# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=332

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

**Page:** 333

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## [Segmentation Transform](https://discourse.slicer.org/t/segmentation-transform/12378)

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**Author:** [@FatihSogukpinar](https://discourse.slicer.org/u/FatihSogukpinar)\
**Replies:** 2\
**Last updated:** [July 6, 2020, 5:39am UTC](https://discourse.slicer.org/t/segmentation-transform/12378 "2020-07-06T05:39:06Z")

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Hi all, I have a segmentation (similar to an atlas but includes only specific anatomical regions) and an MRI and I need to figure out how Slicer aligns them. When I open and plot them in Matlab, they are not aligned. Ba…

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## [Export NRRD image to DICOM](https://discourse.slicer.org/t/export-nrrd-image-to-dicom/946)

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**Author:** [@george1](https://discourse.slicer.org/u/george1)\
**Replies:** 10\
**Last updated:** [July 6, 2020, 3:07am UTC](https://discourse.slicer.org/t/export-nrrd-image-to-dicom/946 "2020-07-06T03:07:26Z")

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## [Adding a widget with Qt Designer to custom module is not functional](https://discourse.slicer.org/t/adding-a-widget-with-qt-designer-to-custom-module-is-not-functional/12380)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 2\
**Last updated:** [July 5, 2020, 7:16pm UTC](https://discourse.slicer.org/t/adding-a-widget-with-qt-designer-to-custom-module-is-not-functional/12380 "2020-07-05T19:16:19Z")

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I could not get a qMRMLNodeComboBox to work in a custom module created by Extension Wizard. It is added to the module’s UI with Qt Designer and its nodeTypes property set to vtkMRMLScalarVolumeNode. The attached screens…

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## [Transforms not loading into Slicer 4.10.2](https://discourse.slicer.org/t/transforms-not-loading-into-slicer-4-10-2/12369)

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**Author:** [@Vinny](https://discourse.slicer.org/u/Vinny)\
**Replies:** 4\
**Last updated:** [July 4, 2020, 1:05pm UTC](https://discourse.slicer.org/t/transforms-not-loading-into-slicer-4-10-2/12369 "2020-07-04T13:05:43Z")

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Hi, I’ve generated acpc transforms in 4.11.0-2020-06-06 that are not loading into the stable Slicer release 4.10.2. The data module is empty and does not display the transform. Any help would be appreciated. Thanks, …

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## [Vtk streamlines not aligning with reference image](https://discourse.slicer.org/t/vtk-streamlines-not-aligning-with-reference-image/12367)

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**Author:** [@Vinny](https://discourse.slicer.org/u/Vinny)\
**Replies:** 2\
**Last updated:** [July 4, 2020, 12:58pm UTC](https://discourse.slicer.org/t/vtk-streamlines-not-aligning-with-reference-image/12367 "2020-07-04T12:58:32Z")

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Hi, I am using 3D Slicer 4.11.0-2020-06-06 and noticed that the imported vtk streamlines do not align with the corresponding reference scan; however, for 3D Slicer version 4.10.2, the streamlines do align. Thanks, Vin…

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## [NRRD to FSL error with DWIConvert](https://discourse.slicer.org/t/nrrd-to-fsl-error-with-dwiconvert/11666)

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**Author:** [@amate](https://discourse.slicer.org/u/amate)\
**Replies:** 11\
**Last updated:** [July 3, 2020, 11:27pm UTC](https://discourse.slicer.org/t/nrrd-to-fsl-error-with-dwiconvert/11666 "2020-07-03T23:27:09Z")

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Operating system: MacOS Mojave 3DSlicer v. 4.10.2 Hi everyone, I have successfully used DWIConvert in Slicer to convert my dicom data to nrrd so I can process it in DTIPrep. However, I am running into problems when tr…

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## [Any way to plot error bars in Slicer?](https://discourse.slicer.org/t/any-way-to-plot-error-bars-in-slicer/12362)

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**Author:** [@xlucox](https://discourse.slicer.org/u/xlucox)\
**Replies:** 1\
**Last updated:** [July 3, 2020, 6:19pm UTC](https://discourse.slicer.org/t/any-way-to-plot-error-bars-in-slicer/12362 "2020-07-03T18:19:14Z")

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Hi!!! I have a data set which has its own standard deviation. I would like to plot in Slicer the error bar of this data. I read in https://www.slicer.org/wiki/Documentation/Nightly/Developers/Plots that VTKPlots can’t d…

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## [How to cite individual modules in 3D Slicer](https://discourse.slicer.org/t/how-to-cite-individual-modules-in-3d-slicer/12354)

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**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 1\
**Last updated:** [July 3, 2020, 6:05pm UTC](https://discourse.slicer.org/t/how-to-cite-individual-modules-in-3d-slicer/12354 "2020-07-03T18:05:16Z")

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How to cite individual modules like model maker and threshold filters. Please guide in this.

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## [Exporting labelmap without croped dimensions](https://discourse.slicer.org/t/exporting-labelmap-without-croped-dimensions/12342)

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**Author:** [@DiamondKMG](https://discourse.slicer.org/u/DiamondKMG)\
**Replies:** 4\
**Last updated:** [July 3, 2020, 4:58pm UTC](https://discourse.slicer.org/t/exporting-labelmap-without-croped-dimensions/12342 "2020-07-03T16:58:51Z")

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Problem report for Slicer 4.11.0-2020-06-30 linux-amd64: When I export a set of segments to a labelmap, if I don’t select a reference volume under the advanced tab of the ‘export/import models and labelmaps’ portion of …

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## [Cannot rename MarkupsFiducial in load data window](https://discourse.slicer.org/t/cannot-rename-markupsfiducial-in-load-data-window/11994)

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**Author:** [@DiamondKMG](https://discourse.slicer.org/u/DiamondKMG)\
**Replies:** 9\
**Last updated:** [July 3, 2020, 2:08pm UTC](https://discourse.slicer.org/t/cannot-rename-markupsfiducial-in-load-data-window/11994 "2020-07-03T14:08:59Z")

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Problem report for Slicer 4.11.0-2020-03-11 linux-amd64: \[please describe expected and actual behavior\] I have a set of .fcsv files that have very similar and long names and I would like to rename each file to a shorte…

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## [All module view doesn't fit on the screen](https://discourse.slicer.org/t/all-module-view-doesnt-fit-on-the-screen/12280)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 11\
**Last updated:** [July 3, 2020, 1:06pm UTC](https://discourse.slicer.org/t/all-module-view-doesnt-fit-on-the-screen/12280 "2020-07-03T13:06:27Z")

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When I expand the Modules to show all modules, it occupies my entire screen, but it is not a full list, nor I can expand or scroll. This is on a laptop with 4K screen. I suspect it is something to do with the scaling

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## [New module finder for selecting modules](https://discourse.slicer.org/t/new-module-finder-for-selecting-modules/12356)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 0\
**Last updated:** [July 3, 2020, 1:05pm UTC](https://discourse.slicer.org/t/new-module-finder-for-selecting-modules/12356 "2020-07-03T13:05:34Z")

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As more modules have been added to Slicer, it has become harder browse and select modules (see \[1\]). To address this, we added a new module finder window. The finder can be displayed by clicking “Search” icon in the modu…

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## [Transform matrix and image coordinates for .fcsv files](https://discourse.slicer.org/t/transform-matrix-and-image-coordinates-for-fcsv-files/12249)

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**Author:** [@FatihSogukpinar](https://discourse.slicer.org/u/FatihSogukpinar)\
**Replies:** 3\
**Last updated:** [July 1, 2020, 1:11pm UTC](https://discourse.slicer.org/t/transform-matrix-and-image-coordinates-for-fcsv-files/12249 "2020-07-01T13:11:41Z")

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Operating system: Windows 10 Slicer version: 4.10.2 Hi all, In Slicer I have an atlas and a .fcsv file. I need to get coordinates of .fcsv file in the image coordinates from Slicer to Matlab (and also the anatomical r…

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## [Create plane perpendicular to MarkupsLine from 1º point](https://discourse.slicer.org/t/create-plane-perpendicular-to-markupsline-from-1-point/12349)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 1\
**Last updated:** [July 2, 2020, 11:56pm UTC](https://discourse.slicer.org/t/create-plane-perpendicular-to-markupsline-from-1-point/12349 "2020-07-02T23:56:09Z")

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I have 2 points in a MarkupsLine and I want to align a model perpendicular to this line from 1º line point. i should like to have a slider to rotate model arround itself throw this custom axis and another slider to trasl…

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## [Importing images in czi file extension](https://discourse.slicer.org/t/importing-images-in-czi-file-extension/12291)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 5\
**Last updated:** [July 2, 2020, 7:58pm UTC](https://discourse.slicer.org/t/importing-images-in-czi-file-extension/12291 "2020-07-02T19:58:10Z")

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Hi All, May I know how to import image files in czi file format generated from Zeiss microscope into Slicer, for performing segmentation? Thanks, Deepa

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## [Segment Editor; Thresholding intensity range not working with discrete Hounsfield Units of \[0,1,2\]](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320)

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**Author:** [@Linford\_Briant](https://discourse.slicer.org/u/Linford_Briant)\
**Replies:** 5\
**Last updated:** [July 2, 2020, 7:26pm UTC](https://discourse.slicer.org/t/segment-editor-thresholding-intensity-range-not-working-with-discrete-hounsfield-units-of-0-1-2/12320 "2020-07-02T19:26:37Z")

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Dear Slicer Community, I have been using the Segment Editor to segment an image that takes on 3 discrete Hounsfield Units (0,1,2). The images contain 2 cells, cell1 is in HU=1, cell2 is in HU=2. The background is HU=0. …

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## [Adding control points with undefined position from Python](https://discourse.slicer.org/t/adding-control-points-with-undefined-position-from-python/12344)

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**Author:** [@smrolfe](https://discourse.slicer.org/u/smrolfe)\
**Replies:** 1\
**Last updated:** [July 2, 2020, 7:10pm UTC](https://discourse.slicer.org/t/adding-control-points-with-undefined-position-from-python/12344 "2020-07-02T19:10:22Z")

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I’d like to create a landmarking template with named, unplaced points. I can unset the position status of a point I have placed, but would like to add points to the node with uninitialized positions. It looks like I coul…

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## [Errors Running Slicer on CentOS using X11](https://discourse.slicer.org/t/errors-running-slicer-on-centos-using-x11/12339)

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**Author:** [@lennymartinez](https://discourse.slicer.org/u/lennymartinez)\
**Replies:** 5\
**Last updated:** [July 2, 2020, 4:52pm UTC](https://discourse.slicer.org/t/errors-running-slicer-on-centos-using-x11/12339 "2020-07-02T16:52:07Z")

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Got Slicer 4.11 installed on a CentOS remote machine mainly to be used for processing. It was working fine the first week, but something seems to have happened in between, or we didn’t notice what was up then. Ideally w…

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## [Increased loading time for multiple segments from numpy array](https://discourse.slicer.org/t/increased-loading-time-for-multiple-segments-from-numpy-array/11026)

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**Author:** [@EricM](https://discourse.slicer.org/u/EricM)\
**Replies:** 6\
**Last updated:** [July 2, 2020, 3:37pm UTC](https://discourse.slicer.org/t/increased-loading-time-for-multiple-segments-from-numpy-array/11026 "2020-07-02T15:37:35Z")

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Hello Slicer community, I have a performance problem, and I would like to reach out to you to see if there is something simple I can do to speed up the process. I have developped an annotation module in Slicer that wor…

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## [load surface in 3dSlicer 4.10.2](https://discourse.slicer.org/t/load-surface-in-3dslicer-4-10-2/12257)

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**Author:** [@Patricia\_Pais](https://discourse.slicer.org/u/Patricia_Pais)\
**Replies:** 3\
**Last updated:** [July 2, 2020, 1:52pm UTC](https://discourse.slicer.org/t/load-surface-in-3dslicer-4-10-2/12257 "2020-07-02T13:52:05Z")

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Operating system: Ubuntu 18.04.4 Slicer version: 4.10.2 Expected behavior: I would like to load a surface generated with freesurfer (e.g., lh.pial) and apply an overlay to it (e.g., overlayInPial.mgh). Actual behavior…

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## [Comparing Density without a known phantom](https://discourse.slicer.org/t/comparing-density-without-a-known-phantom/12326)

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**Author:** [@jamieawren](https://discourse.slicer.org/u/jamieawren)\
**Replies:** 2\
**Last updated:** [July 2, 2020, 5:16am UTC](https://discourse.slicer.org/t/comparing-density-without-a-known-phantom/12326 "2020-07-02T05:16:16Z")

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Hello, I am a very novice use of 3D Slicer, and am still working on fully understanding the conceptual side of image analysis, let alone the “how to” of specific Slicer functions… If I have a group of CT scans, all done…

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## [GE cardiovascular 3d images](https://discourse.slicer.org/t/ge-cardiovascular-3d-images/12263)

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**Author:** [@Rodrigo\_Visconti](https://discourse.slicer.org/u/Rodrigo_Visconti)\
**Replies:** 2\
**Last updated:** [July 2, 2020, 12:47am UTC](https://discourse.slicer.org/t/ge-cardiovascular-3d-images/12263 "2020-07-02T00:47:48Z")

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I’ve known a solution for decrypting GE 3D images using Image3dAPI. Have you heard of these solution? Is it compatible with 3D slicer? So far I couldn’t load GE dicom images with 3D slicer.

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## [Slow DICOM import](https://discourse.slicer.org/t/slow-dicom-import/12324)

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**Author:** [@IMF-Slicer](https://discourse.slicer.org/u/IMF-Slicer)\
**Replies:** 2\
**Last updated:** [July 1, 2020, 9:54pm UTC](https://discourse.slicer.org/t/slow-dicom-import/12324 "2020-07-01T21:54:51Z")

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Hello. I’ve read several prior posts about slow DICOM imports, but don’t see a consistent answer, so thanks for letting me ask the question again. I export a standard CT scan from MIM, about 90 slices, which seems to wo…

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## [Elongation of segments in a 3D volume](https://discourse.slicer.org/t/elongation-of-segments-in-a-3d-volume/12252)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 5\
**Last updated:** [July 1, 2020, 8:14pm UTC](https://discourse.slicer.org/t/elongation-of-segments-in-a-3d-volume/12252 "2020-07-01T20:14:41Z")

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Hello Everyone, I’ve a 3D volume like the following I would like to elongate all the vessel segments (say, by a factor of 5 times the current length). Is there a way to elongate the vessel segments in Slicer?

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## [Help with Vertebra Segmentation Code](https://discourse.slicer.org/t/help-with-vertebra-segmentation-code/12323)

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**Author:** [@vertebra](https://discourse.slicer.org/u/vertebra)\
**Replies:** 1\
**Last updated:** [July 1, 2020, 7:13pm UTC](https://discourse.slicer.org/t/help-with-vertebra-segmentation-code/12323 "2020-07-01T19:13:00Z")

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Please may someone help me sort through this code and give any edits!

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## [Any way to get the mean values for a 4D image ROI](https://discourse.slicer.org/t/any-way-to-get-the-mean-values-for-a-4d-image-roi/12282)

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**Author:** [@xlucox](https://discourse.slicer.org/u/xlucox)\
**Replies:** 4\
**Last updated:** [July 1, 2020, 7:11pm UTC](https://discourse.slicer.org/t/any-way-to-get-the-mean-values-for-a-4d-image-roi/12282 "2020-07-01T19:11:33Z")

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Hi!!! I’m trying to get and array with the mean values of a 4D volume based in a segmentation. I’ve been reading the plugins which use the module segment statistics but I couldn’t find anything helpful. Thank you very …

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## [Using Python Module to Render an Image in 3D](https://discourse.slicer.org/t/using-python-module-to-render-an-image-in-3d/12274)

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**Author:** [@vertebrae](https://discourse.slicer.org/u/vertebrae)\
**Replies:** 20\
**Last updated:** [July 1, 2020, 3:57pm UTC](https://discourse.slicer.org/t/using-python-module-to-render-an-image-in-3d/12274 "2020-07-01T15:57:19Z")

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Hello, I am looking to use a 3D slicer python module to render thresholded spinal data in 3D and to potentially save as an STL file. Does anyone know how to do this?

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## [How to handle .tif file from MIB](https://discourse.slicer.org/t/how-to-handle-tif-file-from-mib/12318)

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**Author:** [@Linford\_Briant](https://discourse.slicer.org/u/Linford_Briant)\
**Replies:** 0\
**Last updated:** [July 1, 2020, 1:11pm UTC](https://discourse.slicer.org/t/how-to-handle-tif-file-from-mib/12318 "2020-07-01T13:11:50Z")

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Dear Slicer Forum, I am new to Slicer, and using it to view in 3D images I have segmented in MIB. (These are serial blockface EM images.) I have saved the images from MIB as a .tif file and I import it into slicer, and …

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## [Problematic behavior of the extension manager](https://discourse.slicer.org/t/problematic-behavior-of-the-extension-manager/10986)

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**Author:** [@rkikinis](https://discourse.slicer.org/u/rkikinis)\
**Replies:** 11\
**Last updated:** [July 1, 2020, 11:44am UTC](https://discourse.slicer.org/t/problematic-behavior-of-the-extension-manager/10986 "2020-07-01T11:44:45Z")

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Operating system: Mac OS 10.15.4 Slicer version: Slicer-4.11.0-2020-04-01-macosx-amd64 Actual behavior: Something is broken/bizarre with the extension manager. I need to click twice for the window to appear and the hi…

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## [Smoothing and bolus](https://discourse.slicer.org/t/smoothing-and-bolus/12225)

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**Author:** [@BORIPHAT](https://discourse.slicer.org/u/BORIPHAT)\
**Replies:** 6\
**Last updated:** [July 1, 2020, 9:07am UTC](https://discourse.slicer.org/t/smoothing-and-bolus/12225 "2020-07-01T09:07:48Z")

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Hello, I’m a beginner for using 3D slicer. I would like to smooth the surface. I use the segment editor Median smoothing method, kernel size 10 mm but It’s still rough and what’s the module to create 3D bolus object. Co…

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