# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=359

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

**Page:** 360

---

## [Issue of hollow shell while creating cardiac segmentation](https://discourse.slicer.org/t/issue-of-hollow-shell-while-creating-cardiac-segmentation/9590)

<div class="topic-metadata">

**Author:** [@sarvpriya1985](https://discourse.slicer.org/u/sarvpriya1985)\
**Replies:** 6\
**Last updated:** [December 24, 2019, 3:38pm UTC](https://discourse.slicer.org/t/issue-of-hollow-shell-while-creating-cardiac-segmentation/9590 "2019-12-24T15:38:29Z")

</div>

Hi everyone, After creating hollow shell (2mm) in cardiac segmentation, when I visualize the structures in virtual reality- The wall appears double-shelled and is not easily understandable and somehow obscures the inter…

---

## [Does Slicer support the batch processing?](https://discourse.slicer.org/t/does-slicer-support-the-batch-processing/2529)

<div class="topic-metadata">

**Author:** [@glhfgg1024](https://discourse.slicer.org/u/glhfgg1024)\
**Replies:** 4\
**Last updated:** [December 24, 2019, 11:50am UTC](https://discourse.slicer.org/t/does-slicer-support-the-batch-processing/2529 "2019-12-24T11:50:26Z")

</div>

Operating system: Windows 10 Slicer version: 4.8.0 Expected behavior: batch processing Actual behavior: Not sure Hi there, I’m on these things: first import the DICOM files into Slicer, then for each patient, I need…

---

## [Application startup script open option is confusing](https://discourse.slicer.org/t/application-startup-script-open-option-is-confusing/9596)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [December 24, 2019, 12:11am UTC](https://discourse.slicer.org/t/application-startup-script-open-option-is-confusing/9596 "2019-12-24T00:11:27Z")

</div>

I find the application startup script setting confusing. The default behavior is to try to open .slicerrc.py file with the editor registered for .py extension. If the user never actually done anything with .py extension…

---

## [Install slicer for all users option on windows](https://discourse.slicer.org/t/install-slicer-for-all-users-option-on-windows/9594)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [December 23, 2019, 7:43pm UTC](https://discourse.slicer.org/t/install-slicer-for-all-users-option-on-windows/9594 "2019-12-23T19:43:15Z")

</div>

While I like that users now can install slicer into their own user space in centrally administered computers, would it be possible to include an option to say ‘install slicer only for this user’ vs ‘install slicer for al…

---

## [Self-registration?](https://discourse.slicer.org/t/self-registration/9515)

<div class="topic-metadata">

**Author:** [@Nathan](https://discourse.slicer.org/u/Nathan)\
**Replies:** 4\
**Last updated:** [December 23, 2019, 7:33pm UTC](https://discourse.slicer.org/t/self-registration/9515 "2019-12-23T19:33:14Z")

</div>

Often in multi-slice MRI, the acquisitions of every other image are acquired separately. Whenthe patient moves between acquisitions, 3D reconstructions are problematic. I am going through images of patients with tremor …

---

## [open .scn image in slicer 3D.](https://discourse.slicer.org/t/open-scn-image-in-slicer-3d/9589)

<div class="topic-metadata">

**Author:** [@itsme](https://discourse.slicer.org/u/itsme)\
**Replies:** 1\
**Last updated:** [December 23, 2019, 3:56pm UTC](https://discourse.slicer.org/t/open-scn-image-in-slicer-3d/9589 "2019-12-23T15:56:03Z")

</div>

How to open .scn image in slicer 3D. Is there any other viewers to view .scn format files?

---

## [Point inside a closed surface/centre](https://discourse.slicer.org/t/point-inside-a-closed-surface-centre/9592)

<div class="topic-metadata">

**Author:** [@Jainey](https://discourse.slicer.org/u/Jainey)\
**Replies:** 3\
**Last updated:** [December 23, 2019, 2:44pm UTC](https://discourse.slicer.org/t/point-inside-a-closed-surface-centre/9592 "2019-12-23T14:44:04Z")

</div>

I m trying to get the centre inside a closed surface/model. Is there a code for this please Thanks

---

## [Python errors in terminal, loading DICOM volume is slow](https://discourse.slicer.org/t/python-errors-in-terminal-loading-dicom-volume-is-slow/9583)

<div class="topic-metadata">

**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 2\
**Last updated:** [December 23, 2019, 1:27pm UTC](https://discourse.slicer.org/t/python-errors-in-terminal-loading-dicom-volume-is-slow/9583 "2019-12-23T13:27:32Z")

</div>

The following errors appear in terminal with home built Slicer unchanged, and not with binaries from your repository : Traceback (most recent call last): File “/home/user/programs/Slicer/lib/Python/lib/python3.6/site-…

---

## [Registration of 2 RT Dose from TPS and Monte Carlo code](https://discourse.slicer.org/t/registration-of-2-rt-dose-from-tps-and-monte-carlo-code/8431)

<div class="topic-metadata">

**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 9\
**Last updated:** [December 23, 2019, 4:56am UTC](https://discourse.slicer.org/t/registration-of-2-rt-dose-from-tps-and-monte-carlo-code/8431 "2019-12-23T04:56:38Z")

</div>

Slicer version:4.10.1 Hi 3D Slicer experts and all I want to compare two RT Dose which are obtained the first from Treatment Planning System(TPS) and the second from Monte Carlo code (Primo software) , by using the Do…

---

## [What is the method to draw Structure of Slicer Rt?](https://discourse.slicer.org/t/what-is-the-method-to-draw-structure-of-slicer-rt/9585)

<div class="topic-metadata">

**Author:** [@11131](https://discourse.slicer.org/u/11131)\
**Replies:** 3\
**Last updated:** [December 23, 2019, 3:44am UTC](https://discourse.slicer.org/t/what-is-the-method-to-draw-structure-of-slicer-rt/9585 "2019-12-23T03:44:13Z")

</div>

Hi, I am working with MR DICOM files and RT Structure. I want to see DICOM and RT Structure in Python. I’m trying to implement pydicom, not the Slicer module, but the value of Image Orientation Patient in MR data that …

---

## [Get Mesh Cell and Modify](https://discourse.slicer.org/t/get-mesh-cell-and-modify/9459)

<div class="topic-metadata">

**Author:** [@lausiv](https://discourse.slicer.org/u/lausiv)\
**Replies:** 9\
**Last updated:** [December 20, 2019, 8:39pm UTC](https://discourse.slicer.org/t/get-mesh-cell-and-modify/9459 "2019-12-20T20:39:36Z")

</div>

for mesh cell 1 …, end of mesh \<== executing all of the mesh Get each mesh cell(below first picture) of all the mesh cells in the volume Modify each cell value(color) referral script code^^ modelNode = slicer…

---

## [Manual segmentation slow to complete a contour](https://discourse.slicer.org/t/manual-segmentation-slow-to-complete-a-contour/9527)

<div class="topic-metadata">

**Author:** [@spaper](https://discourse.slicer.org/u/spaper)\
**Replies:** 9\
**Last updated:** [December 20, 2019, 7:31pm UTC](https://discourse.slicer.org/t/manual-segmentation-slow-to-complete-a-contour/9527 "2019-12-20T19:31:27Z")

</div>

Background: I am currently working on segmenting the articular cartilage and synovial tissue in MRI DICOM images of human knees. The purpose for these segmentations is to compare them to segmentations completed using 3D…

---

## [Nonlinear transforms](https://discourse.slicer.org/t/nonlinear-transforms/9568)

<div class="topic-metadata">

**Author:** [@rprueckl](https://discourse.slicer.org/u/rprueckl)\
**Replies:** 2\
**Last updated:** [December 20, 2019, 3:35pm UTC](https://discourse.slicer.org/t/nonlinear-transforms/9568 "2019-12-20T15:35:41Z")

</div>

Our use-case is that we want to manually adjust a part of a brain atlas to the physiology of an individual subject. Therefore, besides rotation, translation, scaling, we want to transform the part of the atlas also nonli…

---

## [Can you put a module listing under two different categories?](https://discourse.slicer.org/t/can-you-put-a-module-listing-under-two-different-categories/9535)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 6\
**Last updated:** [December 19, 2019, 8:42pm UTC](https://discourse.slicer.org/t/can-you-put-a-module-listing-under-two-different-categories/9535 "2019-12-19T20:42:04Z")

</div>

As part of the SlicerMorph, we want to bundle bunch of extensions that are likely to be use to our users but may get overlooked. A particular example is Fiducial Registration tools within IGT. I would like to make them a…

---

## [RawImageGuess module](https://discourse.slicer.org/t/rawimageguess-module/5697)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 6\
**Last updated:** [December 19, 2019, 3:56pm UTC](https://discourse.slicer.org/t/rawimageguess-module/5697 "2019-12-19T15:56:30Z")

</div>

This project is potentially useful for our user base to facilitate raw image import from microCT scanners without having to create nhdr header to define them. I have tried with a sample data that I have in https://blogs.…

---

## [SlicerIGT Collect Points to Model Node](https://discourse.slicer.org/t/slicerigt-collect-points-to-model-node/9550)

<div class="topic-metadata">

**Author:** [@rprueckl](https://discourse.slicer.org/u/rprueckl)\
**Replies:** 2\
**Last updated:** [December 18, 2019, 4:29pm UTC](https://discourse.slicer.org/t/slicerigt-collect-points-to-model-node/9550 "2019-12-18T16:29:27Z")

</div>

This is probably a bug report: Slicer 4.10.2, SlicerIGT revision 00ff9bf I try to use the ‘Collect Points’ module to collect points into a model node with the following settings (autocollect on): Then, in the transf…

---

## [Additional segments appearing in segment representations](https://discourse.slicer.org/t/additional-segments-appearing-in-segment-representations/9519)

<div class="topic-metadata">

**Author:** [@dominicrushforth](https://discourse.slicer.org/u/dominicrushforth)\
**Replies:** 3\
**Last updated:** [December 18, 2019, 3:47pm UTC](https://discourse.slicer.org/t/additional-segments-appearing-in-segment-representations/9519 "2019-12-18T15:47:39Z")

</div>

I think I have found a bug where segments are not displaying properly. In one scenario I have a segment that includes both the left kidney and the spleen. I then separate this into two seperate segments. Both of these s…

---

## [arrayFromVolume issue](https://discourse.slicer.org/t/arrayfromvolume-issue/9548)

<div class="topic-metadata">

**Author:** [@fraca](https://discourse.slicer.org/u/fraca)\
**Replies:** 3\
**Last updated:** [December 18, 2019, 2:03pm UTC](https://discourse.slicer.org/t/arrayfromvolume-issue/9548 "2019-12-18T14:03:26Z")

</div>

I’ m trying to obtain the array of this volume, but i obtain some errors. Can you help me? labeledImage = self.LabeledVolumeSelector.currentNode().GetImageData() selectedImage = self.SelectedVolumeSelector.currentNode…

---

## [FEM Mesh Analysis & Visualization in Model Module](https://discourse.slicer.org/t/fem-mesh-analysis-visualization-in-model-module/9376)

<div class="topic-metadata">

**Author:** [@lausiv](https://discourse.slicer.org/u/lausiv)\
**Replies:** 37\
**Last updated:** [December 18, 2019, 1:50am UTC](https://discourse.slicer.org/t/fem-mesh-analysis-visualization-in-model-module/9376 "2019-12-18T01:50:35Z")

</div>

FEM Mesh Analysis & Visualization in Model Module (refers below picture :-)) in other words, for example. each mesh, i want to calculate mesh volume and display different color corresponding to the volume.

---

## [How to open .TRE file?](https://discourse.slicer.org/t/how-to-open-tre-file/9533)

<div class="topic-metadata">

**Author:** [@Duy\_H](https://discourse.slicer.org/u/Duy_H)\
**Replies:** 2\
**Last updated:** [December 17, 2019, 9:53pm UTC](https://discourse.slicer.org/t/how-to-open-tre-file/9533 "2019-12-17T21:53:34Z")

</div>

Dataset at “https://public.kitware.com/Wiki/TubeTK/Data” have “VascularNetwork.tre” file. How can i open this file using 3DSlicer?

---

## [Volume Clip with model tool missing !](https://discourse.slicer.org/t/volume-clip-with-model-tool-missing/9532)

<div class="topic-metadata">

**Author:** [@Vignesh\_Sivakumar](https://discourse.slicer.org/u/Vignesh_Sivakumar)\
**Replies:** 1\
**Last updated:** [December 17, 2019, 9:41pm UTC](https://discourse.slicer.org/t/volume-clip-with-model-tool-missing/9532 "2019-12-17T21:41:33Z")

</div>

Hi, I have Slicer 4.10.2 in my Windows PC and have been using it for some time. I have a need to use the “Volume Clip with model” tool that existed in the previous versions which don’t seem to exist in this version. Is …

---

## [Annotations panel](https://discourse.slicer.org/t/annotations-panel/9531)

<div class="topic-metadata">

**Author:** [@Lara\_93](https://discourse.slicer.org/u/Lara_93)\
**Replies:** 1\
**Last updated:** [December 17, 2019, 8:21pm UTC](https://discourse.slicer.org/t/annotations-panel/9531 "2019-12-17T20:21:18Z")

</div>

Operating system: Windows 10 Slicer version: 4.7.0 Expected behavior: Open Annotations panel when I select Annotations module Actual behavior: When I try to open annotations module panel, it doesn’t actually do anythi…

---

## [Z-axis and intensities change from Slicer to fsleyes](https://discourse.slicer.org/t/z-axis-and-intensities-change-from-slicer-to-fsleyes/9513)

<div class="topic-metadata">

**Author:** [@Tommaso\_Di\_Noto](https://discourse.slicer.org/u/Tommaso_Di_Noto)\
**Replies:** 11\
**Last updated:** [December 17, 2019, 3:48pm UTC](https://discourse.slicer.org/t/z-axis-and-intensities-change-from-slicer-to-fsleyes/9513 "2019-12-17T15:48:38Z")

</div>

Hi everyone! Small doubt. I have a DICOM series of a T1 scan. I converted this sequence to nifti with “dcm2niix” from command line and now when I overlap both the original T1 dcm and the T1.nii on Slicer I noticed two w…

---

## [Interactor from old version to 4.10.2](https://discourse.slicer.org/t/interactor-from-old-version-to-4-10-2/9493)

<div class="topic-metadata">

**Author:** [@fraca](https://discourse.slicer.org/u/fraca)\
**Replies:** 4\
**Last updated:** [December 17, 2019, 1:07pm UTC](https://discourse.slicer.org/t/interactor-from-old-version-to-4-10-2/9493 "2019-12-17T13:07:59Z")

</div>

Hi, i’m try to convert this code that was build for 3DSlicer 3.6 to the newest 3DSlicer 4.10.2, but i have some issues to define the interactor. Can you help me? self.RedSliceInteractor=slicer.ApplicationGUI.GetMainSl…

---

## [Registration of MRI to CT for the Spine](https://discourse.slicer.org/t/registration-of-mri-to-ct-for-the-spine/5858)

<div class="topic-metadata">

**Author:** [@triple\_axel](https://discourse.slicer.org/u/triple_axel)\
**Replies:** 2\
**Last updated:** [December 16, 2019, 10:20pm UTC](https://discourse.slicer.org/t/registration-of-mri-to-ct-for-the-spine/5858 "2019-12-16T22:20:01Z")

</div>

Hi, sorry to bother you all again. I have to registered the T1 to T2 scans just fine using the Brainsfit Module, however with regards of T2 to CT scans I am having a bit of trouble. I already used “Fudicial Registration…

---

## [Slicer crash when try to save.](https://discourse.slicer.org/t/slicer-crash-when-try-to-save/9518)

<div class="topic-metadata">

**Author:** [@Carlos\_Montoya](https://discourse.slicer.org/u/Carlos_Montoya)\
**Replies:** 1\
**Last updated:** [December 16, 2019, 3:39pm UTC](https://discourse.slicer.org/t/slicer-crash-when-try-to-save/9518 "2019-12-16T15:39:13Z")

</div>

when I try to save and browse for folder, it crash. Versions 4.8, 4.10 and 4.10.2. Win 10 spanish version. I´ve been working with slicer with no problems ultil last week.

---

## [3D slicer failiing to load the segmentations on iMac](https://discourse.slicer.org/t/3d-slicer-failiing-to-load-the-segmentations-on-imac/9505)

<div class="topic-metadata">

**Author:** [@nayansi.jha](https://discourse.slicer.org/u/nayansi.jha)\
**Replies:** 8\
**Last updated:** [December 16, 2019, 12:42am UTC](https://discourse.slicer.org/t/3d-slicer-failiing-to-load-the-segmentations-on-imac/9505 "2019-12-16T00:42:34Z")

</div>

Slicer is not loading the segmentation files. It shows the progress bar and then it finishes, but nothing opens. Below is the error log, please help ! 2019-12-15 15:44:54.680 Slicer\[953:52097\] Error from CoreDragRequ…

---

## [Encode volume rendering preset in single mrml file](https://discourse.slicer.org/t/encode-volume-rendering-preset-in-single-mrml-file/9504)

<div class="topic-metadata">

**Author:** [@mrm63](https://discourse.slicer.org/u/mrm63)\
**Replies:** 2\
**Last updated:** [December 15, 2019, 3:00pm UTC](https://discourse.slicer.org/t/encode-volume-rendering-preset-in-single-mrml-file/9504 "2019-12-15T15:00:47Z")

</div>

Hi folks–quick question: We are trying to make a very portable version of some volume files with Slicer, such that we could simply send a master .mrml file (along with the .mhd and .raw) files to a user, who could simpl…

---

## [Markup notification](https://discourse.slicer.org/t/markup-notification/7541)

<div class="topic-metadata">

**Author:** [@gcsharp](https://discourse.slicer.org/u/gcsharp)\
**Replies:** 5\
**Last updated:** [December 15, 2019, 2:10pm UTC](https://discourse.slicer.org/t/markup-notification/7541 "2019-12-15T14:10:02Z")

</div>

Hi, I am testing out the repository script “Get a notification if a markup point position is modified”. It is working (stuff being printed in python console) in Slicer 4.10.1, but I am getting no notifications in the v…

---

## [Reading MNI Tag point file in Slicer](https://discourse.slicer.org/t/reading-mni-tag-point-file-in-slicer/9488)

<div class="topic-metadata">

**Author:** [@Tina\_Kapur](https://discourse.slicer.org/u/Tina_Kapur)\
**Replies:** 3\
**Last updated:** [December 14, 2019, 2:46pm UTC](https://discourse.slicer.org/t/reading-mni-tag-point-file-in-slicer/9488 "2019-12-14T14:46:39Z")

</div>

Are there any converters from MNI Tag point file format to any fiducial format supported by Slicer? Here is an example file I am trying to read from the RESECT dataset of intraoperative (brain tumor resection) ultrasoun…

[Previous page](https://discourse.slicer.org/c/support/11.md?page=358)

[Next page](https://discourse.slicer.org/c/support/11.md?page=360)