# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=417

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

**Page:** 418

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## [Create sphere brush to edit voxels values in scanners image without fixed position](https://discourse.slicer.org/t/create-sphere-brush-to-edit-voxels-values-in-scanners-image-without-fixed-position/3521)

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**Author:** [@Laura](https://discourse.slicer.org/u/Laura)\
**Replies:** 9\
**Last updated:** [July 20, 2018, 11:34am UTC](https://discourse.slicer.org/t/create-sphere-brush-to-edit-voxels-values-in-scanners-image-without-fixed-position/3521 "2018-07-20T11:34:48Z")

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Good morning, I would need some help to finish my project as an intern working on segmentation of an organ on 3D Slicer. I have a segmented organ with white pixels over a black background (a vtkMRMLScalarVolumeNode). I…

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## [Reference planes](https://discourse.slicer.org/t/reference-planes/3538)

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**Author:** [@haylea.b](https://discourse.slicer.org/u/haylea.b)\
**Replies:** 0\
**Last updated:** [July 20, 2018, 10:43am UTC](https://discourse.slicer.org/t/reference-planes/3538 "2018-07-20T10:43:12Z")

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Hi everyone, I am wondering how you can make your own reference plane on 3D Slicer? I also need help with calibrating the measurements for the ruler? thanks in advance for your support

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## [Detecting holes](https://discourse.slicer.org/t/detecting-holes/3534)

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**Author:** [@Sadjad\_Abedi](https://discourse.slicer.org/u/Sadjad_Abedi)\
**Replies:** 0\
**Last updated:** [July 20, 2018, 9:01am UTC](https://discourse.slicer.org/t/detecting-holes/3534 "2018-07-20T09:01:58Z")

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I wonder why Slicer can’t detect some small holes in my model. I rose the kernel size even to 25 mm and it takes about 40 min to complete, but the holes remained. I also use some different software such as MeshLab, MeshM…

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## [Cannot find my installed extension in modules](https://discourse.slicer.org/t/cannot-find-my-installed-extension-in-modules/3072)

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**Author:** [@xuec](https://discourse.slicer.org/u/xuec)\
**Replies:** 4\
**Last updated:** [July 20, 2018, 3:58am UTC](https://discourse.slicer.org/t/cannot-find-my-installed-extension-in-modules/3072 "2018-07-20T03:58:06Z")

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Hi, I have just installed the PETDICOM extension (successfully), as I can view it in the manage your extension in the extension manager, however, it is no where to find in the modules. Does anyone perhaps could give me …

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## [Load segment from matrix of integers](https://discourse.slicer.org/t/load-segment-from-matrix-of-integers/3524)

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**Author:** [@alessandronavacchia](https://discourse.slicer.org/u/alessandronavacchia)\
**Replies:** 1\
**Last updated:** [July 19, 2018, 7:00pm UTC](https://discourse.slicer.org/t/load-segment-from-matrix-of-integers/3524 "2018-07-19T19:00:55Z")

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Hi all, I have been exporting and importing segmentation masks as .stl files or other formats that describe the segmented volume as a surface mesh made of triangular elements. I was wondering if it is possible to load …

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## [Segmentation for MRI rat brains](https://discourse.slicer.org/t/segmentation-for-mri-rat-brains/3390)

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**Author:** [@alaleh\_alivar](https://discourse.slicer.org/u/alaleh_alivar)\
**Replies:** 1\
**Last updated:** [July 19, 2018, 2:06pm UTC](https://discourse.slicer.org/t/segmentation-for-mri-rat-brains/3390 "2018-07-19T14:06:07Z")

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Slicer version: 4.9.0 I want to upload an external atlas named as WHS\_SD\_rat\_atlas\_v2 for using it as a reference for brain segmentation. But when I use Em segment with atlas, there is no task defined for this purpose. …

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## [Slicer 4.9.0 build error](https://discourse.slicer.org/t/slicer-4-9-0-build-error/3518)

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**Author:** [@shellyverde](https://discourse.slicer.org/u/shellyverde)\
**Replies:** 3\
**Last updated:** [July 19, 2018, 2:02pm UTC](https://discourse.slicer.org/t/slicer-4-9-0-build-error/3518 "2018-07-19T14:02:44Z")

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Operating system: Windows 10 Slicer version: 4.9.0 check out on July 15, 2018 Expected behavior: Build slicer successfully Actual behavior: Build error occured Use VS 2013 to build, QT 4.8.7. Build mode: debug, x64. …

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## [Improve segmentation : "Paint" and "Erase" (or "Scissors") effects in Segment Editor or Sphere brush?](https://discourse.slicer.org/t/improve-segmentation-paint-and-erase-or-scissors-effects-in-segment-editor-or-sphere-brush/3504)

<div class="topic-metadata">

**Author:** [@Laura](https://discourse.slicer.org/u/Laura)\
**Replies:** 5\
**Last updated:** [July 18, 2018, 3:05pm UTC](https://discourse.slicer.org/t/improve-segmentation-paint-and-erase-or-scissors-effects-in-segment-editor-or-sphere-brush/3504 "2018-07-18T15:05:11Z")

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Good afternoon, First of all, thanks a lot to the one that is going to read my message ! I am currently an intern doing the segmentation of an organ on 3D Slicer (I am so new on 3D Slicer). However, I have some proble…

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## [Resample a 3D CT Image](https://discourse.slicer.org/t/resample-a-3d-ct-image/3505)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 3\
**Last updated:** [July 18, 2018, 1:08pm UTC](https://discourse.slicer.org/t/resample-a-3d-ct-image/3505 "2018-07-18T13:08:34Z")

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Hello! I have read this discussion but couldn’t found the answer I look for. I want to perform a resample similar to the BRAINS resample plugin, BUT not doing interpolation, instead the resample shall average the HU val…

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## [Label statistics calculation (voxel size)](https://discourse.slicer.org/t/label-statistics-calculation-voxel-size/3507)

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**Author:** [@tomo](https://discourse.slicer.org/u/tomo)\
**Replies:** 1\
**Last updated:** [July 17, 2018, 8:51pm UTC](https://discourse.slicer.org/t/label-statistics-calculation-voxel-size/3507 "2018-07-17T20:51:56Z")

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4.6.2 r25516, Mac OS 10.13.6, label volume file created by Freesurfer Label Statistics module: When calculate volume of segmented (labeled) structure the segmentation volume (voxel size 0.75 x 0.75 x0.75 mm3), the outpu…

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## [Import segmentation from model is too coarse](https://discourse.slicer.org/t/import-segmentation-from-model-is-too-coarse/2914)

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**Author:** [@kayarre](https://discourse.slicer.org/u/kayarre)\
**Replies:** 1\
**Last updated:** [May 23, 2018, 7:28pm UTC](https://discourse.slicer.org/t/import-segmentation-from-model-is-too-coarse/2914 "2018-05-23T19:28:59Z")

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When I open a closed surface model and attempt to import it into the segmentation the resulting segmentation is very coarse and doesn’t match the voxel resolution of the background image volume and I don’t see a way to e…

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## [Link to PlmLANDWARP tutorial broken?](https://discourse.slicer.org/t/link-to-plmlandwarp-tutorial-broken/3498)

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**Author:** [@Lowey](https://discourse.slicer.org/u/Lowey)\
**Replies:** 1\
**Last updated:** [July 17, 2018, 4:39am UTC](https://discourse.slicer.org/t/link-to-plmlandwarp-tutorial-broken/3498 "2018-07-17T04:39:03Z")

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Hi there, I was hoping to get access to the PlmLANDWARP tutorial, but I think the link may be broken? https://www.slicer.org/wiki/Documentation/4.8/Modules/PlmLANDWARP Cheers!

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## [Pial surface visualization](https://discourse.slicer.org/t/pial-surface-visualization/3467)

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**Author:** [@MartinaLucignola](https://discourse.slicer.org/u/MartinaLucignola)\
**Replies:** 2\
**Last updated:** [July 13, 2018, 7:57am UTC](https://discourse.slicer.org/t/pial-surface-visualization/3467 "2018-07-13T07:57:20Z")

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Operating system:Windows 10 Slicer version:4.8.1 Expected behavior:- Actual behavior:- Hi everyone, I am looking for Slicer-module allowing pial surface visualization and parametric map overlays. Searching on the w…

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## [Segment statistics problem](https://discourse.slicer.org/t/segment-statistics-problem/3363)

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**Author:** [@Ash\_Alarfaj](https://discourse.slicer.org/u/Ash_Alarfaj)\
**Replies:** 10\
**Last updated:** [July 13, 2018, 7:18pm UTC](https://discourse.slicer.org/t/segment-statistics-problem/3363 "2018-07-13T19:18:18Z")

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Problem report for Slicer 4.8.1 macosx-amd64: \[please describe expected and actual behavior\] When I’ve finished the segmentation and go to segment statistics the apply icon didn’t work and I need to close the programme …

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## [Removing islands in a given range](https://discourse.slicer.org/t/removing-islands-in-a-given-range/3462)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 3\
**Last updated:** [July 13, 2018, 5:00pm UTC](https://discourse.slicer.org/t/removing-islands-in-a-given-range/3462 "2018-07-13T17:00:21Z")

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Greetings Slicers, I’m trying to remove some islands in a given size range (100 voxels to 1000 voxels, for example) using some python code similar to that in SegmentEditorIslandsEffect.py. I can see where vtkITKIslandMa…

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## [model maker- external (binary) nifti mask](https://discourse.slicer.org/t/model-maker-external-binary-nifti-mask/3475)

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**Author:** [@Moran\_Artzi](https://discourse.slicer.org/u/Moran_Artzi)\
**Replies:** 4\
**Last updated:** [July 13, 2018, 4:20am UTC](https://discourse.slicer.org/t/model-maker-external-binary-nifti-mask/3475 "2018-07-13T04:20:57Z")

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Operating system: Win 64 Slicer version: 4.8.1 Hi all, I’m trying to use model maker to do 3D visualization of external (binary) nifti mask On the older Slicer version i used to upload and assign such a mask as label…

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## [Creating 2D mesh from 2D image](https://discourse.slicer.org/t/creating-2d-mesh-from-2d-image/3465)

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**Author:** [@Joseph](https://discourse.slicer.org/u/Joseph)\
**Replies:** 1\
**Last updated:** [July 12, 2018, 2:40am UTC](https://discourse.slicer.org/t/creating-2d-mesh-from-2d-image/3465 "2018-07-12T02:40:13Z")

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From what I can tell, Slicer is used to generate a 3d mesh from 2d images. However, I simply want to segment a 2d image and then create a 2d mesh in order to do a 2d finite element analysis using FEA software. Is this …

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## [Dentalscan reformat/slices](https://discourse.slicer.org/t/dentalscan-reformat-slices/3460)

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**Author:** [@Maxibers](https://discourse.slicer.org/u/Maxibers)\
**Replies:** 2\
**Last updated:** [July 11, 2018, 3:16pm UTC](https://discourse.slicer.org/t/dentalscan-reformat-slices/3460 "2018-07-11T15:16:30Z")

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Greetings, I am a young DDS who is trying to get an OPG looking image from a Cone beam TC. What other softwares let you do is draw a line on a coronal slice and create a 2D picture of the slab around the line. Is it pos…

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## [Show seed points on 3D volume](https://discourse.slicer.org/t/show-seed-points-on-3d-volume/3446)

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**Author:** [@anitakh1](https://discourse.slicer.org/u/anitakh1)\
**Replies:** 3\
**Last updated:** [July 11, 2018, 2:06pm UTC](https://discourse.slicer.org/t/show-seed-points-on-3d-volume/3446 "2018-07-11T14:06:01Z")

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## [Export axial, sagittal, and coronal view of models as volume](https://discourse.slicer.org/t/export-axial-sagittal-and-coronal-view-of-models-as-volume/3455)

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**Author:** [@katharina\_hecker](https://discourse.slicer.org/u/katharina_hecker)\
**Replies:** 1\
**Last updated:** [July 11, 2018, 9:47am UTC](https://discourse.slicer.org/t/export-axial-sagittal-and-coronal-view-of-models-as-volume/3455 "2018-07-11T09:47:50Z")

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Hi everyone, I´m currently working with a lot of integrated models inside one oblect, which is also a model. I was wondering whether you can export the axial, sagittal, and coronal view of models as volumes (for example…

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## [Slicer not loading a radiotherapy plan and dataset](https://discourse.slicer.org/t/slicer-not-loading-a-radiotherapy-plan-and-dataset/3453)

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**Author:** [@Lowey](https://discourse.slicer.org/u/Lowey)\
**Replies:** 5\
**Last updated:** [July 11, 2018, 2:04am UTC](https://discourse.slicer.org/t/slicer-not-loading-a-radiotherapy-plan-and-dataset/3453 "2018-07-11T02:04:59Z")

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Operating system: Windows 7 Slicer version: 4.8.1 Expected behavior: To be able to examine and load a radiotherapy dataset without errors Actual behavior: I receive the following errors when trying to ‘examine’ my dat…

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## [Changing View Group of a Node in View Controllers using Python](https://discourse.slicer.org/t/changing-view-group-of-a-node-in-view-controllers-using-python/3450)

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**Author:** [@cphillips](https://discourse.slicer.org/u/cphillips)\
**Replies:** 1\
**Last updated:** [July 10, 2018, 8:34pm UTC](https://discourse.slicer.org/t/changing-view-group-of-a-node-in-view-controllers-using-python/3450 "2018-07-10T20:34:38Z")

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I want to change the view group of a bunch of different nodes in the View Controllers module as part of a Python script. So far I have only managed to get that vc = slicer.modules.viewcontrollers gives me access to the …

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## [Merging two xrays to form one large FOV image - leg length measurements](https://discourse.slicer.org/t/merging-two-xrays-to-form-one-large-fov-image-leg-length-measurements/3445)

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**Author:** [@bodyimager](https://discourse.slicer.org/u/bodyimager)\
**Replies:** 2\
**Last updated:** [July 10, 2018, 2:10pm UTC](https://discourse.slicer.org/t/merging-two-xrays-to-form-one-large-fov-image-leg-length-measurements/3445 "2018-07-10T14:10:38Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [JPG file stack with different spacings](https://discourse.slicer.org/t/jpg-file-stack-with-different-spacings/3436)

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**Author:** [@Hari\_Simha](https://discourse.slicer.org/u/Hari_Simha)\
**Replies:** 1\
**Last updated:** [July 10, 2018, 4:44am UTC](https://discourse.slicer.org/t/jpg-file-stack-with-different-spacings/3436 "2018-07-10T04:44:16Z")

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Hello I am new to Slicer and am trying to construct a 3d volume from an image stack (jpeg or png). The application is in materials science. The spacing between the images in the stack are not the same. Please advise as…

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## [Rescale type attribute when creating DICOM series](https://discourse.slicer.org/t/rescale-type-attribute-when-creating-dicom-series/3399)

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**Author:** [@awagner](https://discourse.slicer.org/u/awagner)\
**Replies:** 4\
**Last updated:** [July 9, 2018, 7:18pm UTC](https://discourse.slicer.org/t/rescale-type-attribute-when-creating-dicom-series/3399 "2018-07-09T19:18:28Z")

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Hello, I’m using Slicer to create a downsampled CT series, and I was able to do that just fine, except that it appears the “Rescale type” attribute was changed from HU to US. Due to that I cannot export the images anymo…

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## [How to create a label map for heterogeneityCAD?](https://discourse.slicer.org/t/how-to-create-a-label-map-for-heterogeneitycad/3425)

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**Author:** [@danceward](https://discourse.slicer.org/u/danceward)\
**Replies:** 3\
**Last updated:** [July 9, 2018, 7:15pm UTC](https://discourse.slicer.org/t/how-to-create-a-label-map-for-heterogeneitycad/3425 "2018-07-09T19:15:21Z")

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I’m learning texture analysis from CT images, which modules can create right label maps for heterogeneityCAD? Modules such as segment editor and editor can not export right volumes, segment CAD just for MRI, how to do …

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## [Equalize the number of points two CenterlineComputationModels](https://discourse.slicer.org/t/equalize-the-number-of-points-two-centerlinecomputationmodels/3408)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 1\
**Last updated:** [July 9, 2018, 6:09pm UTC](https://discourse.slicer.org/t/equalize-the-number-of-points-two-centerlinecomputationmodels/3408 "2018-07-09T18:09:10Z")

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Hi Slicer Developers I have two models with the names of CenterlineComputationModelMR and CenterlineComputationModelCT with the following information: CenterlineComputationModelMR Mesh Type: Surface Mesh (vtkPolyData) …

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## [Problems with volume rendering (location/deformation/orientation)](https://discourse.slicer.org/t/problems-with-volume-rendering-location-deformation-orientation/3428)

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**Author:** [@torquil](https://discourse.slicer.org/u/torquil)\
**Replies:** 1\
**Last updated:** [July 9, 2018, 5:25pm UTC](https://discourse.slicer.org/t/problems-with-volume-rendering-location-deformation-orientation/3428 "2018-07-09T17:25:25Z")

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Hi! I’m new to Slicer 3d, so hopefully this is not a software problem, but only user error… When I’m doing 3d segmentation, everything seems to work as expected, but when I try volume redering, the 3d volume seems to en…

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## [Setting b-spline grid size](https://discourse.slicer.org/t/setting-b-spline-grid-size/3434)

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**Author:** [@Natasha\_Deans](https://discourse.slicer.org/u/Natasha_Deans)\
**Replies:** 1\
**Last updated:** [July 9, 2018, 5:00pm UTC](https://discourse.slicer.org/t/setting-b-spline-grid-size/3434 "2018-07-09T17:00:39Z")

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## [Enabling models scalars threshold hides the model](https://discourse.slicer.org/t/enabling-models-scalars-threshold-hides-the-model/3396)

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**Author:** [@Fernando](https://discourse.slicer.org/u/Fernando)\
**Replies:** 6\
**Last updated:** [July 9, 2018, 4:54pm UTC](https://discourse.slicer.org/t/enabling-models-scalars-threshold-hides-the-model/3396 "2018-07-09T16:54:54Z")

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Hi all, I’m trying to use the scalars threshold of the Models module for the first time, but when I enable it, the model disappears. I might be doing something wrong. Can you please give me some advice? If you confirm t…

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