# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=206

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

**Page:** 207

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## [Seek for quick registration method](https://discourse.slicer.org/t/seek-for-quick-registration-method/24943)

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**Author:** [@whu](https://discourse.slicer.org/u/whu)\
**Replies:** 11\
**Last updated:** [September 8, 2022, 4:27am UTC](https://discourse.slicer.org/t/seek-for-quick-registration-method/24943 "2022-09-08T04:27:58Z")

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Dear All, Here I got the EM tracker, a STL format Geometric model and corresponding physical object. I want to get three points, both with the EM positon and the Slicer posiontion information. As to the tutorial in IG…

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## [Segment Geometry - number of slices truncated?](https://discourse.slicer.org/t/segment-geometry-number-of-slices-truncated/25122)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 1\
**Last updated:** [September 7, 2022, 11:29pm UTC](https://discourse.slicer.org/t/segment-geometry-number-of-slices-truncated/25122 "2022-09-07T23:29:09Z")

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This question is likely for @jmhuie, as it is a question with the Segment Geometry extension. I noticed that the number of rows in the table for computed values (area in my instance) is the number of slices in the segmen…

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## [How to load custom presets when Slicer starts up](https://discourse.slicer.org/t/how-to-load-custom-presets-when-slicer-starts-up/25127)

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**Author:** [@user4](https://discourse.slicer.org/u/user4)\
**Replies:** 1\
**Last updated:** [September 7, 2022, 2:58pm UTC](https://discourse.slicer.org/t/how-to-load-custom-presets-when-slicer-starts-up/25127 "2022-09-07T14:58:12Z")

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Hi,all. I want to remove the CT presets and add my own presets in volume rendering module when Slicer starts up.I have seen some related topics and currently my idea is divided into two steps. Create my own presets…

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## [Registration transform as sequence bundle format](https://discourse.slicer.org/t/registration-transform-as-sequence-bundle-format/25137)

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**Author:** [@Boris33](https://discourse.slicer.org/u/Boris33)\
**Replies:** 0\
**Last updated:** [September 7, 2022, 8:13am UTC](https://discourse.slicer.org/t/registration-transform-as-sequence-bundle-format/25137 "2022-09-07T08:13:25Z")

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Hello 3DSlicer Community, I have successfully performed registration of my 4D data thanks to the sequence registration module tutorial. I now need to export the volumes and transformation sequences to MatLab to furt…

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## [How to add a calculated (instead of data input from OpenIGTLInk IO) proxy node in SequenceBrowser when recording an ultrasound sequences?](https://discourse.slicer.org/t/how-to-add-a-calculated-instead-of-data-input-from-openigtlink-io-proxy-node-in-sequencebrowser-when-recording-an-ultrasound-sequences/25133)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 0\
**Last updated:** [September 7, 2022, 4:25am UTC](https://discourse.slicer.org/t/how-to-add-a-calculated-instead-of-data-input-from-openigtlink-io-proxy-node-in-sequencebrowser-when-recording-an-ultrasound-sequences/25133 "2022-09-07T04:25:22Z")

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Hi everyone, I am trying to write my first extension module to do a real-time ultrasound annotation. I am now able to write a module for offline annotation with ultrasound sequences recorded as SequenceBrowsers in modu…

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## [How to add an observer to the Sequence-Browser of module Sequences?](https://discourse.slicer.org/t/how-to-add-an-observer-to-the-sequence-browser-of-module-sequences/25129)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 1\
**Last updated:** [September 7, 2022, 3:52am UTC](https://discourse.slicer.org/t/how-to-add-an-observer-to-the-sequence-browser-of-module-sequences/25129 "2022-09-07T03:52:53Z")

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Hi everyone, I am trying to write my first extension module, and would like to synchronize the sequence browser in module Sequences and the module I am working on. How can I add an observer to the Sequence Browser of m…

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## [Turn the Dicom files into .Stl files](https://discourse.slicer.org/t/turn-the-dicom-files-into-stl-files/24963)

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**Author:** [@NativeArcher](https://discourse.slicer.org/u/NativeArcher)\
**Replies:** 3\
**Last updated:** [September 7, 2022, 3:45am UTC](https://discourse.slicer.org/t/turn-the-dicom-files-into-stl-files/24963 "2022-09-07T03:45:36Z")

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I have the Library of Congress stringed Instrument Dicom collection and want to turn the Dicom files into .Stl files and no tutorial that I have seen for this file conversion is really easy to understand. Operating syst…

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## [Bone (ilium, sacrum) segmentation](https://discourse.slicer.org/t/bone-ilium-sacrum-segmentation/25117)

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**Author:** [@yyokoyama](https://discourse.slicer.org/u/yyokoyama)\
**Replies:** 1\
**Last updated:** [September 7, 2022, 3:05am UTC](https://discourse.slicer.org/t/bone-ilium-sacrum-segmentation/25117 "2022-09-07T03:05:22Z")

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version: latest (5.0.3), win11 dataset: dicom file (enhanced dicom) I’m new to slicer, and am working bone segmentations (ilium, sacrum). I’m watching the video (Organ segmentation 1: Bones - YouTube) on how to do it,…

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## [Import bmp data into 3D Slicer](https://discourse.slicer.org/t/import-bmp-data-into-3d-slicer/25058)

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**Author:** [@Trailer](https://discourse.slicer.org/u/Trailer)\
**Replies:** 9\
**Last updated:** [September 6, 2022, 5:49pm UTC](https://discourse.slicer.org/t/import-bmp-data-into-3d-slicer/25058 "2022-09-06T17:49:24Z")

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Hello, I am brand new to slicer 3D. I have a series of .bmp images from a micro-ct from bruker (skyscan). I am trying to import them into slicer 3D but keep getting the error: Error: Loading C:/Users/tommy/Desktop/im…

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## [How to select an existing ROI in LocalTreshold of SegmentEditor with code?](https://discourse.slicer.org/t/how-to-select-an-existing-roi-in-localtreshold-of-segmenteditor-with-code/25100)

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**Author:** [@KKLOVECOCO](https://discourse.slicer.org/u/KKLOVECOCO)\
**Replies:** 8\
**Last updated:** [September 6, 2022, 3:51pm UTC](https://discourse.slicer.org/t/how-to-select-an-existing-roi-in-localtreshold-of-segmenteditor-with-code/25100 "2022-09-06T15:51:51Z")

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Operating system:windows 10 Slicer version: 5.0.3 Hi, all, I just started learning slicer+jupyter and recently I have a problem that I can’t solve, I would appreciate if someone tell me： Before activating LocalTresho…

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## [How to make a smooth transition between different areas?](https://discourse.slicer.org/t/how-to-make-a-smooth-transition-between-different-areas/25069)

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**Author:** [@radiodid](https://discourse.slicer.org/u/radiodid)\
**Replies:** 1\
**Last updated:** [September 6, 2022, 2:14pm UTC](https://discourse.slicer.org/t/how-to-make-a-smooth-transition-between-different-areas/25069 "2022-09-06T14:14:25Z")

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I am working on the creation of a 3D reconstruction of a tooth for a presentation and I need the transition between the enamel and the root to be as smooth as possible, but at the same time, so that these structures do n…

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## [How to calculate %overlap of 2 segmentation objects](https://discourse.slicer.org/t/how-to-calculate-overlap-of-2-segmentation-objects/25112)

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**Author:** [@n3ubie](https://discourse.slicer.org/u/n3ubie)\
**Replies:** 2\
**Last updated:** [September 6, 2022, 2:01pm UTC](https://discourse.slicer.org/t/how-to-calculate-overlap-of-2-segmentation-objects/25112 "2022-09-06T14:01:59Z")

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Hi! I am new to Slicer, and am trying to do segmentation of objects in MRI head. I would like to compare the overlap of 2 manual segmentation objects, how should I go about in doing it in the segmentation statistics? Al…

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## [Measurement for the distance and surface area between joints](https://discourse.slicer.org/t/measurement-for-the-distance-and-surface-area-between-joints/25091)

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**Author:** [@yyokoyama](https://discourse.slicer.org/u/yyokoyama)\
**Replies:** 3\
**Last updated:** [September 6, 2022, 11:24am UTC](https://discourse.slicer.org/t/measurement-for-the-distance-and-surface-area-between-joints/25091 "2022-09-06T11:24:10Z")

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What would be the best way to measure the distance and surface area between sacroiliac joints (blue marked in the attached figure)?

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## [Tips for getting started loading and batch segmenting files with Slicer in python?](https://discourse.slicer.org/t/tips-for-getting-started-loading-and-batch-segmenting-files-with-slicer-in-python/24850)

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**Author:** [@Mike\_Flanigan](https://discourse.slicer.org/u/Mike_Flanigan)\
**Replies:** 3\
**Last updated:** [September 6, 2022, 5:17am UTC](https://discourse.slicer.org/t/tips-for-getting-started-loading-and-batch-segmenting-files-with-slicer-in-python/24850 "2022-09-06T05:17:58Z")

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I’m new to Slicer and am working on a project trying to automate a few Slicer steps for many files by creating a python script and then running it without opening the Slicer GUI. I’ve been reading through sections in th…

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## [Question about the visualization of displacement vector fields](https://discourse.slicer.org/t/question-about-the-visualization-of-displacement-vector-fields/25090)

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**Author:** [@zhangzhehao](https://discourse.slicer.org/u/zhangzhehao)\
**Replies:** 4\
**Last updated:** [September 5, 2022, 9:17pm UTC](https://discourse.slicer.org/t/question-about-the-visualization-of-displacement-vector-fields/25090 "2022-09-05T21:17:39Z")

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Hi all, I am doing image registration between two 3D CTs and have already got the dispalcement vector fields in MHA format with shape (224, 224, 96, 3), where first three dimensions represents the 3D image size. Once I…

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## [PNG data loading into correct orientation](https://discourse.slicer.org/t/png-data-loading-into-correct-orientation/25078)

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**Author:** [@Jojo\_yee88188](https://discourse.slicer.org/u/Jojo_yee88188)\
**Replies:** 2\
**Last updated:** [September 5, 2022, 7:07am UTC](https://discourse.slicer.org/t/png-data-loading-into-correct-orientation/25078 "2022-09-05T07:07:38Z")

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Hi all, I have a quick question about loading png data into the correct orientation. My png data are pelvic MRI in axial, sagittal, and coronal orientation in a separate folder. Therefore, I loaded each plane into the 3…

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## [Ge appsandbox 4 to 3d slicer](https://discourse.slicer.org/t/ge-appsandbox-4-to-3d-slicer/25075)

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**Author:** [@paperhuman465](https://discourse.slicer.org/u/paperhuman465)\
**Replies:** 0\
**Last updated:** [September 4, 2022, 9:01am UTC](https://discourse.slicer.org/t/ge-appsandbox-4-to-3d-slicer/25075 "2022-09-04T09:01:01Z")

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Hi, how do you actually connect GE’s AppSandBox and AppAPI to 3D slicer and achieve real time scanning? Thank you very much.

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## [Connect external appareil to 3D Slicer](https://discourse.slicer.org/t/connect-external-appareil-to-3d-slicer/24774)

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**Author:** [@abdoullah](https://discourse.slicer.org/u/abdoullah)\
**Replies:** 10\
**Last updated:** [September 4, 2022, 12:59am UTC](https://discourse.slicer.org/t/connect-external-appareil-to-3d-slicer/24774 "2022-09-04T00:59:17Z")

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Operating system:Mac OS 12.4 Slicer version:5.0.3 Expected behavior: Actual behavior:

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## [Fill between slices horizontally](https://discourse.slicer.org/t/fill-between-slices-horizontally/14997)

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**Author:** [@Chungmh](https://discourse.slicer.org/u/Chungmh)\
**Replies:** 22\
**Last updated:** [September 3, 2022, 4:21pm UTC](https://discourse.slicer.org/t/fill-between-slices-horizontally/14997 "2022-09-03T16:21:15Z")

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Currently I am trying to segment the cartilages and meniscus. I have already created segments horizontally. however when I tried to fill between slices they are not connecting? Does anyone knows why? I really need thi…

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## [Create Closed Curve from existing Point List in Markups](https://discourse.slicer.org/t/create-closed-curve-from-existing-point-list-in-markups/25050)

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**Author:** [@chris\_nik](https://discourse.slicer.org/u/chris_nik)\
**Replies:** 1\
**Last updated:** [September 3, 2022, 12:54pm UTC](https://discourse.slicer.org/t/create-closed-curve-from-existing-point-list-in-markups/25050 "2022-09-03T12:54:26Z")

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Hello Andras and Community, I have the following question: is it possible to create a Point List by placing multiple Points and then to create a Closed Curve between those points? (the way I go around it at the moment …

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## [Fiducial Marker](https://discourse.slicer.org/t/fiducial-marker/25046)

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**Author:** [@Mohammad](https://discourse.slicer.org/u/Mohammad)\
**Replies:** 4\
**Last updated:** [September 2, 2022, 9:05pm UTC](https://discourse.slicer.org/t/fiducial-marker/25046 "2022-09-02T21:05:42Z")

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Operating system: 10 Slicer version: 4.6 Dear All, I would be grateful if anyone could help me with how I can add some spherical fiducial (Green and Red spheres) (as in the below image) to my CT volume.

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## [Any tips on how I could get a similar result as this picture?](https://discourse.slicer.org/t/any-tips-on-how-i-could-get-a-similar-result-as-this-picture/25015)

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**Author:** [@HT1997](https://discourse.slicer.org/u/HT1997)\
**Replies:** 3\
**Last updated:** [September 2, 2022, 7:13pm UTC](https://discourse.slicer.org/t/any-tips-on-how-i-could-get-a-similar-result-as-this-picture/25015 "2022-09-02T19:13:05Z")

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Hi, I am trying to segment the vessels from the public data LADAF-2020-27 left kidney, given from the Human Organ Atlas website. Is it possible to segment vessels of any kind from these datasets and make a similar result…

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## [Setting Up Unix (Ubuntu) Local Paths?](https://discourse.slicer.org/t/setting-up-unix-ubuntu-local-paths/25049)

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**Author:** [@Matt\_Park](https://discourse.slicer.org/u/Matt_Park)\
**Replies:** 1\
**Last updated:** [September 2, 2022, 12:15pm UTC](https://discourse.slicer.org/t/setting-up-unix-ubuntu-local-paths/25049 "2022-09-02T12:15:44Z")

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I am trying to use the Cervical Vertebra Tools extension on 5.03 r30893/7ea0f43 and am getting a “setup local paths variables” error. Searching has not found a good link. Ubuntu 20.04 I get the following errors: VisSi…

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## [Edit Volume Rendering Module](https://discourse.slicer.org/t/edit-volume-rendering-module/25051)

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**Author:** [@user4](https://discourse.slicer.org/u/user4)\
**Replies:** 1\
**Last updated:** [September 2, 2022, 10:03am UTC](https://discourse.slicer.org/t/edit-volume-rendering-module/25051 "2022-09-02T10:03:59Z")

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Hi,all.I want to add some functions in volume rendering module and create some new widgets.But this C++ built-in module is a .dll file and I have no acess.I wonder if this module is not open source? Is there a way to get…

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## [Bug in Create New Volume Property](https://discourse.slicer.org/t/bug-in-create-new-volume-property/24984)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 4\
**Last updated:** [September 1, 2022, 3:11pm UTC](https://discourse.slicer.org/t/bug-in-create-new-volume-property/24984 "2022-09-01T15:11:21Z")

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I have 16 bit dataset where intensity ranges from 0-65535. When I use volume rendering the very first time on this dataset, I can create a scalar opacity mapping that makes sense for this dataset When I go to volume …

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## [Slicer crash without Error message when calling vtkMRMLSequenceNode.GetNthDataNode(-1)](https://discourse.slicer.org/t/slicer-crash-without-error-message-when-calling-vtkmrmlsequencenode-getnthdatanode-1/25043)

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**Author:** [@sunshine](https://discourse.slicer.org/u/sunshine)\
**Replies:** 0\
**Last updated:** [September 1, 2022, 2:50pm UTC](https://discourse.slicer.org/t/slicer-crash-without-error-message-when-calling-vtkmrmlsequencenode-getnthdatanode-1/25043 "2022-09-01T14:50:23Z")

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Operating system: Win10 Slicer version: 5.1.0-2022-08-16 Expected behavior: Generate an Error message, instead of crashing without any warning or error Actual behavior: Crash directly with no error message This happe…

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## [Using volume import module for 3D Slicer to extract image stacks from .vol files](https://discourse.slicer.org/t/using-volume-import-module-for-3d-slicer-to-extract-image-stacks-from-vol-files/25008)

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**Author:** [@Lastom](https://discourse.slicer.org/u/Lastom)\
**Replies:** 4\
**Last updated:** [September 1, 2022, 1:35pm UTC](https://discourse.slicer.org/t/using-volume-import-module-for-3d-slicer-to-extract-image-stacks-from-vol-files/25008 "2022-09-01T13:35:06Z")

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Hello everyone, I’m pretty new to using the 3D slicer software and recently downloaded it to convert .vol files to image stacks using this plugin by @muratmaga: I managed to already visualize my data in the program a…

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## [Slicer cervical bone](https://discourse.slicer.org/t/slicer-cervical-bone/15783)

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**Author:** [@Siegmund\_Lang](https://discourse.slicer.org/u/Siegmund_Lang)\
**Replies:** 1\
**Last updated:** [September 1, 2022, 1:04pm UTC](https://discourse.slicer.org/t/slicer-cervical-bone/15783 "2022-09-01T13:04:47Z")

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Dear everyone, when using the slicer cervical spine after merking a vertebrae and clicking “Run” I dont get the result but the error message: Extracting to user home done! setup local paths variables… STOPPED: err…

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## [Export transformed 4D image as nifti?](https://discourse.slicer.org/t/export-transformed-4d-image-as-nifti/25032)

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**Author:** [@ch-n](https://discourse.slicer.org/u/ch-n)\
**Replies:** 3\
**Last updated:** [September 1, 2022, 12:54pm UTC](https://discourse.slicer.org/t/export-transformed-4d-image-as-nifti/25032 "2022-09-01T12:54:46Z")

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Hi I would like to apply a bspline transformation I generated with the plastimatch plugin to a 4D image. That works all fine but afterwards I can no longer export the image in nifti format. I need the image for further…

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## [Adjusting the spacial orientation of 2D data loaded as a single slice](https://discourse.slicer.org/t/adjusting-the-spacial-orientation-of-2d-data-loaded-as-a-single-slice/24960)

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**Author:** [@nileshkurwale](https://discourse.slicer.org/u/nileshkurwale)\
**Replies:** 6\
**Last updated:** [September 1, 2022, 4:27am UTC](https://discourse.slicer.org/t/adjusting-the-spacial-orientation-of-2d-data-loaded-as-a-single-slice/24960 "2022-09-01T04:27:09Z")

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Operating system: Mac IOS Big sur 11.6.5 Slicer version: 4.11 Expected behavior: Actual behavior: When I load a single dicom slice in to the scene, it loads it as a volume but by default it loads it in axial view. Is…

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