find the radius at many different point along an uneven cylindrical surface. How can i do this using the vmtk module? Thank you

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## [Unnamed Series as a Scalar Volume](https://discourse.slicer.org/t/unnamed-series-as-a-scalar-volume/22085)

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**Author:** [@dicom](https://discourse.slicer.org/u/dicom)\
**Replies:** 3\
**Last updated:** [February 25, 2022, 3:30pm UTC](https://discourse.slicer.org/t/unnamed-series-as-a-scalar-volume/22085 "2022-02-25T15:30:35Z")

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Dear all, I am new to Dicom and Slicer3D. I am trying to open a Dicom image (PET) with Slicer3D and I got this error message: "DICOM indexer has successfully inserted 200 files \[0.09s\]" "DICOM indexer has successfully…

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## [The voxel value is showing 'invalid'](https://discourse.slicer.org/t/the-voxel-value-is-showing-invalid/22170)

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**Author:** [@parvaneh.a](https://discourse.slicer.org/u/parvaneh.a)\
**Replies:** 4\
**Last updated:** [February 25, 2022, 2:24pm UTC](https://discourse.slicer.org/t/the-voxel-value-is-showing-invalid/22170 "2022-02-25T14:24:33Z")

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I have one image and one segmentation. When I load the image as volume and the segmentation as segmentation everything seems fine with both. There is no NAN voxel value in any of image or segmentation. I use the code bel…

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## [Registration of image adjusted in contrast](https://discourse.slicer.org/t/registration-of-image-adjusted-in-contrast/22160)

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**Author:** [@Engineer90](https://discourse.slicer.org/u/Engineer90)\
**Replies:** 1\
**Last updated:** [February 25, 2022, 10:20am UTC](https://discourse.slicer.org/t/registration-of-image-adjusted-in-contrast/22160 "2022-02-25T10:20:25Z")

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Good morning, I have to perform an image registration, and I would like to do it after changing the contrast, using “adjust window level …” of the two images i’m using. However, if I perform registration of the process…

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## [How to programmatically create the Master Volume for a segmentation node with multiple segments](https://discourse.slicer.org/t/how-to-programmatically-create-the-master-volume-for-a-segmentation-node-with-multiple-segments/22098)

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**Author:** [@PhilipDavis](https://discourse.slicer.org/u/PhilipDavis)\
**Replies:** 5\
**Last updated:** [February 25, 2022, 10:19am UTC](https://discourse.slicer.org/t/how-to-programmatically-create-the-master-volume-for-a-segmentation-node-with-multiple-segments/22098 "2022-02-25T10:19:46Z")

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Hi there, I’m new to 3D Slicer and now I’m developing a Python scripting module. Currently, I want to implement a procedure in python code of my module for calculating the volume value of the overlapping/Intersection p…

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## [Add shortcut to adjust window/level in any mouse mode python script not working](https://discourse.slicer.org/t/add-shortcut-to-adjust-window-level-in-any-mouse-mode-python-script-not-working/21524)

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**Author:** [@Shahnawaz\_Vora](https://discourse.slicer.org/u/Shahnawaz_Vora)\
**Replies:** 1\
**Last updated:** [February 25, 2022, 6:58am UTC](https://discourse.slicer.org/t/add-shortcut-to-adjust-window-level-in-any-mouse-mode-python-script-not-working/21524 "2022-02-25T06:58:50Z")

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I am trying to use this python script for Brightness/contrast shortcut but it gives me error . Can someone help me Traceback (most recent call last): File “”, line 1, in AttributeError: ‘MRMLDisplayableManagerPython.…

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## [Threshold Error on segmentation and does not show 3D reconstruction](https://discourse.slicer.org/t/threshold-error-on-segmentation-and-does-not-show-3d-reconstruction/21999)

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**Author:** [@Andreza](https://discourse.slicer.org/u/Andreza)\
**Replies:** 5\
**Last updated:** [February 24, 2022, 10:52pm UTC](https://discourse.slicer.org/t/threshold-error-on-segmentation-and-does-not-show-3d-reconstruction/21999 "2022-02-24T22:52:04Z")

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Operating system: Windows 10 Pro Slicer version: 4.11.20210226 Hi, I did some segmentations on a TIFF file and obtained the 3D reconstruction of the structures. After some problems with the ruler bar (that I set after…

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## [Problem about pixel value shift and orientation and origin between nifti and converted dicom series](https://discourse.slicer.org/t/problem-about-pixel-value-shift-and-orientation-and-origin-between-nifti-and-converted-dicom-series/22103)

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**Author:** [@Liu\_Lance](https://discourse.slicer.org/u/Liu_Lance)\
**Replies:** 4\
**Last updated:** [February 24, 2022, 3:47pm UTC](https://discourse.slicer.org/t/problem-about-pixel-value-shift-and-orientation-and-origin-between-nifti-and-converted-dicom-series/22103 "2022-02-24T15:47:38Z")

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Hello, I was trying to convert the nifti data to the dicom series. I figure out myself how to use the GUI of 3d slicer to export the loaded volume to dicom series. However, there are some problems in the output. 1. the…

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## [Issue saving fiducials](https://discourse.slicer.org/t/issue-saving-fiducials/22157)

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**Author:** [@anromero](https://discourse.slicer.org/u/anromero)\
**Replies:** 2\
**Last updated:** [February 24, 2022, 3:30pm UTC](https://discourse.slicer.org/t/issue-saving-fiducials/22157 "2022-02-24T15:30:32Z")

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I’ve been using 3D Slicer for a while, but I noticed that last time I opened it and tried landmarking specimens that there is no “Export as…” option when I right click on the markups in the data or markups module. I noti…

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## [Corrupted Slicer RegistrationQA tutorial data](https://discourse.slicer.org/t/corrupted-slicer-registrationqa-tutorial-data/22116)

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**Author:** [@Young\_Wang](https://discourse.slicer.org/u/Young_Wang)\
**Replies:** 6\
**Last updated:** [February 24, 2022, 3:23pm UTC](https://discourse.slicer.org/t/corrupted-slicer-registrationqa-tutorial-data/22116 "2022-02-24T15:23:21Z")

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Hi 3Dslicer community, I’m going through the Slicer RegistrationQA tutorial. However, I noticed that some Slicer RegistrationQA tutorial data is corrupted. I am not sure if this issue comes from my OS(mac os 12.2.1) or …

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## [How to set volume rendering color same as in slices?](https://discourse.slicer.org/t/how-to-set-volume-rendering-color-same-as-in-slices/22020)

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**Author:** [@rasunag27](https://discourse.slicer.org/u/rasunag27)\
**Replies:** 17\
**Last updated:** [February 24, 2022, 2:47pm UTC](https://discourse.slicer.org/t/how-to-set-volume-rendering-color-same-as-in-slices/22020 "2022-02-24T14:47:47Z")

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Hi, I have loaded RGB compatible ‘.dcm’ slices into the 3D slicer. I am able to get the slices in the RGB format as required. But the 3D volume from volume rendering shows grayscale. If I use preset from Volumes, it wil…

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## [Edit Segmentation masks](https://discourse.slicer.org/t/edit-segmentation-masks/22148)

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**Author:** [@Luis\_Santos](https://discourse.slicer.org/u/Luis_Santos)\
**Replies:** 7\
**Last updated:** [February 24, 2022, 1:41pm UTC](https://discourse.slicer.org/t/edit-segmentation-masks/22148 "2022-02-24T13:41:03Z")

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Hello everyone! hope you are doing well. Well. I’m trying to assign my own segmentation algorithm to the input images and put the outoput back in segment editor to edit it. It would help me to improve my model. I alrea…

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## [Vessel Diameter from Centreline](https://discourse.slicer.org/t/vessel-diameter-from-centreline/22154)

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**Author:** [@jpainova](https://discourse.slicer.org/u/jpainova)\
**Replies:** 0\
**Last updated:** [February 24, 2022, 12:28pm UTC](https://discourse.slicer.org/t/vessel-diameter-from-centreline/22154 "2022-02-24T12:28:52Z")

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I’m trying to calculate the diameter of a vessel (segmented from DICOM) at any desired point in the model. I have used VMTK Extract Centreline to plot a centreline with \>200 points to allow for selection of the desired …

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## [How to adjust the object size in 3D only display area?](https://discourse.slicer.org/t/how-to-adjust-the-object-size-in-3d-only-display-area/22152)

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**Author:** [@user4](https://discourse.slicer.org/u/user4)\
**Replies:** 0\
**Last updated:** [February 24, 2022, 7:55am UTC](https://discourse.slicer.org/t/how-to-adjust-the-object-size-in-3d-only-display-area/22152 "2022-02-24T07:55:24Z")

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Hi,all.I am struggling with this task,I will be very grateful if anyone can give me some possible advice. This question is more about vtk. I have a cube(volume) and the information is as follows: image dimensions…

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## [Error with "Fill between slices" ](https://discourse.slicer.org/t/error-with-fill-between-slices/22090)

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**Author:** [@frmrz](https://discourse.slicer.org/u/frmrz)\
**Replies:** 4\
**Last updated:** [February 24, 2022, 7:14am UTC](https://discourse.slicer.org/t/error-with-fill-between-slices/22090 "2022-02-24T07:14:36Z")

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Dear community, I’m trying to propagate the manual annotations I have, using the “Fill between slices” method. In some volume-segmentation pairs, I get the error “Auto-complete operation skipped: all visible segments a…

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## [How can I re-edit a 3D slicer segment in a file I already saved?](https://discourse.slicer.org/t/how-can-i-re-edit-a-3d-slicer-segment-in-a-file-i-already-saved/22140)

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**Author:** [@Andres\_Dominguez\_Vaz](https://discourse.slicer.org/u/Andres_Dominguez_Vaz)\
**Replies:** 1\
**Last updated:** [February 24, 2022, 7:09am UTC](https://discourse.slicer.org/t/how-can-i-re-edit-a-3d-slicer-segment-in-a-file-i-already-saved/22140 "2022-02-24T07:09:40Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [How to turn off the visibility of 3D models](https://discourse.slicer.org/t/how-to-turn-off-the-visibility-of-3d-models/22143)

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**Author:** [@WilliamDaniel](https://discourse.slicer.org/u/WilliamDaniel)\
**Replies:** 1\
**Last updated:** [February 24, 2022, 7:07am UTC](https://discourse.slicer.org/t/how-to-turn-off-the-visibility-of-3d-models/22143 "2022-02-24T07:07:05Z")

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Hello! Hope you are doing well! As shown in figure below, I’ve created a ‘Segmentation’ node for ‘MRHead’ which contains two segments: Segment\_1(with threshold 50-279), Segment\_2(with threshold 80-279). I imported th…

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## [Extensions for macOS not being build after February 15](https://discourse.slicer.org/t/extensions-for-macos-not-being-build-after-february-15/22125)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 3\
**Last updated:** [February 24, 2022, 6:19am UTC](https://discourse.slicer.org/t/extensions-for-macos-not-being-build-after-february-15/22125 "2022-02-24T06:19:09Z")

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Since february 15 there are no builds for Slicer Elastix extension available, see CDash

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## [DICOM and STL don't match.](https://discourse.slicer.org/t/dicom-and-stl-dont-match/22114)

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**Author:** [@Asagami-Fujino](https://discourse.slicer.org/u/Asagami-Fujino)\
**Replies:** 7\
**Last updated:** [February 24, 2022, 2:46am UTC](https://discourse.slicer.org/t/dicom-and-stl-dont-match/22114 "2022-02-24T02:46:50Z")

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I loaded the DICOM (it is a TRUS image) and the STL (the segmentation result) but the result turned out like this. The DICOM volume and the STL model did not match. So how to solve this problem?

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## [Tutorial about how to wriite a segmentation Editor Effects plugin](https://discourse.slicer.org/t/tutorial-about-how-to-wriite-a-segmentation-editor-effects-plugin/22147)

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**Author:** [@Yang\_Li](https://discourse.slicer.org/u/Yang_Li)\
**Replies:** 0\
**Last updated:** [February 24, 2022, 2:17am UTC](https://discourse.slicer.org/t/tutorial-about-how-to-wriite-a-segmentation-editor-effects-plugin/22147 "2022-02-24T02:17:49Z")

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Hi there! Currently I want to implement a seg. algorithm with the help of Slicer Segementation Editor. My question is is there any guide/tutorials to begin? I have already downloaded the plugins such as Nvidia AIAA et…

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## [How to programmatically split the RGB channels and store them separately as a segmentation node](https://discourse.slicer.org/t/how-to-programmatically-split-the-rgb-channels-and-store-them-separately-as-a-segmentation-node/22122)

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**Author:** [@PhilipDavis](https://discourse.slicer.org/u/PhilipDavis)\
**Replies:** 8\
**Last updated:** [February 23, 2022, 7:45pm UTC](https://discourse.slicer.org/t/how-to-programmatically-split-the-rgb-channels-and-store-them-separately-as-a-segmentation-node/22122 "2022-02-23T19:45:35Z")

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Hi there, I’m new to 3D Slicer, as this title mentions, here is a RGB stack TIFF image: RGB STACK and now I’d like to implement a procedure in python that splits the RGB channels and converts/stores the RGB channels i…

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## [Running slicer from mac terminal](https://discourse.slicer.org/t/running-slicer-from-mac-terminal/18908)

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**Author:** [@Panda](https://discourse.slicer.org/u/Panda)\
**Replies:** 4\
**Last updated:** [February 23, 2022, 7:41pm UTC](https://discourse.slicer.org/t/running-slicer-from-mac-terminal/18908 "2022-02-23T19:41:37Z")

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Hello, There are two issues I am facing - not really clear what’s happening. Quite basic actually: How do you initiate Slicer from mac terminal and run a python script without GUI -the documentation has stuff for Wind…

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## [Soft tissue deformation](https://discourse.slicer.org/t/soft-tissue-deformation/22128)

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**Author:** [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Replies:** 0\
**Last updated:** [February 23, 2022, 12:56pm UTC](https://discourse.slicer.org/t/soft-tissue-deformation/22128 "2022-02-23T12:56:37Z")

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Hello sir I have some doubts regarding soft tissue deformation , when I am going to fiducial registration wizard and adding some points then performing deformation but when I am going to other coronal sections and addin…

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## [Virtual septoplasty in 3D slicer](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329)

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**Author:** [@Sliceeeeee](https://discourse.slicer.org/u/Sliceeeeee)\
**Replies:** 25\
**Last updated:** [February 23, 2022, 7:50am UTC](https://discourse.slicer.org/t/virtual-septoplasty-in-3d-slicer/20329 "2022-02-23T07:50:05Z")

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i am going to make 3D model of nasal airway with 3D slicer ,but from a data of nasal septum deviation i want to make a corrected nasal airway by virtual septoplasty , how i can do that in 3D slicer ?

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## [How to creat .stl model from DICOM USING 3D Slicer?](https://discourse.slicer.org/t/how-to-creat-stl-model-from-dicom-using-3d-slicer/22100)

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**Author:** [@Moh\_d\_Al-Watary](https://discourse.slicer.org/u/Moh_d_Al-Watary)\
**Replies:** 1\
**Last updated:** [February 23, 2022, 7:14am UTC](https://discourse.slicer.org/t/how-to-creat-stl-model-from-dicom-using-3d-slicer/22100 "2022-02-23T07:14:22Z")

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Dear Friend, wish you are doing fine. I am working on a project in which I need to use .stl files from CT scan in DICOM format. So I need to change the format to. stl and creat 3d model how could this be done? Also, I …

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## [Lung tumour segmentation](https://discourse.slicer.org/t/lung-tumour-segmentation/22111)

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**Author:** [@ni5h](https://discourse.slicer.org/u/ni5h)\
**Replies:** 4\
**Last updated:** [February 23, 2022, 12:57am UTC](https://discourse.slicer.org/t/lung-tumour-segmentation/22111 "2022-02-23T00:57:46Z")

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Hi, for complex lung tumours, other than grow from seeds and fill between slices etc, is there an extension that can annotate a lung tumours? I have found completing this via GfS as not very accurate - imaging dataset is…

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## [Registration QA extension, jacobian determinant](https://discourse.slicer.org/t/registration-qa-extension-jacobian-determinant/13531)

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**Author:** [@Ana1890](https://discourse.slicer.org/u/Ana1890)\
**Replies:** 3\
**Last updated:** [February 22, 2022, 8:44pm UTC](https://discourse.slicer.org/t/registration-qa-extension-jacobian-determinant/13531 "2022-02-22T20:44:51Z")

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Hi everyone! I’m using Registration QA to calculate the Jacobian Determinant, but I want to calculate this with several regions of interest (ROI), individually. At this moment I’m creating several files to do that, and I…

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