# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=219

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

**Page:** 220

---

## [How to convert 3D numpy array to vtk and save the .vtk file?](https://discourse.slicer.org/t/how-to-convert-3d-numpy-array-to-vtk-and-save-the-vtk-file/22327)

<div class="topic-metadata">

**Author:** [@user4](https://discourse.slicer.org/u/user4)\
**Replies:** 7\
**Last updated:** [June 16, 2022, 2:36am UTC](https://discourse.slicer.org/t/how-to-convert-3d-numpy-array-to-vtk-and-save-the-vtk-file/22327 "2022-06-16T02:36:42Z")

</div>

Hi,all.Sorry for my little knowledge about VTK. Here is the thing I want to do: I have a scalar volume (3D numpy array) I want to add some information describing the image and then save it as a .vtk file as follows: …

---

## [Question about instancing efficiency between vtk8.2 and vtk9.0](https://discourse.slicer.org/t/question-about-instancing-efficiency-between-vtk8-2-and-vtk9-0/23885)

<div class="topic-metadata">

**Author:** [@xianger-qi](https://discourse.slicer.org/u/xianger-qi)\
**Replies:** 1\
**Last updated:** [June 15, 2022, 12:10pm UTC](https://discourse.slicer.org/t/question-about-instancing-efficiency-between-vtk8-2-and-vtk9-0/23885 "2022-06-15T12:10:29Z")

</div>

Hey guys, i took a test about variable instancing efficiency between vtk8.2 and vtk9.0 on different class. Here was what i got: testing times: 10000 Statistical method: average instancing time the method instancing: …

---

## [Visualize models inside volume rendering?](https://discourse.slicer.org/t/visualize-models-inside-volume-rendering/23839)

<div class="topic-metadata">

**Author:** [@sunwei921119](https://discourse.slicer.org/u/sunwei921119)\
**Replies:** 12\
**Last updated:** [June 15, 2022, 6:59am UTC](https://discourse.slicer.org/t/visualize-models-inside-volume-rendering/23839 "2022-06-15T06:59:19Z")

</div>

hello，The enclosed visibility enables the point to perspective in volume rendering. Is there a plug-in that can perspective models in volume rendering?

---

## [Artificial Coloring of Structures](https://discourse.slicer.org/t/artificial-coloring-of-structures/23878)

<div class="topic-metadata">

**Author:** [@scott.young](https://discourse.slicer.org/u/scott.young)\
**Replies:** 1\
**Last updated:** [June 15, 2022, 6:50am UTC](https://discourse.slicer.org/t/artificial-coloring-of-structures/23878 "2022-06-15T06:50:34Z")

</div>

I want to be able to color different segments different colors. They do not need to be realistic. I am working with Anatomy students and want to be able to “turn on” highlighted color so the students can easily see the r…

---

## [Convert STL file to high-resolution TIFF stack](https://discourse.slicer.org/t/convert-stl-file-to-high-resolution-tiff-stack/15949)

<div class="topic-metadata">

**Author:** [@FLRonan](https://discourse.slicer.org/u/FLRonan)\
**Replies:** 12\
**Last updated:** [June 15, 2022, 3:10am UTC](https://discourse.slicer.org/t/convert-stl-file-to-high-resolution-tiff-stack/15949 "2022-06-15T03:10:13Z")

</div>

Hello, I am running a python script to slice an .stl file into a tif stack as per previous forum posts and the script repo. I have been having issues with certain stl files causing slicer to crash. Slicer will exit/cr…

---

## [Animator Module - Not exporting correctly](https://discourse.slicer.org/t/animator-module-not-exporting-correctly/17016)

<div class="topic-metadata">

**Author:** [@ebryson](https://discourse.slicer.org/u/ebryson)\
**Replies:** 11\
**Last updated:** [June 15, 2022, 2:40am UTC](https://discourse.slicer.org/t/animator-module-not-exporting-correctly/17016 "2022-06-15T02:40:22Z")

</div>

Hello! I’m running into a small problem with the Animator module. I’m trying to export a GIF of my model but when I select the directory destination and click export a window showing the GIF pops up, but the file itself …

---

## [Introductory workshop](https://discourse.slicer.org/t/introductory-workshop/23877)

<div class="topic-metadata">

**Author:** [@epicsaga](https://discourse.slicer.org/u/epicsaga)\
**Replies:** 1\
**Last updated:** [June 14, 2022, 9:44pm UTC](https://discourse.slicer.org/t/introductory-workshop/23877 "2022-06-14T21:44:08Z")

</div>

Good morning, Does anyone know of any introductory workshops for using 3D Slicer for image processing? Thanks, Carlos

---

## [UKF tractography fails for large scans (~1.5mm iso)](https://discourse.slicer.org/t/ukf-tractography-fails-for-large-scans-1-5mm-iso/23863)

<div class="topic-metadata">

**Author:** [@phoebeimms](https://discourse.slicer.org/u/phoebeimms)\
**Replies:** 1\
**Last updated:** [June 14, 2022, 3:46pm UTC](https://discourse.slicer.org/t/ukf-tractography-fails-for-large-scans-1-5mm-iso/23863 "2022-06-14T15:46:40Z")

</div>

Hi! We are running whole brain 2-tensor UKF tractography, using 5 seeds ver voxel and otherwise default parameters, on a large range of scans (from various online repositories, e.g., HCP, UKBB, etc). Depending on the ac…

---

## [Maintenance of download.slicer.org, slicer.kitware.com and slicer-packages.kitware.com planned for June 3rd 2022 - 12:00pm to 13:30pm ET](https://discourse.slicer.org/t/maintenance-of-download-slicer-org-slicer-kitware-com-and-slicer-packages-kitware-com-planned-for-june-3rd-2022-12-00pm-to-13-30pm-et/23687)

<div class="topic-metadata">

**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 4\
**Last updated:** [June 14, 2022, 8:08am UTC](https://discourse.slicer.org/t/maintenance-of-download-slicer-org-slicer-kitware-com-and-slicer-packages-kitware-com-planned-for-june-3rd-2022-12-00pm-to-13-30pm-et/23687 "2022-06-14T08:08:14Z")

</div>

The following system will be temporarily unavailable while system updates are deployed on the corresponding virtual machines. Server Description download.slicer.org Site allowing to download preview and stable a…

---

## [Rotational transformation matrix & surface registration of models](https://discourse.slicer.org/t/rotational-transformation-matrix-surface-registration-of-models/23680)

<div class="topic-metadata">

**Author:** [@mdhan](https://discourse.slicer.org/u/mdhan)\
**Replies:** 5\
**Last updated:** [June 13, 2022, 10:09pm UTC](https://discourse.slicer.org/t/rotational-transformation-matrix-surface-registration-of-models/23680 "2022-06-13T22:09:38Z")

</div>

Hello, Sorry for troubling you all, but I’d be grateful if you could kindly help with me with something I’m struggling with. I’ve been having trouble utilizing the rotational transformation matrix to suit my needs, and …

---

## [Fiducial arrow pointer is missing from toolbar](https://discourse.slicer.org/t/fiducial-arrow-pointer-is-missing-from-toolbar/23859)

<div class="topic-metadata">

**Author:** [@Avri\_Lev](https://discourse.slicer.org/u/Avri_Lev)\
**Replies:** 1\
**Last updated:** [June 13, 2022, 8:04pm UTC](https://discourse.slicer.org/t/fiducial-arrow-pointer-is-missing-from-toolbar/23859 "2022-06-13T20:04:37Z")

</div>

Hello all, I used to work with ver 4.11 where the fiducial marker was placed on the toolbar. Now in ver 5.0.2 it is no longer there… Any help will be appriciated. Dr. Avri

---

## [Show the full volume and not only slices](https://discourse.slicer.org/t/show-the-full-volume-and-not-only-slices/23848)

<div class="topic-metadata">

**Author:** [@hmaguilera](https://discourse.slicer.org/u/hmaguilera)\
**Replies:** 2\
**Last updated:** [June 13, 2022, 1:39pm UTC](https://discourse.slicer.org/t/show-the-full-volume-and-not-only-slices/23848 "2022-06-13T13:39:36Z")

</div>

Hi, I was wondering if it is possible to show the entire volume cone, and not only the three slices as shown in the bottom right corner.

---

## [Sending Transformed Ultrasound Data to Unity for AR Overlay](https://discourse.slicer.org/t/sending-transformed-ultrasound-data-to-unity-for-ar-overlay/7925)

<div class="topic-metadata">

**Author:** [@David\_Asgar-Deen](https://discourse.slicer.org/u/David_Asgar-Deen)\
**Replies:** 5\
**Last updated:** [June 13, 2022, 1:16pm UTC](https://discourse.slicer.org/t/sending-transformed-ultrasound-data-to-unity-for-ar-overlay/7925 "2022-06-13T13:16:46Z")

</div>

Hello, Thank you for taking the time to read this post. I am currently working on visualizing ultrasound slice data through a semi-transparent mirror AR display and was hoping to get some help sending the data to Unity.…

---

## [Missing segmentation parts after applying 'grow from seeds' ](https://discourse.slicer.org/t/missing-segmentation-parts-after-applying-grow-from-seeds/23853)

<div class="topic-metadata">

**Author:** [@Roos](https://discourse.slicer.org/u/Roos)\
**Replies:** 1\
**Last updated:** [June 13, 2022, 12:45pm UTC](https://discourse.slicer.org/t/missing-segmentation-parts-after-applying-grow-from-seeds/23853 "2022-06-13T12:45:04Z")

</div>

Operating system: 3D Slicer Slicer version: 5.0.2 Expected behavior: similarity between initial and applied segmentation Actual behavior: Missing parts of initial segmentation after applying grow from seeds

---

## [Canine skull stripping](https://discourse.slicer.org/t/canine-skull-stripping/23820)

<div class="topic-metadata">

**Author:** [@Josefa\_Garcia](https://discourse.slicer.org/u/Josefa_Garcia)\
**Replies:** 7\
**Last updated:** [June 12, 2022, 10:26pm UTC](https://discourse.slicer.org/t/canine-skull-stripping/23820 "2022-06-12T22:26:02Z")

</div>

Hi, I am trying to do this with MRI images of the canine brain, I’ve provided an atlas volume and mask volume of an atlas I’ve found on internet, but the algorithm is not working, It selects the entire image and not just…

---

## [Measure Inside a Model](https://discourse.slicer.org/t/measure-inside-a-model/23817)

<div class="topic-metadata">

**Author:** [@dbgraf20](https://discourse.slicer.org/u/dbgraf20)\
**Replies:** 2\
**Last updated:** [June 12, 2022, 12:27am UTC](https://discourse.slicer.org/t/measure-inside-a-model/23817 "2022-06-12T00:27:13Z")

</div>

I am having some problems measuring inside my model. When I use the ruler, the tool I am trying to use locks onto the outside of the model. I need to measure the inside. How can I do this?

---

## [Isodose module not showing colorwash](https://discourse.slicer.org/t/isodose-module-not-showing-colorwash/23756)

<div class="topic-metadata">

**Author:** [@TomNB](https://discourse.slicer.org/u/TomNB)\
**Replies:** 4\
**Last updated:** [June 10, 2022, 10:31pm UTC](https://discourse.slicer.org/t/isodose-module-not-showing-colorwash/23756 "2022-06-10T22:31:39Z")

</div>

The dose is calculated using the orthovoltage engine, fig 1. I wonder if it is not compatible with isodose module because when I switch to Isodose module the colorwash disappears, fig 2. However when I calculate the isod…

---

## [Rodent skull stripping](https://discourse.slicer.org/t/rodent-skull-stripping/2677)

<div class="topic-metadata">

**Author:** [@djrowland](https://discourse.slicer.org/u/djrowland)\
**Replies:** 1\
**Last updated:** [April 25, 2018, 1:48am UTC](https://discourse.slicer.org/t/rodent-skull-stripping/2677 "2018-04-25T01:48:30Z")

</div>

Hello, I am interested in performing skull stripping and bias corrections for rodent data from a Bruker scanner. Since I have become comfortable with Slicer and working with DTI data in it, I was hoping that there might…

---

## [Unable to load DICOM segmentation](https://discourse.slicer.org/t/unable-to-load-dicom-segmentation/22947)

<div class="topic-metadata">

**Author:** [@koeglfryderyk](https://discourse.slicer.org/u/koeglfryderyk)\
**Replies:** 15\
**Last updated:** [June 10, 2022, 8:36pm UTC](https://discourse.slicer.org/t/unable-to-load-dicom-segmentation/22947 "2022-06-10T20:36:20Z")

</div>

Operating system: Mac M1Pro macOS 12.3.1 Slicer version: 4.13.0-2022-04-12 (also tested on 2022-04-04) Expected behaviour: Load DICOM segmentation Actual behaviour: Unable to load - error message I’m trying to load a…

---

## [Windows Defender quarantined Slicer.exe](https://discourse.slicer.org/t/windows-defender-quarantined-slicer-exe/23613)

<div class="topic-metadata">

**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 4\
**Last updated:** [June 10, 2022, 5:10pm UTC](https://discourse.slicer.org/t/windows-defender-quarantined-slicer-exe/23613 "2022-06-10T17:10:53Z")

</div>

On my university-managed computer, Slicer.exe disappeared from the install tree. Windows Defender quarantined the executable due to “potentially unwanted behavior”. It states that it detected Program:Win32/Beareuws.A!…

---

## [Segment visibility Hotkey](https://discourse.slicer.org/t/segment-visibility-hotkey/23811)

<div class="topic-metadata">

**Author:** [@volkodavmyx](https://discourse.slicer.org/u/volkodavmyx)\
**Replies:** 1\
**Last updated:** [June 10, 2022, 3:03pm UTC](https://discourse.slicer.org/t/segment-visibility-hotkey/23811 "2022-06-10T15:03:41Z")

</div>

Hi everyone! In our project we work with low-contrasted CT scans, and manual segmentación. So we need often switch segment visibility. Does exist Hotkey to on/off segment visibility, or the way to add this hotkeys fo o…

---

## [Failed loading of nii.gz file](https://discourse.slicer.org/t/failed-loading-of-nii-gz-file/23769)

<div class="topic-metadata">

**Author:** [@James\_Goldfarb](https://discourse.slicer.org/u/James_Goldfarb)\
**Replies:** 1\
**Last updated:** [June 10, 2022, 2:52pm UTC](https://discourse.slicer.org/t/failed-loading-of-nii-gz-file/23769 "2022-06-10T14:52:12Z")

</div>

Having trouble loading a CT series after conversion from dicom to nii.gz . with dicom2nifti.convert\_directory() ITKsnap loads the nii.gz file without error. Original dicom files are read by 3dslicer without error. Oth…

---

## [Unable to set Logical effect's parameter from another effect](https://discourse.slicer.org/t/unable-to-set-logical-effects-parameter-from-another-effect/23790)

<div class="topic-metadata">

**Author:** [@Dwij\_Mistry](https://discourse.slicer.org/u/Dwij_Mistry)\
**Replies:** 2\
**Last updated:** [June 10, 2022, 2:05pm UTC](https://discourse.slicer.org/t/unable-to-set-logical-effects-parameter-from-another-effect/23790 "2022-06-10T14:05:02Z")

</div>

use case: in one of our custom effect we want to perform union operation from logical effect. problem: when we are setting # selecting UNION OPERATION slicer.util.getModuleWidget("SegmentationEditor").editor.OptionsG…

---

## [Monai server launch failing](https://discourse.slicer.org/t/monai-server-launch-failing/23757)

<div class="topic-metadata">

**Author:** [@Nayra\_Pumar](https://discourse.slicer.org/u/Nayra_Pumar)\
**Replies:** 8\
**Last updated:** [June 10, 2022, 1:49pm UTC](https://discourse.slicer.org/t/monai-server-launch-failing/23757 "2022-06-10T13:49:39Z")

</div>

I’ve cloned the MONAIlabel github repository (GitHub - Project-MONAI/MONAILabel: MONAI Label is an intelligent open source image labeling and learning tool.), set up a python 3.9 python environment, installed cuda and th…

---

## [Windows security warning on Stable](https://discourse.slicer.org/t/windows-security-warning-on-stable/23804)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 1\
**Last updated:** [June 10, 2022, 4:22am UTC](https://discourse.slicer.org/t/windows-security-warning-on-stable/23804 "2022-06-10T04:22:07Z")

</div>

I am seeing this message for the stable on my Windows 11 machine.

---

## [How can give more than one segments different color in the same volume?](https://discourse.slicer.org/t/how-can-give-more-than-one-segments-different-color-in-the-same-volume/23788)

<div class="topic-metadata">

**Author:** [@MAXFAXSURGEON](https://discourse.slicer.org/u/MAXFAXSURGEON)\
**Replies:** 7\
**Last updated:** [June 10, 2022, 4:18am UTC](https://discourse.slicer.org/t/how-can-give-more-than-one-segments-different-color-in-the-same-volume/23788 "2022-06-10T04:18:23Z")

</div>

Dears in 3D Slicer support team, I want to know how could I color different regions with different colors in the same model! As you can seen in this screenshot below: Want to color the fractured segments (small ones)…

---

## [Heat Map for multiple segmentations](https://discourse.slicer.org/t/heat-map-for-multiple-segmentations/23782)

<div class="topic-metadata">

**Author:** [@zells](https://discourse.slicer.org/u/zells)\
**Replies:** 4\
**Last updated:** [June 9, 2022, 4:35pm UTC](https://discourse.slicer.org/t/heat-map-for-multiple-segmentations/23782 "2022-06-09T16:35:24Z")

</div>

I have a bunch of lesions here (with organs) but I want the colors of the lesions to be denoted in a manner that if they are overlapping with other lesions it changes color. ie if the two yellow lesions (in the middle …

---

## [Diferrence Between Subtraction in ForeGround and Background and Subtract Scalar Volumes](https://discourse.slicer.org/t/diferrence-between-subtraction-in-foreground-and-background-and-subtract-scalar-volumes/23799)

<div class="topic-metadata">

**Author:** [@Ayush\_Gupta](https://discourse.slicer.org/u/Ayush_Gupta)\
**Replies:** 0\
**Last updated:** [June 9, 2022, 3:54pm UTC](https://discourse.slicer.org/t/diferrence-between-subtraction-in-foreground-and-background-and-subtract-scalar-volumes/23799 "2022-06-09T15:54:31Z")

</div>

Hello there I want to subtract two volumes one is a CT Scan and another is CT Angiography, when I use scalar subtraction I get a different output from subtraction in foreground and background(I registered both the images…

---

## [Can I get a specific vertex number surface model from lung CT and its segmentation？](https://discourse.slicer.org/t/can-i-get-a-specific-vertex-number-surface-model-from-lung-ct-and-its-segmentation/23795)

<div class="topic-metadata">

**Author:** [@qod\_rec](https://discourse.slicer.org/u/qod_rec)\
**Replies:** 0\
**Last updated:** [June 9, 2022, 1:36pm UTC](https://discourse.slicer.org/t/can-i-get-a-specific-vertex-number-surface-model-from-lung-ct-and-its-segmentation/23795 "2022-06-09T13:36:30Z")

</div>

Hello，I’m trying to do some deep learning quest on 3d reconstruction from lung x-rays (CT’s DRR). I want to take some features from DRR and use this to transform a initial template lung mesh to the ground-truth mesh, wh…

---

## [Exporting png-files as stacks after registration](https://discourse.slicer.org/t/exporting-png-files-as-stacks-after-registration/23587)

<div class="topic-metadata">

**Author:** [@j.v.d](https://discourse.slicer.org/u/j.v.d)\
**Replies:** 3\
**Last updated:** [June 9, 2022, 10:19am UTC](https://discourse.slicer.org/t/exporting-png-files-as-stacks-after-registration/23587 "2022-06-09T10:19:18Z")

</div>

Hey everyone! Lately I wanted to align two different CT-modalities with 3D Slicer so that corresponding anatomic structures are positioned exactly over each other. This worked out quite well so far with “Transforms” and…

[Previous page](https://discourse.slicer.org/c/support/11.md?page=218)

[Next page](https://discourse.slicer.org/c/support/11.md?page=220)