# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=335

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

**Page:** 336

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## [Number of pixels after segmentation](https://discourse.slicer.org/t/number-of-pixels-after-segmentation/12074)

<div class="topic-metadata">

**Author:** [@cotozakot](https://discourse.slicer.org/u/cotozakot)\
**Replies:** 3\
**Last updated:** [June 18, 2020, 10:45am UTC](https://discourse.slicer.org/t/number-of-pixels-after-segmentation/12074 "2020-06-18T10:45:44Z")

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Can I read the number of pixels / voxels somewhere after segmentation? Not only their volume, I mean their quantity. So far, I have been able to obtain results from the Segment Statistic module.

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## [MRI Brain data and label map question](https://discourse.slicer.org/t/mri-brain-data-and-label-map-question/12083)

<div class="topic-metadata">

**Author:** [@harry1511](https://discourse.slicer.org/u/harry1511)\
**Replies:** 0\
**Last updated:** [June 18, 2020, 2:49am UTC](https://discourse.slicer.org/t/mri-brain-data-and-label-map-question/12083 "2020-06-18T02:49:34Z")

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Hi, I am working on a visualization project, and has acquired few datasets of healthy brain (NIFTI format). I managed to open and extract the datasets out as series of .png, and this is used as a flipbook texture that w…

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## [Creating spheric segment 2cm](https://discourse.slicer.org/t/creating-spheric-segment-2cm/12063)

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**Author:** [@Zhanat](https://discourse.slicer.org/u/Zhanat)\
**Replies:** 3\
**Last updated:** [June 18, 2020, 1:24am UTC](https://discourse.slicer.org/t/creating-spheric-segment-2cm/12063 "2020-06-18T01:24:11Z")

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Hello! How I can creat spheric segment with 2cm radius? I’m using Segment Editor, but I don’t know how to change spheres radius. Thank you for your answers!

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## [Perimeter of model](https://discourse.slicer.org/t/perimeter-of-model/12076)

<div class="topic-metadata">

**Author:** [@cotozakot](https://discourse.slicer.org/u/cotozakot)\
**Replies:** 0\
**Last updated:** [June 17, 2020, 6:23pm UTC](https://discourse.slicer.org/t/perimeter-of-model/12076 "2020-06-17T18:23:46Z")

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Hi, I wanted to know how to measure the perimeter of the 3D volume data (model 3D) Thanks in advance!

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## [Resampling a volume and Image Spacing](https://discourse.slicer.org/t/resampling-a-volume-and-image-spacing/12066)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 6\
**Last updated:** [June 17, 2020, 5:13pm UTC](https://discourse.slicer.org/t/resampling-a-volume-and-image-spacing/12066 "2020-06-17T17:13:42Z")

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Hi All, I have got a volume with the following dimensions 1702 x1678 x 251. I want to reduce the resolution in xy direction and leave z unaltered. May I know which module can be used to do the above? I’ve checked t…

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## [Question on using Scissors](https://discourse.slicer.org/t/question-on-using-scissors/12071)

<div class="topic-metadata">

**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 2\
**Last updated:** [June 17, 2020, 3:49pm UTC](https://discourse.slicer.org/t/question-on-using-scissors/12071 "2020-06-17T15:49:03Z")

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Hello, I have loaded 2D slices using Image Stacks. Before reconstructing 3D volume using these slices, I’d like to use the Scissors effect in Segment Editor to edit only the region shown in the image below (rectangle -y…

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## [why are preview result and apply result different in threshold segmentation？ ](https://discourse.slicer.org/t/why-are-preview-result-and-apply-result-different-in-threshold-segmentation/12050)

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**Author:** [@SummerZ2020](https://discourse.slicer.org/u/SummerZ2020)\
**Replies:** 2\
**Last updated:** [June 17, 2020, 6:38am UTC](https://discourse.slicer.org/t/why-are-preview-result-and-apply-result-different-in-threshold-segmentation/12050 "2020-06-17T06:38:06Z")

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Operating system:windows Slicer version:4.10.2 and 4.11 Expected behavior:the segmentation result after the “Apply” button is clicked should be same with the preview result in Threshold segmentation. Actual behavior: …

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## [The window center and window width cannot be adjusted in Segment editor in 6.11(2020.6.15)](https://discourse.slicer.org/t/the-window-center-and-window-width-cannot-be-adjusted-in-segment-editor-in-6-11-2020-6-15/12056)

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**Author:** [@SummerZ2020](https://discourse.slicer.org/u/SummerZ2020)\
**Replies:** 2\
**Last updated:** [June 17, 2020, 6:37am UTC](https://discourse.slicer.org/t/the-window-center-and-window-width-cannot-be-adjusted-in-segment-editor-in-6-11-2020-6-15/12056 "2020-06-17T06:37:15Z")

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Operating system:windows Slicer version:6.11(2020.6.10) and 6.11(2020.6.15) Expected behavior:The window width and center can be adjusted by clicking left mouse button and dragging mouse. Actual behavior:The window wi…

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## [Exporting decimated vtkPolyData](https://discourse.slicer.org/t/exporting-decimated-vtkpolydata/12036)

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**Author:** [@Queen\_Rei](https://discourse.slicer.org/u/Queen_Rei)\
**Replies:** 4\
**Last updated:** [June 16, 2020, 9:41pm UTC](https://discourse.slicer.org/t/exporting-decimated-vtkpolydata/12036 "2020-06-16T21:41:31Z")

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My current objective is to decimate a segmentation and export it. I have been looking around for the proper way to do this with vtkDecimatePro and the vtkSegmentationNode. I wanted to know how I may export this decimated…

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## [qSlicerScalarVolumeDisplayWidget updates threshold bounds automatically for float volumes](https://discourse.slicer.org/t/qslicerscalarvolumedisplaywidget-updates-threshold-bounds-automatically-for-float-volumes/12058)

<div class="topic-metadata">

**Author:** [@rat01](https://discourse.slicer.org/u/rat01)\
**Replies:** 2\
**Last updated:** [June 16, 2020, 7:17pm UTC](https://discourse.slicer.org/t/qslicerscalarvolumedisplaywidget-updates-threshold-bounds-automatically-for-float-volumes/12058 "2020-06-16T19:17:55Z")

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I have a scenario where I’m dynamically updating a scalar float volume with a modified numpy array with every update of a slider. Specifically, I’m masking various regions of the original volume with NANs. I’m using NANs…

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## [Data privacy with SlicerJupyter on the binder](https://discourse.slicer.org/t/data-privacy-with-slicerjupyter-on-the-binder/12057)

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**Author:** [@tbillah](https://discourse.slicer.org/u/tbillah)\
**Replies:** 1\
**Last updated:** [June 16, 2020, 4:10pm UTC](https://discourse.slicer.org/t/data-privacy-with-slicerjupyter-on-the-binder/12057 "2020-06-16T16:10:38Z")

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If I use the binder | slicer from here, I believe it instantiates an image of the docker container to run a Notebook for me. If I upload data to the container/virtual machine, whatever we call it– Does anyone have acce…

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## [First click-and-drag on 3D view](https://discourse.slicer.org/t/first-click-and-drag-on-3d-view/12035)

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**Author:** [@ada](https://discourse.slicer.org/u/ada)\
**Replies:** 6\
**Last updated:** [June 16, 2020, 1:03pm UTC](https://discourse.slicer.org/t/first-click-and-drag-on-3d-view/12035 "2020-06-16T13:03:43Z")

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Hi all, After a first 3D loading, the volume is well displayed and I want to use the mouse to rotate the 3D view. I do not know why but the first click-and-drag event with the mouse moves one of the ROI side (I control…

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## [Remove Orthopedic cast with segmentation](https://discourse.slicer.org/t/remove-orthopedic-cast-with-segmentation/12030)

<div class="topic-metadata">

**Author:** [@eran\_bam](https://discourse.slicer.org/u/eran_bam)\
**Replies:** 4\
**Last updated:** [June 16, 2020, 6:26am UTC](https://discourse.slicer.org/t/remove-orthopedic-cast-with-segmentation/12030 "2020-06-16T06:26:36Z")

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Hi everyone, After I try to remove the orthopedic cast from the CT image, I get the image that I attached. Untitled2222|598x455 How can I fill the holes in the image to get the correct image without all these holes?

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## [My DCM files aren't showing up in 3D View?](https://discourse.slicer.org/t/my-dcm-files-arent-showing-up-in-3d-view/12049)

<div class="topic-metadata">

**Author:** [@Wolf1471](https://discourse.slicer.org/u/Wolf1471)\
**Replies:** 1\
**Last updated:** [June 16, 2020, 2:38am UTC](https://discourse.slicer.org/t/my-dcm-files-arent-showing-up-in-3d-view/12049 "2020-06-16T02:38:25Z")

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So I’m following along with this tutorial provided on their documentation page: To turn some .dcm files i was provided with into either .stl or .obj to import into Maya or 3ds Max. I followed up to 4 minute…

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## [Problem loading png. in coronal and sagital vindows + Editor segmentation diabeled ](https://discourse.slicer.org/t/problem-loading-png-in-coronal-and-sagital-vindows-editor-segmentation-diabeled/12040)

<div class="topic-metadata">

**Author:** [@hpok](https://discourse.slicer.org/u/hpok)\
**Replies:** 1\
**Last updated:** [June 15, 2020, 7:32pm UTC](https://discourse.slicer.org/t/problem-loading-png-in-coronal-and-sagital-vindows-editor-segmentation-diabeled/12040 "2020-06-15T19:32:27Z")

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Hello, I have encountered a few problems when loading png data and subsequently segmenting them. I aim to segment a hippocampus from a set of png. images. When I load it into Slicer, the axial view port is all right bu…

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## [Using fit volume](https://discourse.slicer.org/t/using-fit-volume/12038)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 1\
**Last updated:** [June 15, 2020, 6:29pm UTC](https://discourse.slicer.org/t/using-fit-volume/12038 "2020-06-15T18:29:04Z")

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Hello, I’d like to know how to use Fit to Volume In the volume shown in the below snapshot, the cube is not fit around the vessel segment. I find a lot of void space. . Any suggestions will be of great help.

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## [Centerline Computation](https://discourse.slicer.org/t/centerline-computation/12025)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 10\
**Last updated:** [June 15, 2020, 5:45pm UTC](https://discourse.slicer.org/t/centerline-computation/12025 "2020-06-15T17:45:57Z")

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Hello Everyone, I’m using VMTK module in Slicer to run Centerline Computation for this model input using the latest Preview release. The task has run for nearly 10 hours but it was unsuccessful. The notice that the…

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## [Heap space for Slicer](https://discourse.slicer.org/t/heap-space-for-slicer/12031)

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**Author:** [@Deepa](https://discourse.slicer.org/u/Deepa)\
**Replies:** 4\
**Last updated:** [June 15, 2020, 5:44pm UTC](https://discourse.slicer.org/t/heap-space-for-slicer/12031 "2020-06-15T17:44:38Z")

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Hi All, I am facing memory issues while running tasks like centerline line extraction using Slicer installed on a server. I’d like to know how to increase the heap space for Slicer.

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## [Deepinfer - run time in 4.10.2 and availability in 4.11.0 (29117)](https://discourse.slicer.org/t/deepinfer-run-time-in-4-10-2-and-availability-in-4-11-0-29117/12026)

<div class="topic-metadata">

**Author:** [@NiinaIn3D](https://discourse.slicer.org/u/NiinaIn3D)\
**Replies:** 1\
**Last updated:** [June 15, 2020, 4:05pm UTC](https://discourse.slicer.org/t/deepinfer-run-time-in-4-10-2-and-availability-in-4-11-0-29117/12026 "2020-06-15T16:05:24Z")

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Hi again, I’ve been trying to get DeepInfer to work in ver. 4.10.2 but either there’s something wrong or my computer is just not coping with the extension. After 40 minutes it’s still sitting at 15%, I’d imagine this is…

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## [Issue with Mean diffusivity scalar measurement](https://discourse.slicer.org/t/issue-with-mean-diffusivity-scalar-measurement/12034)

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**Author:** [@KatS](https://discourse.slicer.org/u/KatS)\
**Replies:** 0\
**Last updated:** [June 15, 2020, 2:16pm UTC](https://discourse.slicer.org/t/issue-with-mean-diffusivity-scalar-measurement/12034 "2020-06-15T14:16:49Z")

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Dear all, I’m facing issues when trying to create a Mean Diffusivity output from my DTI data. I’m using Slicer 4.10.1 and the DMRI Extension and imported my data (acquired at 3T, Siemens Skyra, 41 gradient directions) …

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## [How can I speed up the registration process in the Elastix module?](https://discourse.slicer.org/t/how-can-i-speed-up-the-registration-process-in-the-elastix-module/11998)

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**Author:** [@kuba\_grepl](https://discourse.slicer.org/u/kuba_grepl)\
**Replies:** 4\
**Last updated:** [June 15, 2020, 12:27pm UTC](https://discourse.slicer.org/t/how-can-i-speed-up-the-registration-process-in-the-elastix-module/11998 "2020-06-15T12:27:26Z")

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Hello everybody. I use Elastix module for deformable multimodal registration of 3DCT and 3DMRI scans of human head and neck. It works very well. Thank you for this amazing software tool!!! Unfortunately, one registrati…

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## [Sandbox - Curved Planar Reformat module not installing?](https://discourse.slicer.org/t/sandbox-curved-planar-reformat-module-not-installing/11768)

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**Author:** [@NiinaIn3D](https://discourse.slicer.org/u/NiinaIn3D)\
**Replies:** 11\
**Last updated:** [June 15, 2020, 4:06am UTC](https://discourse.slicer.org/t/sandbox-curved-planar-reformat-module-not-installing/11768 "2020-06-15T04:06:32Z")

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Hi all, I’ve recently started to use 3D Slicer and was looking for a curved planar reformat tool to use with anatomical features. I noticed the module should be included in the Sandbox extension, but when I install it th…

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## [Extension manager for the sake of deep learning](https://discourse.slicer.org/t/extension-manager-for-the-sake-of-deep-learning/12015)

<div class="topic-metadata">

**Author:** [@khikho](https://discourse.slicer.org/u/khikho)\
**Replies:** 1\
**Last updated:** [June 14, 2020, 2:58pm UTC](https://discourse.slicer.org/t/extension-manager-for-the-sake-of-deep-learning/12015 "2020-06-14T14:58:55Z")

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hi Is there Extension manager for the sake of deep learning?

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## [Opening nightly saved segmentation files on stable version](https://discourse.slicer.org/t/opening-nightly-saved-segmentation-files-on-stable-version/10852)

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**Author:** [@Aep93](https://discourse.slicer.org/u/Aep93)\
**Replies:** 3\
**Last updated:** [June 14, 2020, 2:56pm UTC](https://discourse.slicer.org/t/opening-nightly-saved-segmentation-files-on-stable-version/10852 "2020-06-14T14:56:34Z")

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Hello all, I used the slicer nightly version and generated several seg.nrrd files. However, for some reason, I should use the stable version for now. The problem is that the stable version does not completely read the s…

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## [About scissors with airway segmentation](https://discourse.slicer.org/t/about-scissors-with-airway-segmentation/11898)

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**Author:** [@anitakh1](https://discourse.slicer.org/u/anitakh1)\
**Replies:** 8\
**Last updated:** [June 14, 2020, 5:57am UTC](https://discourse.slicer.org/t/about-scissors-with-airway-segmentation/11898 "2020-06-14T05:57:27Z")

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i used ‘segment lung airway’ module for airway segmentation. there are some leakages which i want to cut from volume. how can i do that. segment editor scissor only chops the selection made there during processing. how c…

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## [Can I use markup angles to edit a segmentation?](https://discourse.slicer.org/t/can-i-use-markup-angles-to-edit-a-segmentation/12010)

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**Author:** [@Mohammad\_Tanjib\_Rahm](https://discourse.slicer.org/u/Mohammad_Tanjib_Rahm)\
**Replies:** 5\
**Last updated:** [June 14, 2020, 5:10am UTC](https://discourse.slicer.org/t/can-i-use-markup-angles-to-edit-a-segmentation/12010 "2020-06-14T05:10:50Z")

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I am trying to keep only the region of segmentation that is inside the markup angle and get rid of the rest. So far I have tried the scissor tool. It gets the job done. But I am looking for a faster method. Is there any …

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## [Error message when running slicerCIP](https://discourse.slicer.org/t/error-message-when-running-slicercip/11897)

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**Author:** [@shahrokh](https://discourse.slicer.org/u/shahrokh)\
**Replies:** 3\
**Last updated:** [June 13, 2020, 2:21pm UTC](https://discourse.slicer.org/t/error-message-when-running-slicercip/11897 "2020-06-13T14:21:15Z")

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Hello Developers and Users 3DSlicer I want to run SlicerCIP (SlicerCIP4-10-2) in my computer with the following specifications: sn@MP:~$ uname --all Linux MP 5.3.0-53-generic #47~18.04.1-Ubuntu SMP Thu May 7 13:10:50…

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## [3D models from mrb files](https://discourse.slicer.org/t/3d-models-from-mrb-files/12007)

<div class="topic-metadata">

**Author:** [@IanH](https://discourse.slicer.org/u/IanH)\
**Replies:** 1\
**Last updated:** [June 12, 2020, 11:52pm UTC](https://discourse.slicer.org/t/3d-models-from-mrb-files/12007 "2020-06-12T23:52:36Z")

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I’m an undergrad student using Slicer to model soybean nodules. I’ve been segmenting the data and saving them as .mrb files. I’m able to generate a 3D preview, but have not been able to figure out how to generate a file …

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## [Problem with nrrd file](https://discourse.slicer.org/t/problem-with-nrrd-file/11902)

<div class="topic-metadata">

**Author:** [@Adrian\_Izaguirre](https://discourse.slicer.org/u/Adrian_Izaguirre)\
**Replies:** 3\
**Last updated:** [June 12, 2020, 4:05pm UTC](https://discourse.slicer.org/t/problem-with-nrrd-file/11902 "2020-06-12T16:05:35Z")

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Hi I’am a student new both to the forum and the software, for a project i hadto find a baby ultrasound and make a 3d model of it, but when i try to upload the data to 3DSlicer the images are show in just one axis instead…

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## [Refresh volume rendering](https://discourse.slicer.org/t/refresh-volume-rendering/11847)

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**Author:** [@ada](https://discourse.slicer.org/u/ada)\
**Replies:** 8\
**Last updated:** [June 12, 2020, 4:04pm UTC](https://discourse.slicer.org/t/refresh-volume-rendering/11847 "2020-06-12T16:04:33Z")

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Hi developpers, I am writing a scripted module with python to hide the volume and only display slices into the 3d view using following functions : red = slicer.util.getNode(‘vtkMRMLSliceNodeRed’) red.SetSliceVisible(1…

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