# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=351

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

**Page:** 352

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## [Grow from seeds problem](https://discourse.slicer.org/t/grow-from-seeds-problem/10414)

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**Author:** [@rlazol](https://discourse.slicer.org/u/rlazol)\
**Replies:** 4\
**Last updated:** [February 26, 2020, 5:37pm UTC](https://discourse.slicer.org/t/grow-from-seeds-problem/10414 "2020-02-26T17:37:34Z")

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Dear All, we tried to segmentate the bones in an elephants’ limb using grow from seeds. My collague marked each bone extensively for a different segmentation using “paint” and then initiated the Grow from seeds. The res…

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## [MRI normnalization](https://discourse.slicer.org/t/mri-normnalization/10443)

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**Author:** [@Ceylan](https://discourse.slicer.org/u/Ceylan)\
**Replies:** 0\
**Last updated:** [February 26, 2020, 3:25pm UTC](https://discourse.slicer.org/t/mri-normnalization/10443 "2020-02-26T15:25:13Z")

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

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## [General Registration (BRAINS) error](https://discourse.slicer.org/t/general-registration-brains-error/10383)

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**Author:** [@Saima](https://discourse.slicer.org/u/Saima)\
**Replies:** 5\
**Last updated:** [February 26, 2020, 12:31pm UTC](https://discourse.slicer.org/t/general-registration-brains-error/10383 "2020-02-26T12:31:10Z")

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## [CBCT generated Lateral Cephalometry](https://discourse.slicer.org/t/cbct-generated-lateral-cephalometry/10365)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 3\
**Last updated:** [February 25, 2020, 11:48pm UTC](https://discourse.slicer.org/t/cbct-generated-lateral-cephalometry/10365 "2020-02-25T23:48:58Z")

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One of my colleagues came across this article and we tried to do the same with 3D Slicer. I It says two algorithms are used for generation of cephalograms from CBCT data. maximum intensity projection RayCast – 3D…

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## [Nightly Doxygen out of date](https://discourse.slicer.org/t/nightly-doxygen-out-of-date/10428)

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**Author:** [@Sunderlandkyl](https://discourse.slicer.org/u/Sunderlandkyl)\
**Replies:** 2\
**Last updated:** [February 25, 2020, 7:31pm UTC](https://discourse.slicer.org/t/nightly-doxygen-out-of-date/10428 "2020-02-25T19:31:24Z")

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The current nightly Doxygen doesn’t show the latest version of the API (Last updated January 30th). How often is the documentation updated? @jcfr @Sam\_Horvath

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## [SlicerMarkupsToModel does not build : since Slicer commit 997de030a6](https://discourse.slicer.org/t/slicermarkupstomodel-does-not-build-since-slicer-commit-997de030a6/10402)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 5\
**Last updated:** [February 25, 2020, 7:25pm UTC](https://discourse.slicer.org/t/slicermarkupstomodel-does-not-build-since-slicer-commit-997de030a6/10402 "2020-02-25T19:25:07Z")

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Since Slicer commit 997de030a6cd340b9f389c5bf54e8cacb55ddced, SlicerMarkupsToModel fails to build on Linux with missing curveGenerator-\>SetInputPoints and curveGenerator-\>GetOutputPoints. These are indeed discarded in th…

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## [How to superimpose two CT/CBCTs?](https://discourse.slicer.org/t/how-to-superimpose-two-ct-cbcts/10322)

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**Author:** [@ddii](https://discourse.slicer.org/u/ddii)\
**Replies:** 5\
**Last updated:** [February 25, 2020, 6:53pm UTC](https://discourse.slicer.org/t/how-to-superimpose-two-ct-cbcts/10322 "2020-02-25T18:53:32Z")

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How do you superimpose two scans? or even move the VR side by side? Thanks

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## [How to segment multiple volumes at once?](https://discourse.slicer.org/t/how-to-segment-multiple-volumes-at-once/10280)

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**Author:** [@Xi\_Fang](https://discourse.slicer.org/u/Xi_Fang)\
**Replies:** 11\
**Last updated:** [February 25, 2020, 6:31pm UTC](https://discourse.slicer.org/t/how-to-segment-multiple-volumes-at-once/10280 "2020-02-25T18:31:55Z")

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Currently I can make use of Clara model in 3D slicer to segment CT scans one by one. But I have tens of scans to segment. Loading and segmenting take a lot of time. Thus I wonder if I can segment tens of volumes at once …

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## [why my PNG stack from SlicerFab is colorful and very large?](https://discourse.slicer.org/t/why-my-png-stack-from-slicerfab-is-colorful-and-very-large/10415)

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**Author:** [@Lei](https://discourse.slicer.org/u/Lei)\
**Replies:** 7\
**Last updated:** [February 25, 2020, 6:24pm UTC](https://discourse.slicer.org/t/why-my-png-stack-from-slicerfab-is-colorful-and-very-large/10415 "2020-02-25T18:24:49Z")

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Operating system: win 10 Slicer version: 4.10.2 Expected behavior: black and white PNG stack from Bitmap generator (600\*300dpi) Actual behavior: very large and clolorful images, not covering the whole area

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## [Where can I found Editor module](https://discourse.slicer.org/t/where-can-i-found-editor-module/10408)

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**Author:** [@pooyesh](https://discourse.slicer.org/u/pooyesh)\
**Replies:** 9\
**Last updated:** [February 25, 2020, 4:26pm UTC](https://discourse.slicer.org/t/where-can-i-found-editor-module/10408 "2020-02-25T16:26:41Z")

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Hi I am beginner in 3D Slicer. I want to segment the Brain Corpus callosum and Cerebellum. In training movies I found the “Editor” models that can be helpful but in latest installed version (4.10.2 r28257) and in exten…

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## [Fractional anisotropy nrrd to dicom](https://discourse.slicer.org/t/fractional-anisotropy-nrrd-to-dicom/10352)

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**Author:** [@HariES](https://discourse.slicer.org/u/HariES)\
**Replies:** 6\
**Last updated:** [February 25, 2020, 4:44am UTC](https://discourse.slicer.org/t/fractional-anisotropy-nrrd-to-dicom/10352 "2020-02-25T04:44:07Z")

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Dear Sir I would like to export nrrd as dicom and save. I tried using dicom export, create dicom series and under data module. Nothing is worked properly. I may enter some information which I dont know. Kindly guide …

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## [DICOM cardiac CT image time series appears as moving line](https://discourse.slicer.org/t/dicom-cardiac-ct-image-time-series-appears-as-moving-line/10368)

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**Author:** [@ravi\_nataraj](https://discourse.slicer.org/u/ravi_nataraj)\
**Replies:** 4\
**Last updated:** [February 25, 2020, 4:40am UTC](https://discourse.slicer.org/t/dicom-cardiac-ct-image-time-series-appears-as-moving-line/10368 "2020-02-25T04:40:14Z")

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Hi, everyone. I’m pretty new to 3D Slicer and Imaging in general. I’m trying to volume render a heart from a 2-chamber CT view, however, the format of the DICOM file is problematic. I have 20 instances (files) and every …

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## [Extraction the vector components using python](https://discourse.slicer.org/t/extraction-the-vector-components-using-python/10394)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 3\
**Last updated:** [February 25, 2020, 12:26am UTC](https://discourse.slicer.org/t/extraction-the-vector-components-using-python/10394 "2020-02-25T00:26:57Z")

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Operating system:Linux Slicer version:4.11.0 Hi 3D Slicer experts and all I have a BSplin Transform which contains displacement fields. I want to extract its vector components. for this purpose I converted it to a vol…

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## [Best way to compare and contrast drilling trajectories](https://discourse.slicer.org/t/best-way-to-compare-and-contrast-drilling-trajectories/10382)

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**Author:** [@mccarthyvetsurg](https://discourse.slicer.org/u/mccarthyvetsurg)\
**Replies:** 4\
**Last updated:** [February 21, 2020, 5:36pm UTC](https://discourse.slicer.org/t/best-way-to-compare-and-contrast-drilling-trajectories/10382 "2020-02-21T17:36:29Z")

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Operating system: Windows 10 Expected behavior: unsure? Actual behavior: unsure? Does anyone know if 3D slicer can compare a preoperative drill trajectory to a post drill trajectory with STLs or if we can compare an…

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## [Flickering when using segmentation effects](https://discourse.slicer.org/t/flickering-when-using-segmentation-effects/10380)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 17\
**Last updated:** [February 25, 2020, 12:21am UTC](https://discourse.slicer.org/t/flickering-when-using-segmentation-effects/10380 "2020-02-25T00:21:15Z")

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While the use of segmentation effects in python scripts in slicer works really well, it creates flickering in the Slicer GUI when using full screen mode in mac. Using windowed mode makes no flickering, only full screen m…

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## [How to Convert MRI nii files into a series of tiff files using 3D Slicer 4.10?](https://discourse.slicer.org/t/how-to-convert-mri-nii-files-into-a-series-of-tiff-files-using-3d-slicer-4-10/10376)

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**Author:** [@Ali\_khattak](https://discourse.slicer.org/u/Ali_khattak)\
**Replies:** 1\
**Last updated:** [February 25, 2020, 12:11am UTC](https://discourse.slicer.org/t/how-to-convert-mri-nii-files-into-a-series-of-tiff-files-using-3d-slicer-4-10/10376 "2020-02-25T00:11:51Z")

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Hello all, this is my first question in this forum please guide me I am using ADNI images for my project of Alzheimer disease detection and classification using CNN but I have 3D images which need high performance GPU …

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## [How to add multi-metric inputs function to SlicerElastix?](https://discourse.slicer.org/t/how-to-add-multi-metric-inputs-function-to-slicerelastix/10202)

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**Author:** [@James753](https://discourse.slicer.org/u/James753)\
**Replies:** 2\
**Last updated:** [February 24, 2020, 5:50am UTC](https://discourse.slicer.org/t/how-to-add-multi-metric-inputs-function-to-slicerelastix/10202 "2020-02-24T05:50:44Z")

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Good extension! A quick question. How to add multi-metric inputs function ? Thx.

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## [Matching volume size with linear transformation](https://discourse.slicer.org/t/matching-volume-size-with-linear-transformation/10406)

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**Author:** [@mbutler808](https://discourse.slicer.org/u/mbutler808)\
**Replies:** 1\
**Last updated:** [February 24, 2020, 3:30am UTC](https://discourse.slicer.org/t/matching-volume-size-with-linear-transformation/10406 "2020-02-24T03:30:39Z")

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I have uCTscans of small frogs and we are trying to segment the hindlimb muscles for a study on locomotion. They were scanned in arbitrary orientations, which make it hard to identify the muscles. I would like to transf…

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## [How to add node selector on the loadable module of the Slicer](https://discourse.slicer.org/t/how-to-add-node-selector-on-the-loadable-module-of-the-slicer/10400)

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**Author:** [@sungminkim](https://discourse.slicer.org/u/sungminkim)\
**Replies:** 1\
**Last updated:** [February 23, 2020, 3:26pm UTC](https://discourse.slicer.org/t/how-to-add-node-selector-on-the-loadable-module-of-the-slicer/10400 "2020-02-23T15:26:40Z")

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Hi all, I have developed script module (Python module) of the Slicer for my research. Recently, I have started to develop new module with loadable module (C++ module) for the new purpose. But, I have faced to the prob…

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## [How to make segments from vtkMRMLModelNode by code](https://discourse.slicer.org/t/how-to-make-segments-from-vtkmrmlmodelnode-by-code/10389)

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**Author:** [@apparrilla](https://discourse.slicer.org/u/apparrilla)\
**Replies:** 4\
**Last updated:** [February 22, 2020, 10:27am UTC](https://discourse.slicer.org/t/how-to-make-segments-from-vtkmrmlmodelnode-by-code/10389 "2020-02-22T10:27:43Z")

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Hi, I have some ModelNodes from .vtk files attacked to lineartransforms. With this code i get new segments for each model in segmentation but with wrong location. How to fix segments position? name = model.GetName() …

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## [When Install via conda,Why the radiomics pyradiomics packages are not available from current channels?](https://discourse.slicer.org/t/when-install-via-conda-why-the-radiomics-pyradiomics-packages-are-not-available-from-current-channels/10392)

<div class="topic-metadata">

**Author:** [@382831265](https://discourse.slicer.org/u/382831265)\
**Replies:** 2\
**Last updated:** [February 22, 2020, 3:29am UTC](https://discourse.slicer.org/t/when-install-via-conda-why-the-radiomics-pyradiomics-packages-are-not-available-from-current-channels/10392 "2020-02-22T03:29:15Z")

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Operating system:win 10 professional Slicer version: Expected behavior: Actual behavior:

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## [Get a vector at specific voxel coordinates](https://discourse.slicer.org/t/get-a-vector-at-specific-voxel-coordinates/10366)

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**Author:** [@loubna](https://discourse.slicer.org/u/loubna)\
**Replies:** 11\
**Last updated:** [February 21, 2020, 4:57pm UTC](https://discourse.slicer.org/t/get-a-vector-at-specific-voxel-coordinates/10366 "2020-02-21T16:57:11Z")

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Hi, I have applied a 3d sobel filter on vtkImageData like this: vtkSmartPointer\<vtkImageSobel3D\> sobelFilter = vtkSmartPointer\<vtkImageSobel3D\>::New(); sobelFilter-\>SetInputData(image); sobelFilter-\>Update(); My quest…

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## [When estimating the volume of a segmented region using this software, do we need to consider the gap between the slices??](https://discourse.slicer.org/t/when-estimating-the-volume-of-a-segmented-region-using-this-software-do-we-need-to-consider-the-gap-between-the-slices/10311)

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**Author:** [@Eshani](https://discourse.slicer.org/u/Eshani)\
**Replies:** 2\
**Last updated:** [February 21, 2020, 4:42pm UTC](https://discourse.slicer.org/t/when-estimating-the-volume-of-a-segmented-region-using-this-software-do-we-need-to-consider-the-gap-between-the-slices/10311 "2020-02-21T16:42:49Z")

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

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## [Surface generation from label map volume](https://discourse.slicer.org/t/surface-generation-from-label-map-volume/10372)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 4\
**Last updated:** [February 21, 2020, 4:32pm UTC](https://discourse.slicer.org/t/surface-generation-from-label-map-volume/10372 "2020-02-21T16:32:52Z")

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Hello all, I am trying a code for generating surface from a label map volume. When I enter the following command: reconstructSurface.SetInputConnection(threshold.GetOutputPort()) reconstructSurface.SetProjectionPlaneM…

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## [Turning off mouse adjustment of contrast and brightness](https://discourse.slicer.org/t/turning-off-mouse-adjustment-of-contrast-and-brightness/596)

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**Author:** [@bobread](https://discourse.slicer.org/u/bobread)\
**Replies:** 10\
**Last updated:** [February 21, 2020, 3:47pm UTC](https://discourse.slicer.org/t/turning-off-mouse-adjustment-of-contrast-and-brightness/596 "2020-02-21T15:47:02Z")

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Is it possible to turn off the left mouse button adjustment of contrast and brightness in the Segment Editor? When manually painting a segment I keep accidentally changing the values and it is driving me up the wall!

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## [Segmenting a Entire Slice!](https://discourse.slicer.org/t/segmenting-a-entire-slice/10381)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 3\
**Last updated:** [February 21, 2020, 2:39pm UTC](https://discourse.slicer.org/t/segmenting-a-entire-slice/10381 "2020-02-21T14:39:06Z")

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The my Micro CT data are reformated with " Fit slice plane to markup fiducials " script. I expected to fill the entire selected slice with Scissor effect by drawing a rectangle. (Same with the paint). However there are a…

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## [Special characters in filenames and strings are now allowed](https://discourse.slicer.org/t/special-characters-in-filenames-and-strings-are-now-allowed/10375)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 0\
**Last updated:** [February 21, 2020, 4:12am UTC](https://discourse.slicer.org/t/special-characters-in-filenames-and-strings-are-now-allowed/10375 "2020-02-21T04:12:47Z")

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Starting from Slicer Preview Release 4.11.0-2020-02-21, special characters are permitted in file names and in any other user-defined text (such as node names, string parameters, etc.). It was a large change throughout S…

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## [Vmtk Vesselness Filtering without seed point?](https://discourse.slicer.org/t/vmtk-vesselness-filtering-without-seed-point/8468)

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**Author:** [@Tommaso\_Di\_Noto](https://discourse.slicer.org/u/Tommaso_Di_Noto)\
**Replies:** 14\
**Last updated:** [February 21, 2020, 10:53am UTC](https://discourse.slicer.org/t/vmtk-vesselness-filtering-without-seed-point/8468 "2020-02-21T10:53:00Z")

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Hi everyone! I was studying tutorials about vmtk and I saw the Vesselness Filtering module. I find it really useful for a single patient, and I manged to make it work by manually specifying the initial seed (fiducial) p…

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## [BSpline to deformation field Error](https://discourse.slicer.org/t/bspline-to-deformation-field-error/503)

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**Author:** [@eladam](https://discourse.slicer.org/u/eladam)\
**Replies:** 4\
**Last updated:** [June 14, 2017, 6:15pm UTC](https://discourse.slicer.org/t/bspline-to-deformation-field-error/503 "2017-06-14T18:15:35Z")

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Hello, I have been trying to work with the BSpline to deformation field module, but it doesn't seem to work. As an input I provided the transform that I acquired from the General Registration (BRAINS) module through …

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## [Build Slicer in Windows subsystem complaining rename permission denied](https://discourse.slicer.org/t/build-slicer-in-windows-subsystem-complaining-rename-permission-denied/10370)

<div class="topic-metadata">

**Author:** [@Zhiy](https://discourse.slicer.org/u/Zhiy)\
**Replies:** 1\
**Last updated:** [February 21, 2020, 1:41am UTC](https://discourse.slicer.org/t/build-slicer-in-windows-subsystem-complaining-rename-permission-denied/10370 "2020-02-21T01:41:08Z")

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I tried to build Slicer nightly code in Ubuntu 18 (subsystem of windows 10). The cmake version is 3.13.4. The gcc/g++ versions are both 7.4. I ran cmake -DCMAKE\_BUILD\_TYPE:STRING=Debug -DQt5\_DIR:PATH=/home/me/Qt/5.14.…

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