# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=423

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

**Page:** 424

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## [VTK merge to create 3D image](https://discourse.slicer.org/t/vtk-merge-to-create-3d-image/2876)

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**Author:** [@Alex\_Wiley](https://discourse.slicer.org/u/Alex_Wiley)\
**Replies:** 5\
**Last updated:** [May 24, 2018, 5:55pm UTC](https://discourse.slicer.org/t/vtk-merge-to-create-3d-image/2876 "2018-05-24T17:55:01Z")

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Operating system: Slicer version: 4.3.1 Expected behavior: Actual behaviour: I am trying to merge VTK files to stitch together a 3D image.

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## [Elastix fails to update resampled image and transform](https://discourse.slicer.org/t/elastix-fails-to-update-resampled-image-and-transform/2909)

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**Author:** [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Replies:** 5\
**Last updated:** [May 24, 2018, 3:15pm UTC](https://discourse.slicer.org/t/elastix-fails-to-update-resampled-image-and-transform/2909 "2018-05-24T15:15:32Z")

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I am using a downloaded Slicer 4.9.0-2018-05-04 r27180. Using sample data MRBrainTumor1 and MRBrainTumor2, I try to register them using SlicerElastix extension. I tried a couple of presets (3D MRI, monomodal (brain) amon…

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## [Load table from txt format](https://discourse.slicer.org/t/load-table-from-txt-format/2910)

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**Author:** [@Davide\_Punzo](https://discourse.slicer.org/u/Davide_Punzo)\
**Replies:** 3\
**Last updated:** [May 24, 2018, 8:27am UTC](https://discourse.slicer.org/t/load-table-from-txt-format/2910 "2018-05-24T08:27:04Z")

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Hi @lassoan, what is the syntax for a table in txt format to be properly loaded? For example I have this table https://www.dropbox.com/s/eqwrs03bohn4bs4/WEIN069\_cat.txt?dl=0 and it will loaded as only one column (also…

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## [Spatial registration of meshes](https://discourse.slicer.org/t/spatial-registration-of-meshes/2859)

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**Author:** [@Bio\_Medical](https://discourse.slicer.org/u/Bio_Medical)\
**Replies:** 8\
**Last updated:** [May 24, 2018, 4:45am UTC](https://discourse.slicer.org/t/spatial-registration-of-meshes/2859 "2018-05-24T04:45:19Z")

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Can we perform Digital image coorelation in 3D slicer?

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## [Vessel tracking algorithm on lung CT](https://discourse.slicer.org/t/vessel-tracking-algorithm-on-lung-ct/2913)

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**Author:** [@anitakh1](https://discourse.slicer.org/u/anitakh1)\
**Replies:** 0\
**Last updated:** [May 23, 2018, 1:16pm UTC](https://discourse.slicer.org/t/vessel-tracking-algorithm-on-lung-ct/2913 "2018-05-23T13:16:37Z")

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## [Application of pyradiomics](https://discourse.slicer.org/t/application-of-pyradiomics/2894)

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**Author:** [@Abdullah1](https://discourse.slicer.org/u/Abdullah1)\
**Replies:** 0\
**Last updated:** [May 23, 2018, 5:39am UTC](https://discourse.slicer.org/t/application-of-pyradiomics/2894 "2018-05-23T05:39:51Z")

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I have a project topic on application of pyradiomics and 3d slicer to Medical image analysis and I really need help on step by step instructions on how to make use of the radiomics module on the 3D slicer.

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## [Export segmentation to FEA software](https://discourse.slicer.org/t/export-segmentation-to-fea-software/2893)

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**Author:** [@saeed\_mouloodi](https://discourse.slicer.org/u/saeed_mouloodi)\
**Replies:** 1\
**Last updated:** [May 23, 2018, 4:50am UTC](https://discourse.slicer.org/t/export-segmentation-to-fea-software/2893 "2018-05-23T04:50:16Z")

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## [LabelMap vs Segment Editor](https://discourse.slicer.org/t/labelmap-vs-segment-editor/2888)

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**Author:** [@cphillips](https://discourse.slicer.org/u/cphillips)\
**Replies:** 1\
**Last updated:** [May 22, 2018, 7:18pm UTC](https://discourse.slicer.org/t/labelmap-vs-segment-editor/2888 "2018-05-22T19:18:26Z")

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Operating system: Windows 7 Slicer version: 4.8.1 I have been using the Grow From Seeds effect (in the Segment Editor) to segment out an infarct from a T2W MRI and calculate its volume. I initially tried the GrowCut Ef…

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## [Can you make a difference overlay of two scalar overlays?](https://discourse.slicer.org/t/can-you-make-a-difference-overlay-of-two-scalar-overlays/2867)

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**Author:** [@srb\_4](https://discourse.slicer.org/u/srb_4)\
**Replies:** 7\
**Last updated:** [May 22, 2018, 7:14pm UTC](https://discourse.slicer.org/t/can-you-make-a-difference-overlay-of-two-scalar-overlays/2867 "2018-05-22T19:14:51Z")

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If I have two scalar overlays for the same model, is there a way to create a new overlay that gives me the difference between overlay 1 and overlay 2? Operating system: Windows 10 Slicer version: 4.8.1

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## [.vtp to segmentation & load segmentation in Python](https://discourse.slicer.org/t/vtp-to-segmentation-load-segmentation-in-python/2883)

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**Author:** [@trnhx001](https://discourse.slicer.org/u/trnhx001)\
**Replies:** 1\
**Last updated:** [May 22, 2018, 6:20pm UTC](https://discourse.slicer.org/t/vtp-to-segmentation-load-segmentation-in-python/2883 "2018-05-22T18:20:33Z")

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Hi, I saved my segmentation as .vtp. Is there anyway to convert it back to Segmentation (.nrrd probably) in python or using 3D Slicers existing tools. Moreover, I am trying to load segmentation data into 3D matrix in P…

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## [Scene view not starting](https://discourse.slicer.org/t/scene-view-not-starting/2881)

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**Author:** [@HLee](https://discourse.slicer.org/u/HLee)\
**Replies:** 2\
**Last updated:** [May 22, 2018, 6:11pm UTC](https://discourse.slicer.org/t/scene-view-not-starting/2881 "2018-05-22T18:11:51Z")

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Hello all, I am quite new to Slicer but have used recent versions of Slicer (one year). Recently I noticed that when I started the program (several different versions… I am currently on 4.9.0 but it is the same for 4.6) …

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## [Cannot import "sample data"](https://discourse.slicer.org/t/cannot-import-sample-data/2849)

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**Author:** [@nirotu](https://discourse.slicer.org/u/nirotu)\
**Replies:** 5\
**Last updated:** [May 22, 2018, 5:07pm UTC](https://discourse.slicer.org/t/cannot-import-sample-data/2849 "2018-05-22T17:07:36Z")

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I use PC desktop. Unable to dooanload sample data for learning. Thank you,

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## [import directory of Grayscale Word image slice files](https://discourse.slicer.org/t/import-directory-of-grayscale-word-image-slice-files/2873)

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**Author:** [@john\_micrima](https://discourse.slicer.org/u/john_micrima)\
**Replies:** 4\
**Last updated:** [May 22, 2018, 2:53pm UTC](https://discourse.slicer.org/t/import-directory-of-grayscale-word-image-slice-files/2873 "2018-05-22T14:53:44Z")

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Operating system: Window 10 Slicer version: 4.8.1 Expected behavior: I expect to see an 3D image in the 3D pane Actual behavior: I see an empty cube and grayscale images in the other three panes My first question is,…

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## [convert dicom rt structure](https://discourse.slicer.org/t/convert-dicom-rt-structure/2872)

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**Author:** [@Jana.az](https://discourse.slicer.org/u/Jana.az)\
**Replies:** 1\
**Last updated:** [May 22, 2018, 11:49am UTC](https://discourse.slicer.org/t/convert-dicom-rt-structure/2872 "2018-05-22T11:49:24Z")

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I have imported a dicom rt structure, have done segmentation and then to models. How can i convert a specific model (like tumor or eyes) to an .stl format??

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## [move slicerDICOMdatabase ](https://discourse.slicer.org/t/move-slicerdicomdatabase/2858)

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**Author:** [@lambrosone](https://discourse.slicer.org/u/lambrosone)\
**Replies:** 1\
**Last updated:** [May 21, 2018, 12:40pm UTC](https://discourse.slicer.org/t/move-slicerdicomdatabase/2858 "2018-05-21T12:40:04Z")

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Operating system:win 10 Slicer version: 4.8.1 Expected behavior: Actual behavior: simple question. Is it possible to tell slicer to move the dicom database out of documents onto another drive? Thanks

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## [How to make the edge of the segment smoother?](https://discourse.slicer.org/t/how-to-make-the-edge-of-the-segment-smoother/2723)

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**Author:** [@trnhx001](https://discourse.slicer.org/u/trnhx001)\
**Replies:** 10\
**Last updated:** [May 21, 2018, 11:13am UTC](https://discourse.slicer.org/t/how-to-make-the-edge-of-the-segment-smoother/2723 "2018-05-21T11:13:46Z")

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Hi, I am a new intern, and my boss requires me to make the edge/border of a segment looks smooth. I am trying to have segment of Aorta. He calls it something like contour/mesh. Right now, the border looks very rough (li…

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## [About using Slicer with command line in windows](https://discourse.slicer.org/t/about-using-slicer-with-command-line-in-windows/2851)

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**Author:** [@Nater14](https://discourse.slicer.org/u/Nater14)\
**Replies:** 2\
**Last updated:** [May 21, 2018, 12:26am UTC](https://discourse.slicer.org/t/about-using-slicer-with-command-line-in-windows/2851 "2018-05-21T00:26:25Z")

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Operating system: Windows (10) Slicer version: Slicer4 Expected behavior: Images Registration through Elastix extension on Slicer 4 with command line Actual behavior: Don’t know how to do. Hello, I need some help. Be…

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## [2D Mixed Map MRI Viewing](https://discourse.slicer.org/t/2d-mixed-map-mri-viewing/2848)

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**Author:** [@cphillips](https://discourse.slicer.org/u/cphillips)\
**Replies:** 1\
**Last updated:** [May 18, 2018, 3:33pm UTC](https://discourse.slicer.org/t/2d-mixed-map-mri-viewing/2848 "2018-05-18T15:33:12Z")

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Operating system: Windows Slicer version: 4.8.1 Expected behavior: Actual behavior: I am attempting to view a 2D Mixed Map MRI scan in Slicer, but the slicer slider appears to be non-functional. Granted, there is onl…

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## [Fill “holes” in an image (T1-weighted)](https://discourse.slicer.org/t/fill-holes-in-an-image-t1-weighted/2612)

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**Author:** [@Frederic](https://discourse.slicer.org/u/Frederic)\
**Replies:** 8\
**Last updated:** [May 18, 2018, 1:05pm UTC](https://discourse.slicer.org/t/fill-holes-in-an-image-t1-weighted/2612 "2018-05-18T13:05:58Z")

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Hi all! I would like to fill holes of a binary input 3D image (cf. image and the code on it). It’s possible with Scipy (link), but Scipy is not installed in slicer. How could I do that? Thanks in advance.! Slicer\_ho…

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## [Load segmentation and export surface mesh as model .ply](https://discourse.slicer.org/t/load-segmentation-and-export-surface-mesh-as-model-ply/2646)

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**Author:** [@ladybug](https://discourse.slicer.org/u/ladybug)\
**Replies:** 10\
**Last updated:** [May 18, 2018, 11:36am UTC](https://discourse.slicer.org/t/load-segmentation-and-export-surface-mesh-as-model-ply/2646 "2018-05-18T11:36:08Z")

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Hello, I’m new to creating modules and my programming skills are rather basic, so I encountered problems in loading segmentation from subdirectories, and in exporting and saving the mesh models. The first issue looks l…

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## [2D ultrasound to 3D mesh ](https://discourse.slicer.org/t/2d-ultrasound-to-3d-mesh/2833)

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**Author:** [@ror\_input](https://discourse.slicer.org/u/ror_input)\
**Replies:** 3\
**Last updated:** [May 17, 2018, 4:46pm UTC](https://discourse.slicer.org/t/2d-ultrasound-to-3d-mesh/2833 "2018-05-17T16:46:00Z")

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Hi, I have a set of tiff images of 2D ultrasound (likely will get DICOM in the future) that I am hoping to convert to a 3D mesh and export as an STL file. The goal here is to do some image segmentation on breast tumors …

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## [load DICOM import](https://discourse.slicer.org/t/load-dicom-import/2839)

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**Author:** [@HwangJeongUk](https://discourse.slicer.org/u/HwangJeongUk)\
**Replies:** 2\
**Last updated:** [May 17, 2018, 1:03pm UTC](https://discourse.slicer.org/t/load-dicom-import/2839 "2018-05-17T13:03:50Z")

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Operating system: windows7 Slicer version: 4.9.0 Expected behavior: DICOM load Actual behavior: There is no change after loading the DICOM file. If you drag the DICOM folder to the Slicer window and click “Load di…

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## [Loading DICOM DWI Data](https://discourse.slicer.org/t/loading-dicom-dwi-data/2829)

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**Author:** [@cphillips](https://discourse.slicer.org/u/cphillips)\
**Replies:** 3\
**Last updated:** [May 16, 2018, 9:14pm UTC](https://discourse.slicer.org/t/loading-dicom-dwi-data/2829 "2018-05-16T21:14:43Z")

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Operating system: Windows 7 Slicer version: 4.8.1 Expected behavior: DICOM DWI Data loads normally Actual behavior: DICOM DWI Data appears garbled I am using the DICOM Browser to import and load MRI data. The importe…

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## [Paring a needle model with a vtktransform through python code](https://discourse.slicer.org/t/paring-a-needle-model-with-a-vtktransform-through-python-code/2827)

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**Author:** [@lgroves](https://discourse.slicer.org/u/lgroves)\
**Replies:** 1\
**Last updated:** [May 16, 2018, 8:15pm UTC](https://discourse.slicer.org/t/paring-a-needle-model-with-a-vtktransform-through-python-code/2827 "2018-05-16T20:15:09Z")

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I am trying to pair an already existing needle model with tracking data streaming in through the Plus server to view the needle in the 3D view. Currently I am performing this through using the data module and dragging my…

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## [How to save a model made by different parts from an atlas?](https://discourse.slicer.org/t/how-to-save-a-model-made-by-different-parts-from-an-atlas/2777)

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**Author:** [@marta](https://discourse.slicer.org/u/marta)\
**Replies:** 11\
**Last updated:** [May 16, 2018, 2:23pm UTC](https://discourse.slicer.org/t/how-to-save-a-model-made-by-different-parts-from-an-atlas/2777 "2018-05-16T14:23:43Z")

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Hello to everyone, I downloaded an atlas from the 3d slicer library and I selected the anatomical parts that interest me. Now I need to save the model as an stl file. In this model every anatomical part has to be a dif…

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## [Access slicer modules and libraries in pycharm](https://discourse.slicer.org/t/access-slicer-modules-and-libraries-in-pycharm/2765)

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**Author:** [@hadasara](https://discourse.slicer.org/u/hadasara)\
**Replies:** 4\
**Last updated:** [May 15, 2018, 7:54pm UTC](https://discourse.slicer.org/t/access-slicer-modules-and-libraries-in-pycharm/2765 "2018-05-15T19:54:31Z")

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Hi, I’d like to know why when I try to call slicer modules\\libraries (vtk, numpy), they are not recognized, unless I’m in the remote-debug mode, and run some loadable module, while there is a breakpoint somewhere in the…

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## [saggital and coronal views not loading ](https://discourse.slicer.org/t/saggital-and-coronal-views-not-loading/2818)

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**Author:** [@Sydney\_Brannoch](https://discourse.slicer.org/u/Sydney_Brannoch)\
**Replies:** 1\
**Last updated:** [May 15, 2018, 6:10pm UTC](https://discourse.slicer.org/t/saggital-and-coronal-views-not-loading/2818 "2018-05-15T18:10:46Z")

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Hello! I am new to 3D slicer and have tried to upload my micro-CT dataset after successfully following a tutorial using pre-loaded data. I am unable to load saggital and coronal views of the dataset however. When I have…

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## [Creating single DICOM file with the segmentation marked on MRI](https://discourse.slicer.org/t/creating-single-dicom-file-with-the-segmentation-marked-on-mri/2822)

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**Author:** [@Abhishek\_Behera](https://discourse.slicer.org/u/Abhishek_Behera)\
**Replies:** 0\
**Last updated:** [May 15, 2018, 1:30pm UTC](https://discourse.slicer.org/t/creating-single-dicom-file-with-the-segmentation-marked-on-mri/2822 "2018-05-15T13:30:24Z")

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Operating system: Windows 10 Slicer version: 4.8.1 Expected behavior: Actual behavior: I am working with an MRI dataset (3D Sag T1). I wish to segment (a single gyrus) an area using slicer and then change the corresp…

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## [Data missing from registration library](https://discourse.slicer.org/t/data-missing-from-registration-library/2816)

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**Author:** [@dzenanz](https://discourse.slicer.org/u/dzenanz)\
**Replies:** 1\
**Last updated:** [May 14, 2018, 8:30pm UTC](https://discourse.slicer.org/t/data-missing-from-registration-library/2816 "2018-05-14T20:30:38Z")

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Case 39 from here is missing the data. More precisely, when I try to download either .mrb, I get an empty zip file.

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## [Unable to load and view data](https://discourse.slicer.org/t/unable-to-load-and-view-data/2812)

<div class="topic-metadata">

**Author:** [@itakeitapart](https://discourse.slicer.org/u/itakeitapart)\
**Replies:** 5\
**Last updated:** [May 14, 2018, 8:07pm UTC](https://discourse.slicer.org/t/unable-to-load-and-view-data/2812 "2018-05-14T20:07:15Z")

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Operating system:windows 7 Slicer version:4.8.1 Expected behavior: Actual behavior: Hello All, I am a very novice user. Around 6-9 months ago I was working with some of the demo videos found on you tube. I had use…

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