# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=375

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

**Page:** 376

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## [Help with "Grow From Seeds" command](https://discourse.slicer.org/t/help-with-grow-from-seeds-command/7520)

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**Author:** [@Ricardo](https://discourse.slicer.org/u/Ricardo)\
**Replies:** 9\
**Last updated:** [August 13, 2019, 8:52am UTC](https://discourse.slicer.org/t/help-with-grow-from-seeds-command/7520 "2019-08-13T08:52:24Z")

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Hi all. Recently started to work with 3DSlicer and would like to know if it’s possibly for the community to help with some issue I’m having with the “Grow From Seeds” command. I’m trying the a human heart segmentation …

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## [Export deformable transform to DICOM](https://discourse.slicer.org/t/export-deformable-transform-to-dicom/7997)

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**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 0\
**Last updated:** [August 13, 2019, 2:40am UTC](https://discourse.slicer.org/t/export-deformable-transform-to-dicom/7997 "2019-08-13T02:40:00Z")

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Thanks for the clarification. I have succeeded in installing the extensions using yesterday’s preview release version. But I still have two other questions. I want to export deformable transform, but when I install “…

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## [Extension installation](https://discourse.slicer.org/t/extension-installation/7984)

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**Author:** [@labixin](https://discourse.slicer.org/u/labixin)\
**Replies:** 1\
**Last updated:** [August 12, 2019, 2:56pm UTC](https://discourse.slicer.org/t/extension-installation/7984 "2019-08-12T14:56:52Z")

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Hi all, I have downloaded the latest Slicer Windows Version 4.11.0 (Preview Release, revision 28433, built 2019-08-12). But when I went to Extension Manager, it showed that both “SlicerRT” and “SlicerElastix” cannot be …

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## [Create a DICOM Series for batch of images](https://discourse.slicer.org/t/create-a-dicom-series-for-batch-of-images/7996)

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**Author:** [@pateld](https://discourse.slicer.org/u/pateld)\
**Replies:** 1\
**Last updated:** [August 13, 2019, 12:08am UTC](https://discourse.slicer.org/t/create-a-dicom-series-for-batch-of-images/7996 "2019-08-13T00:08:54Z")

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I am able to convert a nrrd file to a DICOM series manually using the Create a DICOM Series module, however, I can’t find a way to conduct this process automatically and I have 200 image sets that each need to be convert…

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## [MatlabBridge not working in Windows Preview version](https://discourse.slicer.org/t/matlabbridge-not-working-in-windows-preview-version/7991)

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**Author:** [@Prashant\_Pandey](https://discourse.slicer.org/u/Prashant_Pandey)\
**Replies:** 0\
**Last updated:** [August 12, 2019, 8:13pm UTC](https://discourse.slicer.org/t/matlabbridge-not-working-in-windows-preview-version/7991 "2019-08-12T20:13:46Z")

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Using the preview version on windows 10 MatlabBridge modules aren’t working. I tried the default (thresholding example) module which is automatically created by the generator and I get the error: test-module standard e…

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## [Changing voxel size](https://discourse.slicer.org/t/changing-voxel-size/7804)

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**Author:** [@Andrew\_Kanawati](https://discourse.slicer.org/u/Andrew_Kanawati)\
**Replies:** 4\
**Last updated:** [August 12, 2019, 3:19pm UTC](https://discourse.slicer.org/t/changing-voxel-size/7804 "2019-08-12T15:19:21Z")

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Can you please explain the steps to change the voxel size of the models. I am finding the dimensions of printed tubes and cylinders to be smaller or larger than the planned dimension. I have tried reducing the ‘spacing s…

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## [Inconsistency between Slicer 3.6 and Slicer 4.10.2 in mhd header](https://discourse.slicer.org/t/inconsistency-between-slicer-3-6-and-slicer-4-10-2-in-mhd-header/7980)

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**Author:** [@Xiaogai\_Li](https://discourse.slicer.org/u/Xiaogai_Li)\
**Replies:** 6\
**Last updated:** [August 12, 2019, 8:15am UTC](https://discourse.slicer.org/t/inconsistency-between-slicer-3-6-and-slicer-4-10-2-in-mhd-header/7980 "2019-08-12T08:15:03Z")

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Dear all, When open exactly the same image (hdr + img format), and save into mhd format using Slicer 3.6 and Slicer 4.10.2 gives different .mhd file regarding RAI VS RPI and transformation Matrix as below and attached p…

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## [Matplotlib problems](https://discourse.slicer.org/t/matplotlib-problems/7981)

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**Author:** [@garbulinskamaja](https://discourse.slicer.org/u/garbulinskamaja)\
**Replies:** 3\
**Last updated:** [August 12, 2019, 7:40am UTC](https://discourse.slicer.org/t/matplotlib-problems/7981 "2019-08-12T07:40:47Z")

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Hi! I am new to Slicer. I am trying to save a plot by script plt.scatter(np.arange(1, 20, 1), np.arange(1,20, 1)) plt.savefig(os.path.join(results\_path, "plotloss.png")) from slicer. The plot has some additional values…

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## [How to increase the size of mesh triangles](https://discourse.slicer.org/t/how-to-increase-the-size-of-mesh-triangles/7895)

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**Author:** [@Mohsen\_Taheri](https://discourse.slicer.org/u/Mohsen_Taheri)\
**Replies:** 7\
**Last updated:** [August 11, 2019, 7:45pm UTC](https://discourse.slicer.org/t/how-to-increase-the-size-of-mesh-triangles/7895 "2019-08-11T19:45:28Z")

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Hi, For a specific purpose I need to coarsen the mesh or increase the area of mesh triangles. I appreciate if anyone help me

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## [DVH for resampled RT Dose](https://discourse.slicer.org/t/dvh-for-resampled-rt-dose/7978)

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**Author:** [@aseman](https://discourse.slicer.org/u/aseman)\
**Replies:** 1\
**Last updated:** [August 11, 2019, 1:54pm UTC](https://discourse.slicer.org/t/dvh-for-resampled-rt-dose/7978 "2019-08-11T13:54:17Z")

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Slicer version:4.10.1 Hi 3D Slicer experts and all I exported RT Dose(Dimension:62x46x88) from TPS and I converted it to a volume (Dimension: 256x256x89) using Resample Scalar Volume Module. I want to calculate DVH fo…

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## [Grow From Seeds Not Working](https://discourse.slicer.org/t/grow-from-seeds-not-working/7614)

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**Author:** [@Tyrus](https://discourse.slicer.org/u/Tyrus)\
**Replies:** 9\
**Last updated:** [August 11, 2019, 12:10pm UTC](https://discourse.slicer.org/t/grow-from-seeds-not-working/7614 "2019-08-11T12:10:09Z")

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Hi everyone, I have a question about the “Grow from seeds” effect in Segment Editor. I have been using it pretty seamlessly in the past, but this morning when I tried to use it, its effect is to remove everything I have…

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## [Can I display a binary numpy array on Slicer as a segmentation volume?](https://discourse.slicer.org/t/can-i-display-a-binary-numpy-array-on-slicer-as-a-segmentation-volume/7952)

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**Author:** [@ISJ0392](https://discourse.slicer.org/u/ISJ0392)\
**Replies:** 2\
**Last updated:** [August 10, 2019, 6:09pm UTC](https://discourse.slicer.org/t/can-i-display-a-binary-numpy-array-on-slicer-as-a-segmentation-volume/7952 "2019-08-10T18:09:12Z")

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I have a numpy array with dimensions 512 \* 512 \* 64 \* 5. This represents 5 3D arrays, and the arrays have only 1 or 0 values representing voxels in a segmentation volume. Is there anyway I can display this saved .npy fil…

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## [Can anyone help me with extraction of arteries from CT angiography of brain?](https://discourse.slicer.org/t/can-anyone-help-me-with-extraction-of-arteries-from-ct-angiography-of-brain/7974)

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**Author:** [@Ritu\_Karela](https://discourse.slicer.org/u/Ritu_Karela)\
**Replies:** 1\
**Last updated:** [August 10, 2019, 5:50pm UTC](https://discourse.slicer.org/t/can-anyone-help-me-with-extraction-of-arteries-from-ct-angiography-of-brain/7974 "2019-08-10T17:50:02Z")

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Operating system: Windows 10 Slicer version: 4.10.2

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## [Changing window/level and index slice for a volume loaded from the command line](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924)

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**Author:** [@matt-warkentin](https://discourse.slicer.org/u/matt-warkentin)\
**Replies:** 5\
**Last updated:** [August 10, 2019, 4:58pm UTC](https://discourse.slicer.org/t/changing-window-level-and-index-slice-for-a-volume-loaded-from-the-command-line/7924 "2019-08-10T16:58:00Z")

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Hi, I am trying to write a piece of code that will open the Slicer GUI from the command-line, and load a particular volume, with a chosen window/level, and some fiducials pre-loaded into the scene. The code below partia…

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## [Grow from seeds not giving any results](https://discourse.slicer.org/t/grow-from-seeds-not-giving-any-results/7645)

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**Author:** [@dfafalis](https://discourse.slicer.org/u/dfafalis)\
**Replies:** 7\
**Last updated:** [August 10, 2019, 1:05pm UTC](https://discourse.slicer.org/t/grow-from-seeds-not-giving-any-results/7645 "2019-08-10T13:05:43Z")

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Operating system:Window 7 Enterprise Slicer version: 4.11.0 Expected behavior: create segments after applying “Grow from seeds” effect Actual behavior: no segments created; the seeds remained as initially painted Hel…

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## [Windows build is not updating](https://discourse.slicer.org/t/windows-build-is-not-updating/7970)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [August 10, 2019, 12:52pm UTC](https://discourse.slicer.org/t/windows-build-is-not-updating/7970 "2019-08-10T12:52:07Z")

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Preview windows build seems stuck at revision 28425.

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## [Prevent transformix running in Slicer Elastix](https://discourse.slicer.org/t/prevent-transformix-running-in-slicer-elastix/7902)

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**Author:** [@Prashant\_Pandey](https://discourse.slicer.org/u/Prashant_Pandey)\
**Replies:** 10\
**Last updated:** [August 10, 2019, 12:49pm UTC](https://discourse.slicer.org/t/prevent-transformix-running-in-slicer-elastix/7902 "2019-08-10T12:49:04Z")

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Using Slicer 4.10.2 I am writing a runtime sensitive registration module which makes use of the slicer elastix module. As you can imagine elastix registration takes some time to run (about ~2 minutes for the data and pa…

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## [MakeModelEffect Error. The file cannot be saved.](https://discourse.slicer.org/t/makemodeleffect-error-the-file-cannot-be-saved/7957)

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**Author:** [@11127](https://discourse.slicer.org/u/11127)\
**Replies:** 1\
**Last updated:** [August 9, 2019, 8:55pm UTC](https://discourse.slicer.org/t/makemodeleffect-error-the-file-cannot-be-saved/7957 "2019-08-09T20:55:37Z")

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Operating system: window10 Slicer version:4.10.2 Expected behavior: Save the cropped as a STL file. Actual behavior: Fail in the last step.(Model Maker) Hello. I want to use this program to extract the ears from the…

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## [Installation issues: macOS Mojave 10.14.6](https://discourse.slicer.org/t/installation-issues-macos-mojave-10-14-6/7950)

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**Author:** [@unnmdnwb3](https://discourse.slicer.org/u/unnmdnwb3)\
**Replies:** 2\
**Last updated:** [August 9, 2019, 11:32am UTC](https://discourse.slicer.org/t/installation-issues-macos-mojave-10-14-6/7950 "2019-08-09T11:32:20Z")

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Hello everyone, I’ve tried to locally install and compile Slicer to use its modules for an extension, on which I will be working on. However, I’m struggling with some issues and would appreciate some help. My setup is…

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## [Change display range of .raw file](https://discourse.slicer.org/t/change-display-range-of-raw-file/6320)

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**Author:** [@anitakh1](https://discourse.slicer.org/u/anitakh1)\
**Replies:** 20\
**Last updated:** [August 9, 2019, 5:56am UTC](https://discourse.slicer.org/t/change-display-range-of-raw-file/6320 "2019-08-09T05:56:57Z")

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

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## [Visualize arrays stored in h5](https://discourse.slicer.org/t/visualize-arrays-stored-in-h5/7953)

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**Author:** [@rogertrullo](https://discourse.slicer.org/u/rogertrullo)\
**Replies:** 1\
**Last updated:** [August 9, 2019, 12:25am UTC](https://discourse.slicer.org/t/visualize-arrays-stored-in-h5/7953 "2019-08-09T00:25:05Z")

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Hi, I know that hdf5 is just a container as discussed in here , however I think it can be a greate feature to have some kind of option to display 3d arrays in 3D slicer. The format is widely used in the machine learning…

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## [Problems with python](https://discourse.slicer.org/t/problems-with-python/7944)

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**Author:** [@zahiraabdala](https://discourse.slicer.org/u/zahiraabdala)\
**Replies:** 1\
**Last updated:** [August 9, 2019, 12:13am UTC](https://discourse.slicer.org/t/problems-with-python/7944 "2019-08-09T00:13:28Z")

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hi, i\`m trying to use python but when i download a dicom, appear this Geometric issues were found with 1 of the series. Please use caution. Loading with imageIOName: GDCM Irregular volume geometry detected, but maximu…

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## [How to assign default color table to a node](https://discourse.slicer.org/t/how-to-assign-default-color-table-to-a-node/7936)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 1\
**Last updated:** [August 8, 2019, 12:38pm UTC](https://discourse.slicer.org/t/how-to-assign-default-color-table-to-a-node/7936 "2019-08-08T12:38:27Z")

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I wonder if this is too trivial for appearing here but I struggle for weeks before realizing that you can easily assign a color table to a node in python # First access the color table by name, the name is the one that …

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## [Different coordinate systems when exporting stl files from 3D Slicer to matlab](https://discourse.slicer.org/t/different-coordinate-systems-when-exporting-stl-files-from-3d-slicer-to-matlab/2491)

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**Author:** [@Clara\_Korting](https://discourse.slicer.org/u/Clara_Korting)\
**Replies:** 5\
**Last updated:** [May 9, 2018, 4:07am UTC](https://discourse.slicer.org/t/different-coordinate-systems-when-exporting-stl-files-from-3d-slicer-to-matlab/2491 "2018-05-09T04:07:36Z")

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Hej, I am using 3D Slicer 4.8.1 to create models of muscles of the lower leg. I just stumbled upon a problem which is the following. I export the models from slicer as .stl files. I then read and display those files in…

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## [How to Reformat slice with Python Interator?](https://discourse.slicer.org/t/how-to-reformat-slice-with-python-interator/7931)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 0\
**Last updated:** [August 8, 2019, 5:41am UTC](https://discourse.slicer.org/t/how-to-reformat-slice-with-python-interator/7931 "2019-08-08T05:41:20Z")

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Hi Dears 3DSlicer developers and users I have 3D CT volume images.I want to change slice properties such as its center and orientation. For example I want to get slice with the center in the certain location (r0, a0, s0…

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## [Display a segmented data in Slicer 3D view](https://discourse.slicer.org/t/display-a-segmented-data-in-slicer-3d-view/7889)

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**Author:** [@mikecsu](https://discourse.slicer.org/u/mikecsu)\
**Replies:** 2\
**Last updated:** [August 8, 2019, 3:20am UTC](https://discourse.slicer.org/t/display-a-segmented-data-in-slicer-3d-view/7889 "2019-08-08T03:20:02Z")

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Operating system:win 10 Slicer version:4.10 Expected behavior: Actual behavior: Hi，everyone. I would like to know" Is it possible to display a segmented data with " nrrd " format in slicer 3D view ?“. Here " segm…

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## [Loaded tiff file looks too bright/oversaturated](https://discourse.slicer.org/t/loaded-tiff-file-looks-too-bright-oversaturated/2697)

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**Author:** [@romip](https://discourse.slicer.org/u/romip)\
**Replies:** 2\
**Last updated:** [August 7, 2019, 9:04pm UTC](https://discourse.slicer.org/t/loaded-tiff-file-looks-too-bright-oversaturated/2697 "2019-08-07T21:04:21Z")

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Hi Everyone, Probably a silly question, but I am struggling to open my CLSM images. I couldn’t open my original file (.lsm) so I converted the stack to images using imagej (save as → Image sequence), but something weir…

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## [Elastix general registration](https://discourse.slicer.org/t/elastix-general-registration/7888)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 4\
**Last updated:** [August 7, 2019, 5:38pm UTC](https://discourse.slicer.org/t/elastix-general-registration/7888 "2019-08-07T17:38:39Z")

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Hi In elastix general registration mask volume option doesn’t allow me to select anything. It jus give the option none. I created a mask beforehand and then selected my fixed and moving volumes, Can someone help pleas…

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## [PLUS with Optitrack Prime13](https://discourse.slicer.org/t/plus-with-optitrack-prime13/7894)

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**Author:** [@BGWH](https://discourse.slicer.org/u/BGWH)\
**Replies:** 2\
**Last updated:** [August 7, 2019, 12:00pm UTC](https://discourse.slicer.org/t/plus-with-optitrack-prime13/7894 "2019-08-07T12:00:38Z")

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Dear all, I tried to use SliceIGT and PLUS (PlusApp-2.9.0.20190802-Win64) in combination with Optitrack Prime 13 cameras (Motive version 2.0.0). To design the configuration file I have followed this guide: http://perk-…

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## [Different Dimensions in the original image and segmentation](https://discourse.slicer.org/t/different-dimensions-in-the-original-image-and-segmentation/7909)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 0\
**Last updated:** [August 7, 2019, 2:58am UTC](https://discourse.slicer.org/t/different-dimensions-in-the-original-image-and-segmentation/7909 "2019-08-07T02:58:38Z")

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Operating system: windows 10 Slicer version: 4.10.1 Expected behavior: the original image and segmentation are in the same dimension after being exported in ‘.nrrd’ format Actual behavior: the segmenation is cropped b…

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