# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=372

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

**Page:** 373

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## [Transforming a data node on to linear transform](https://discourse.slicer.org/t/transforming-a-data-node-on-to-linear-transform/8232)

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**Author:** [@Jainey](https://discourse.slicer.org/u/Jainey)\
**Replies:** 4\
**Last updated:** [September 5, 2019, 12:52pm UTC](https://discourse.slicer.org/t/transforming-a-data-node-on-to-linear-transform/8232 "2019-09-05T12:52:48Z")

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hi all, apologies for all this non-software persons queries. I have done registration of models and created linear transform files. (from 3 to 10) The I have created a mark ups node applying mark ups on my first model…

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## [Export two aligned STL model from Meshlab to SLICER3D for deviation Measurement](https://discourse.slicer.org/t/export-two-aligned-stl-model-from-meshlab-to-slicer3d-for-deviation-measurement/8264)

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**Author:** [@ss\_sabz](https://discourse.slicer.org/u/ss_sabz)\
**Replies:** 2\
**Last updated:** [September 5, 2019, 12:03pm UTC](https://discourse.slicer.org/t/export-two-aligned-stl-model-from-meshlab-to-slicer3d-for-deviation-measurement/8264 "2019-09-05T12:03:33Z")

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Hi: I need to find Deviation between two STL model points, So i found this link: How to compare/quantify (populate) two .stl models having shape difference to see result as color stl file and bar telling plus and minus…

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## [Working with GE medical images and corresponding direction file](https://discourse.slicer.org/t/working-with-ge-medical-images-and-corresponding-direction-file/8281)

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**Author:** [@mshah](https://discourse.slicer.org/u/mshah)\
**Replies:** 9\
**Last updated:** [September 4, 2019, 8:24pm UTC](https://discourse.slicer.org/t/working-with-ge-medical-images-and-corresponding-direction-file/8281 "2019-09-04T20:24:03Z")

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Hello, I am working with a set of GE medical DTI and DWI images. It seems that the directional gradients (in 26 directions) of these images are a in a separate .txt file. If these anyway I can integrate these directions…

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## [Export grid with segmentation information](https://discourse.slicer.org/t/export-grid-with-segmentation-information/8298)

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**Author:** [@iacarr](https://discourse.slicer.org/u/iacarr)\
**Replies:** 1\
**Last updated:** [September 4, 2019, 6:39pm UTC](https://discourse.slicer.org/t/export-grid-with-segmentation-information/8298 "2019-09-04T18:39:10Z")

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I’m looking to obtain a file with a 3D cartesian grid containing the segmentations I’ve created. I’ve worked a bit with the Segment Mesher module but have not found a way to export a simple cartesian grid of a prescribed…

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## [Exporting models by script](https://discourse.slicer.org/t/exporting-models-by-script/8289)

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**Author:** [@Ihsan\_MUTLU](https://discourse.slicer.org/u/Ihsan_MUTLU)\
**Replies:** 2\
**Last updated:** [September 4, 2019, 6:12pm UTC](https://discourse.slicer.org/t/exporting-models-by-script/8289 "2019-09-04T18:12:48Z")

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Hi! I am having a problem exporting models as obj files. I have created a model hierarcy node and filled it as follows: exportedModelsNode = slicer.mrmlScene.AddNewNodeByClass(‘vtkMRMLModelHierarchyNode’) slicer.modu…

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## [How to perform 3D-cinematic rendering?](https://discourse.slicer.org/t/how-to-perform-3d-cinematic-rendering/7313)

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**Author:** [@Egor](https://discourse.slicer.org/u/Egor)\
**Replies:** 30\
**Last updated:** [September 4, 2019, 4:38pm UTC](https://discourse.slicer.org/t/how-to-perform-3d-cinematic-rendering/7313 "2019-09-04T16:38:53Z")

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Is it possible to perform 3D-cinematic rendering from MDCT by 3D Slicer? Is there any modules to do that?

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## [OpenIGTIF Trajectory Message](https://discourse.slicer.org/t/openigtif-trajectory-message/8280)

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**Author:** [@burnhamd](https://discourse.slicer.org/u/burnhamd)\
**Replies:** 6\
**Last updated:** [September 4, 2019, 3:29pm UTC](https://discourse.slicer.org/t/openigtif-trajectory-message/8280 "2019-09-04T15:29:35Z")

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Does the OpenIGTIF extension have support to receive and send trajectory messages? I cant seem to find mention of it.

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## [Object-transformation rotate = OK translate doesn´t work, what´s wrong](https://discourse.slicer.org/t/object-transformation-rotate-ok-translate-doesn-t-work-what-s-wrong/8291)

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**Author:** [@norus](https://discourse.slicer.org/u/norus)\
**Replies:** 2\
**Last updated:** [September 4, 2019, 2:39pm UTC](https://discourse.slicer.org/t/object-transformation-rotate-ok-translate-doesn-t-work-what-s-wrong/8291 "2019-09-04T14:39:50Z")

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Hello, only a small problem: to translate an object in Transforms-workbench doesn´t work, it´s activated. rotation is ok. version 4.10.2 win 10 Dell M4800 RAM 16 GB May I didn´t check something. Thank you for …

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## [Determine voxel spacing in anatomical coordinate system](https://discourse.slicer.org/t/determine-voxel-spacing-in-anatomical-coordinate-system/8286)

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**Author:** [@Leon](https://discourse.slicer.org/u/Leon)\
**Replies:** 2\
**Last updated:** [September 4, 2019, 1:15pm UTC](https://discourse.slicer.org/t/determine-voxel-spacing-in-anatomical-coordinate-system/8286 "2019-09-04T13:15:12Z")

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Who can explain this to me? In the ‘Volumes’ module, the dimensions are displayed in three columns. If I understand it correctly (but correct me if I’m wrong), then the order from left to right is axial - coronal - sagi…

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## [Loading wrong serie](https://discourse.slicer.org/t/loading-wrong-serie/7951)

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**Author:** [@Harlock1978](https://discourse.slicer.org/u/Harlock1978)\
**Replies:** 3\
**Last updated:** [September 4, 2019, 12:44pm UTC](https://discourse.slicer.org/t/loading-wrong-serie/7951 "2019-09-04T12:44:22Z")

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Operating system: Windows 10 Slicer version: 4.10.2 Expected behavior: When I open Dicom Browser and I search a patient writing the Patient ID the right patient is shown and I expect that when clicking load this patie…

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## [Watermark feature](https://discourse.slicer.org/t/watermark-feature/8252)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [September 4, 2019, 3:14am UTC](https://discourse.slicer.org/t/watermark-feature/8252 "2019-09-04T03:14:43Z")

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@jcfr @pieper @lassoan. We finished our first SlicerMorph workshop and our trainees pretty much feel in love with Slicer and its capabilities (check out https://twitter.com/SlicerMorph/status/1168022612313686016 for som…

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## [DTI Analysis using Nifti file](https://discourse.slicer.org/t/dti-analysis-using-nifti-file/8283)

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**Author:** [@nirav](https://discourse.slicer.org/u/nirav)\
**Replies:** 2\
**Last updated:** [September 3, 2019, 8:13pm UTC](https://discourse.slicer.org/t/dti-analysis-using-nifti-file/8283 "2019-09-03T20:13:31Z")

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Hello Everyone, I am working with the .nii files to perform the DTI analysis and the .nii images are converted from Bruker file using Matlab. The problem I am facing is when using the Volumes module the software is not …

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## [Histogram of volume in regions defined by segments](https://discourse.slicer.org/t/histogram-of-volume-in-regions-defined-by-segments/2236)

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**Author:** [@drusmanbashir](https://discourse.slicer.org/u/drusmanbashir)\
**Replies:** 9\
**Last updated:** [September 3, 2019, 5:14pm UTC](https://discourse.slicer.org/t/histogram-of-volume-in-regions-defined-by-segments/2236 "2019-09-03T17:14:20Z")

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Hi. I am trying to apply a mask (LabelMap) to a volume in slicer to plot histograms of intensities within the masked region of interest. The necessary requisite is that I do all this programmatically using segmentation …

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## [Remove 3D view axis labels in python script](https://discourse.slicer.org/t/remove-3d-view-axis-labels-in-python-script/8276)

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**Author:** [@ezemikulan](https://discourse.slicer.org/u/ezemikulan)\
**Replies:** 2\
**Last updated:** [September 3, 2019, 1:58pm UTC](https://discourse.slicer.org/t/remove-3d-view-axis-labels-in-python-script/8276 "2019-09-03T13:58:20Z")

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Hi, I’m trying to save images of a volume render via a python script and I would like to toggle off the axis labels but I’m unable to do so. I’ve searched inside various objects, layoutManager.threeDWidget(0).threeDView…

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## [Is there a way to do conversion between vtkCollection and vtkMRMLNode?](https://discourse.slicer.org/t/is-there-a-way-to-do-conversion-between-vtkcollection-and-vtkmrmlnode/8243)

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**Author:** [@aiden.zhu](https://discourse.slicer.org/u/aiden.zhu)\
**Replies:** 4\
**Last updated:** [September 2, 2019, 3:26pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-do-conversion-between-vtkcollection-and-vtkmrmlnode/8243 "2019-09-02T15:26:32Z")

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Excuse my silly question if it is silly or it has been addressed somewhere else (please forward a link to me then, Thanks.). Anyway I have been confused a lot by this–\> In the class vtkMRMLScen, the following methods: …

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## [Export of voxel-true surface mesh](https://discourse.slicer.org/t/export-of-voxel-true-surface-mesh/8212)

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**Author:** [@fabian](https://discourse.slicer.org/u/fabian)\
**Replies:** 6\
**Last updated:** [September 2, 2019, 2:17pm UTC](https://discourse.slicer.org/t/export-of-voxel-true-surface-mesh/8212 "2019-09-02T14:17:17Z")

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Hi everyone! I’m new to Slicer and I apologise if this question is trivial or has been discussed elsewhere. I have a segmented volume and I’d like to export the surface of this volume as an (ideally triangular) mesh (e.…

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## [Beware of the STL file format](https://discourse.slicer.org/t/beware-of-the-stl-file-format/7642)

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**Author:** [@Chris\_Rorden](https://discourse.slicer.org/u/Chris_Rorden)\
**Replies:** 16\
**Last updated:** [September 2, 2019, 1:56am UTC](https://discourse.slicer.org/t/beware-of-the-stl-file-format/7642 "2019-09-02T01:56:46Z")

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Many topics on this forum mention the STL format. While it is great that Slicer supports so many formats, I would advocate that Slicer discourage users from exporting to STL (e.g. from the “Save Scene and Unsaved Data” d…

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## [Nightly Release - Data Probe not working for Red Slice](https://discourse.slicer.org/t/nightly-release-data-probe-not-working-for-red-slice/8240)

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**Author:** [@Greydon\_Gilmore](https://discourse.slicer.org/u/Greydon_Gilmore)\
**Replies:** 5\
**Last updated:** [August 30, 2019, 11:21pm UTC](https://discourse.slicer.org/t/nightly-release-data-probe-not-working-for-red-slice/8240 "2019-08-30T23:21:10Z")

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Hi all, I haven’t found a solution so I’m asking here. I can’t seem to activate the data probe instance for the Red Slice. It is working for Yellow and Green. The widget appears empty when hovering over the Red slice. I…

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## [Test extension in Docker](https://discourse.slicer.org/t/test-extension-in-docker/8120)

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**Author:** [@unnmdnwb3](https://discourse.slicer.org/u/unnmdnwb3)\
**Replies:** 14\
**Last updated:** [August 30, 2019, 12:40pm UTC](https://discourse.slicer.org/t/test-extension-in-docker/8120 "2019-08-30T12:40:38Z")

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Hello everyone, I’d like to set up a CI-pipeline with Gitlab CI, which should enable continuous testing of our extension (in python). However, it’s not quite obvious to me which dependencies I therefore have to integrat…

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## [Screen capture has issues if scaling is set to 2.0x or larger](https://discourse.slicer.org/t/screen-capture-has-issues-if-scaling-is-set-to-2-0x-or-larger/8219)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [August 29, 2019, 9:53pm UTC](https://discourse.slicer.org/t/screen-capture-has-issues-if-scaling-is-set-to-2-0x-or-larger/8219 "2019-08-29T21:53:09Z")

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When I try to do a screen capture of the 3D rendering window at magnification equal or greater to 2.0x, it superimposes two images. This only happens with 3D view only setting. Also Screen shot window stays behind t…

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## [Quitting Slicer kills my entire VNC session](https://discourse.slicer.org/t/quitting-slicer-kills-my-entire-vnc-session/8216)

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**Author:** [@hbraunDSP](https://discourse.slicer.org/u/hbraunDSP)\
**Replies:** 4\
**Last updated:** [August 29, 2019, 4:14pm UTC](https://discourse.slicer.org/t/quitting-slicer-kills-my-entire-vnc-session/8216 "2019-08-29T16:14:25Z")

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I’m having a problem where closing slicer causes the entire VNC session in which it’s running to quit. My setup: I’m on Computer 1 (Windows 10) My vnc session is on Computer 2 (RHEL 5.11) From Computer 2, I ssh to Com…

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## [How should I pass arguments when running Slicer in batch mode?](https://discourse.slicer.org/t/how-should-i-pass-arguments-when-running-slicer-in-batch-mode/8217)

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**Author:** [@hbraunDSP](https://discourse.slicer.org/u/hbraunDSP)\
**Replies:** 1\
**Last updated:** [August 29, 2019, 3:24pm UTC](https://discourse.slicer.org/t/how-should-i-pass-arguments-when-running-slicer-in-batch-mode/8217 "2019-08-29T15:24:53Z")

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I want to run slicer from within python, to execute a script that builds a scene automatically from a JSON file telling it what files to load. I think I’ve solved everything except how to tell slicer the location of the …

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## [Suggestion: Display progress bar while saving MRB](https://discourse.slicer.org/t/suggestion-display-progress-bar-while-saving-mrb/8222)

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**Author:** [@rprueckl](https://discourse.slicer.org/u/rprueckl)\
**Replies:** 0\
**Last updated:** [August 29, 2019, 7:50am UTC](https://discourse.slicer.org/t/suggestion-display-progress-bar-while-saving-mrb/8222 "2019-08-29T07:50:29Z")

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Currently, a progress bar is presented while loading a MRB file, whereas this is not the case while saving. It would be worth considering to have one as saving large scenes can take some time.

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## [Slicer Application Settings: User](https://discourse.slicer.org/t/slicer-application-settings-user/8141)

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**Author:** [@RayCui](https://discourse.slicer.org/u/RayCui)\
**Replies:** 5\
**Last updated:** [August 29, 2019, 1:47am UTC](https://discourse.slicer.org/t/slicer-application-settings-user/8141 "2019-08-29T01:47:55Z")

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I found that there are user settings in the Application Settings of Slicer, which can record Name, Login, Email, Organization, etc. How can these user information be used? Will the user information be saved to a file whe…

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## [Models not Transparent in Slicer 4.10.1](https://discourse.slicer.org/t/models-not-transparent-in-slicer-4-10-1/6538)

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**Author:** [@Nicole\_Seider](https://discourse.slicer.org/u/Nicole_Seider)\
**Replies:** 16\
**Last updated:** [August 28, 2019, 9:15pm UTC](https://discourse.slicer.org/t/models-not-transparent-in-slicer-4-10-1/6538 "2019-08-28T21:15:36Z")

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Dear all, We are currently working with Slicer 4.4.0 and Slicer 4.10.1. In Slicer 4.4, we can make models transparent using the opacity button: in the image below, the gray ‘leftpial’ surface is at .5 opacity, the gree…

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## [Wondering if I can create segmentation label from imported STL object?](https://discourse.slicer.org/t/wondering-if-i-can-create-segmentation-label-from-imported-stl-object/8201)

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**Author:** [@Shangcheng\_Wang](https://discourse.slicer.org/u/Shangcheng_Wang)\
**Replies:** 4\
**Last updated:** [August 28, 2019, 8:18pm UTC](https://discourse.slicer.org/t/wondering-if-i-can-create-segmentation-label-from-imported-stl-object/8201 "2019-08-28T20:18:43Z")

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Hi community, I had a MRI data set and segmented bone models in STL format. Could I create segmentation label from these 3D models? I also imported a cylindrical pin (create from CAD software) into slicer, and I am won…

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## [Can erase segment but not draw](https://discourse.slicer.org/t/can-erase-segment-but-not-draw/8210)

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**Author:** [@JoeCrozier](https://discourse.slicer.org/u/JoeCrozier)\
**Replies:** 4\
**Last updated:** [August 28, 2019, 5:35pm UTC](https://discourse.slicer.org/t/can-erase-segment-but-not-draw/8210 "2019-08-28T17:35:22Z")

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Slicer 4.11.0 Windows 10 Pro Hello, hopefully this question has not been answered before. If so, please point me in the right direction. I have a patient I am trying to create segmentation for, in order to 3d print t…

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## [Python script for transferring markup fiducial (fcsv file) to Excel](https://discourse.slicer.org/t/python-script-for-transferring-markup-fiducial-fcsv-file-to-excel/4447)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 5\
**Last updated:** [August 28, 2019, 11:08am UTC](https://discourse.slicer.org/t/python-script-for-transferring-markup-fiducial-fcsv-file-to-excel/4447 "2019-08-28T11:08:28Z")

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Hi All, could someone help me to write a python script to transfer fssv data (Real time RAS coordinates) in a transformed sequence to excel please. I have no programming knowledge, I am afraid. Thanks

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## [Fail to load pet/ct Gemini](https://discourse.slicer.org/t/fail-to-load-pet-ct-gemini/8158)

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**Author:** [@hu\_shuang](https://discourse.slicer.org/u/hu_shuang)\
**Replies:** 10\
**Last updated:** [August 28, 2019, 3:05am UTC](https://discourse.slicer.org/t/fail-to-load-pet-ct-gemini/8158 "2019-08-28T03:05:24Z")

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Operating system: Mac OS X Slicer version:4.10.2 Expected behavior: load pet/ct acquired by Phillips Gemini Actual behavior: It returns to “Could not load: 7: bone as a Scalar Volume”, the metadata is as following. No…

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## [DWI and DICOM Volume Rendering](https://discourse.slicer.org/t/dwi-and-dicom-volume-rendering/8199)

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**Author:** [@eliseberning](https://discourse.slicer.org/u/eliseberning)\
**Replies:** 4\
**Last updated:** [August 27, 2019, 8:16pm UTC](https://discourse.slicer.org/t/dwi-and-dicom-volume-rendering/8199 "2019-08-27T20:16:52Z")

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Operating system: Windows 10 Slicer version: 4.10.2 Hello, I have routinely been loading MRI DICOM images and performing a volume rendering for my data analysis. The DICOM files are a folder of IMA files and I save th…

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