# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=283

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

**Page:** 284

---

## [How run VMTK script?](https://discourse.slicer.org/t/how-run-vmtk-script/17395)

<div class="topic-metadata">

**Author:** [@alessia](https://discourse.slicer.org/u/alessia)\
**Replies:** 0\
**Last updated:** [April 30, 2021, 2:27pm UTC](https://discourse.slicer.org/t/how-run-vmtk-script/17395 "2021-04-30T14:27:17Z")

</div>

After installing VMTK thanks ANACONDA, how can I run VMTK script? Anaconda doesn’t recognize the command : 1. source path-to-vmtk\_env.sh Thank you

---

## [Is there a way to change the ROI to a sphere](https://discourse.slicer.org/t/is-there-a-way-to-change-the-roi-to-a-sphere/15650)

<div class="topic-metadata">

**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 9\
**Last updated:** [April 30, 2021, 2:26pm UTC](https://discourse.slicer.org/t/is-there-a-way-to-change-the-roi-to-a-sphere/15650 "2021-04-30T14:26:56Z")

</div>

As this picture shows, the ROI is a cube, and sometimes it may be better to change it to a sphere. Of course, this function PRISM rendering can be implemented, but it will be more convenient if you can directly adjust th…

---

## [Fill holes in 3D model](https://discourse.slicer.org/t/fill-holes-in-3d-model/13508)

<div class="topic-metadata">

**Author:** [@ru6928](https://discourse.slicer.org/u/ru6928)\
**Replies:** 11\
**Last updated:** [April 30, 2021, 2:29am UTC](https://discourse.slicer.org/t/fill-holes-in-3d-model/13508 "2021-04-30T02:29:15Z")

</div>

Hi all, I would like to fill the holes in the 3D model using some sort of interpolation. How do I do it in 3DSlicer? These are segmentations obtained from a deep learning algorithm for cardiac MR images. The myocardi…

---

## [How to convert .nii MRI mask files to 3D volume that could be meshed with 3D element types later?](https://discourse.slicer.org/t/how-to-convert-nii-mri-mask-files-to-3d-volume-that-could-be-meshed-with-3d-element-types-later/17231)

<div class="topic-metadata">

**Author:** [@Mohsen](https://discourse.slicer.org/u/Mohsen)\
**Replies:** 2\
**Last updated:** [April 30, 2021, 12:18am UTC](https://discourse.slicer.org/t/how-to-convert-nii-mri-mask-files-to-3d-volume-that-could-be-meshed-with-3d-element-types-later/17231 "2021-04-30T00:18:09Z")

</div>

Hello, I am trying to convert a .nii MRI mask (binary 3D mask) file to a 3D volume mesh or any 3D volume format, so I could mesh the model with 3D element types and do Finite Element Analysis. I would appreciate it if …

---

## [Segmentations translocating upon loading of saved data](https://discourse.slicer.org/t/segmentations-translocating-upon-loading-of-saved-data/17308)

<div class="topic-metadata">

**Author:** [@Isaac.Annal](https://discourse.slicer.org/u/Isaac.Annal)\
**Replies:** 4\
**Last updated:** [April 29, 2021, 12:18am UTC](https://discourse.slicer.org/t/segmentations-translocating-upon-loading-of-saved-data/17308 "2021-04-29T00:18:56Z")

</div>

Hi all! I’ve been trying to really get going with 3D slicer for a while now and I can’t seem to figure out a resolution to this issue. I am currently working on the segmentation of skink skulls. When I load saved data, …

---

## [Volumetric assessment](https://discourse.slicer.org/t/volumetric-assessment/17062)

<div class="topic-metadata">

**Author:** [@rmarahman](https://discourse.slicer.org/u/rmarahman)\
**Replies:** 8\
**Last updated:** [April 28, 2021, 11:39pm UTC](https://discourse.slicer.org/t/volumetric-assessment/17062 "2021-04-28T23:39:48Z")

</div>

Dear Users, I am using 3D Slicer version 4.11. Over 10 years ago I used the program to do volumetric assessments on white matter disease in the brain. I am now attempting to do volumetric assessments on brain tumours an…

---

## [Change Axis Labels from RAS to XYZ (or something else custom)](https://discourse.slicer.org/t/change-axis-labels-from-ras-to-xyz-or-something-else-custom/17356)

<div class="topic-metadata">

**Author:** [@Jonathan\_Lesage](https://discourse.slicer.org/u/Jonathan_Lesage)\
**Replies:** 5\
**Last updated:** [April 28, 2021, 3:54pm UTC](https://discourse.slicer.org/t/change-axis-labels-from-ras-to-xyz-or-something-else-custom/17356 "2021-04-28T15:54:40Z")

</div>

I was wondering if it is possible to change the RAS labels on the axes to XYZ? I am attempting to make using slicer more attractive to folks in the Nondestructive Testing world and being able to change RAS to XYZ will ma…

---

## [Export Markups Data (Distance, Angle)?](https://discourse.slicer.org/t/export-markups-data-distance-angle/17363)

<div class="topic-metadata">

**Author:** [@lazymark2](https://discourse.slicer.org/u/lazymark2)\
**Replies:** 3\
**Last updated:** [April 28, 2021, 3:37pm UTC](https://discourse.slicer.org/t/export-markups-data-distance-angle/17363 "2021-04-28T15:37:20Z")

</div>

Operating system:Linux Slicer version:4.11.20210226 Hi everyone, recently I want to measure the data of crown length and root length. And I used markupsline tool in Markups Mode. But I can’t find a way to export the de…

---

## [ROI on slice intersection](https://discourse.slicer.org/t/roi-on-slice-intersection/17350)

<div class="topic-metadata">

**Author:** [@Vincebisca](https://discourse.slicer.org/u/Vincebisca)\
**Replies:** 3\
**Last updated:** [April 28, 2021, 8:25am UTC](https://discourse.slicer.org/t/roi-on-slice-intersection/17350 "2021-04-28T08:25:57Z")

</div>

Hello, I have been trying to create a custom workflow GUI on a Slicelet used for segmentation. part of this workflow is a Crop Volume to select only a precise part of the DICOM I try to segment. I managed pretty well (c…

---

## [Misalignment between Eigen Artemis DICOM image and segmentation](https://discourse.slicer.org/t/misalignment-between-eigen-artemis-dicom-image-and-segmentation/17008)

<div class="topic-metadata">

**Author:** [@sulaimanvesal](https://discourse.slicer.org/u/sulaimanvesal)\
**Replies:** 16\
**Last updated:** [April 28, 2021, 6:11am UTC](https://discourse.slicer.org/t/misalignment-between-eigen-artemis-dicom-image-and-segmentation/17008 "2021-04-28T06:11:26Z")

</div>

Hi, I wanted to ask this point, that why my segmentation output during export placed at the corner of NRRD volume. Even though the volume origin is at (0.0, 0.0, 0.0). Below is the code that I am using to export a vtk …

---

## [Rotate the tracker coordinates](https://discourse.slicer.org/t/rotate-the-tracker-coordinates/16998)

<div class="topic-metadata">

**Author:** [@WangZhen1175701153](https://discourse.slicer.org/u/WangZhen1175701153)\
**Replies:** 8\
**Last updated:** [April 28, 2021, 4:39am UTC](https://discourse.slicer.org/t/rotate-the-tracker-coordinates/16998 "2021-04-28T04:39:52Z")

</div>

My tracker doesn’t align with the needle model. How do I rotate the coordinates that the physics tracker passed in?

---

## [Building Slicer on Linux with TBB](https://discourse.slicer.org/t/building-slicer-on-linux-with-tbb/17352)

<div class="topic-metadata">

**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 1\
**Last updated:** [April 28, 2021, 1:20am UTC](https://discourse.slicer.org/t/building-slicer-on-linux-with-tbb/17352 "2021-04-28T01:20:34Z")

</div>

Following this discussion. Slicer builds on Arch Linux with TBB by passing Slicer\_VTK\_SMP\_IMPLEMENTATION\_TYPE:STRING=TBB to cmake. However, VTK failed initially : \[ 7%\] Built target vtkCommonComputationalGeometryObje…

---

## [Segmentation smoothing brush](https://discourse.slicer.org/t/segmentation-smoothing-brush/14724)

<div class="topic-metadata">

**Author:** [@Hannnonk](https://discourse.slicer.org/u/Hannnonk)\
**Replies:** 5\
**Last updated:** [April 27, 2021, 8:48pm UTC](https://discourse.slicer.org/t/segmentation-smoothing-brush/14724 "2021-04-27T20:48:57Z")

</div>

Could someone point me in the direction of how to obtain the segmentation smoothing brush? It says it is in the Slicer Preview Releases (Slicer-4.13)…but for the life of me I can not find this. Do I have to download a n…

---

## [Problem with CIP 3d model and exportation](https://discourse.slicer.org/t/problem-with-cip-3d-model-and-exportation/11113)

<div class="topic-metadata">

**Author:** [@javierfuster](https://discourse.slicer.org/u/javierfuster)\
**Replies:** 1\
**Last updated:** [April 27, 2021, 8:17pm UTC](https://discourse.slicer.org/t/problem-with-cip-3d-model-and-exportation/11113 "2021-04-27T20:17:39Z")

</div>

Hi everyone, I am making the lobe lung segmentation (Iteractive Lobe Segmentation) with the extension CIP. Everything works fine but at the moment that I want to make a 3D model it results imposible with the lobe segmen…

---

## [How to crop a DICOM 3D dose file and save it in a DICOM 3D dose file (not DICOM series)](https://discourse.slicer.org/t/how-to-crop-a-dicom-3d-dose-file-and-save-it-in-a-dicom-3d-dose-file-not-dicom-series/11873)

<div class="topic-metadata">

**Author:** [@vietlebao](https://discourse.slicer.org/u/vietlebao)\
**Replies:** 0\
**Last updated:** [June 5, 2020, 5:03am UTC](https://discourse.slicer.org/t/how-to-crop-a-dicom-3d-dose-file-and-save-it-in-a-dicom-3d-dose-file-not-dicom-series/11873 "2020-06-05T05:03:57Z")

</div>

Hi every one, I am cropping a DICOM dose file (single file) and then save it in a single DICOM dose file as well (not a DICOM series). I have a DICOM 3D dose (single file) file that inputs to 3D Slicer, then I crop it …

---

## [Updated FAQ with sample data link](https://discourse.slicer.org/t/updated-faq-with-sample-data-link/4465)

<div class="topic-metadata">

**Author:** [@pieper](https://discourse.slicer.org/u/pieper)\
**Replies:** 0\
**Last updated:** [October 19, 2018, 3:07pm UTC](https://discourse.slicer.org/t/updated-faq-with-sample-data-link/4465 "2018-10-19T15:07:41Z")

</div>

FYI to troubleshooters: Related to this post I updated the FAQ for the Nightly and 4.10 wiki pages to include a link to sample dicom data that people can use to test their slicer installation. https://www.slicer.org/w/i…

---

## [Plotting Registration Results from Elastix](https://discourse.slicer.org/t/plotting-registration-results-from-elastix/15959)

<div class="topic-metadata">

**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 0\
**Last updated:** [February 11, 2021, 9:04pm UTC](https://discourse.slicer.org/t/plotting-registration-results-from-elastix/15959 "2021-02-11T21:04:50Z")

</div>

Hello, I want to plot my registration results to compare different metric values and also the amount of translation in x, y, z direction. I found some code from SimpleITK here: SimpleITK-Notebooks/60\_Registration\_Introd…

---

## [Calculate the ADC for different b values in Breast DWI images](https://discourse.slicer.org/t/calculate-the-adc-for-different-b-values-in-breast-dwi-images/17241)

<div class="topic-metadata">

**Author:** [@Mgi](https://discourse.slicer.org/u/Mgi)\
**Replies:** 7\
**Last updated:** [April 27, 2021, 6:55pm UTC](https://discourse.slicer.org/t/calculate-the-adc-for-different-b-values-in-breast-dwi-images/17241 "2021-04-27T18:55:05Z")

</div>

Operating system: Windows 10 Slicer version: 4.11.20200930 Expected behavior: I used the DWModeling module to calculate the ADC from Breast DWI images with b values 0-400-700-1100. Actual behavior: I can not see the r…

---

## [Line profile : Intensity matching](https://discourse.slicer.org/t/line-profile-intensity-matching/11291)

<div class="topic-metadata">

**Author:** [@Fritta](https://discourse.slicer.org/u/Fritta)\
**Replies:** 0\
**Last updated:** [April 24, 2020, 1:19pm UTC](https://discourse.slicer.org/t/line-profile-intensity-matching/11291 "2020-04-24T13:19:49Z")

</div>

Hi, I’m using 3D Slicer to process two different images ( RT Dose volume and MRI volume ) of the same phantom and I would like to compare them in terms of relative intensity. In other words I would like to test if the i…

---

## [How to quantify the measurements obtained from the vtk file](https://discourse.slicer.org/t/how-to-quantify-the-measurements-obtained-from-the-vtk-file/11874)

<div class="topic-metadata">

**Author:** [@danila](https://discourse.slicer.org/u/danila)\
**Replies:** 0\
**Last updated:** [June 5, 2020, 8:08am UTC](https://discourse.slicer.org/t/how-to-quantify-the-measurements-obtained-from-the-vtk-file/11874 "2020-06-05T08:08:02Z")

</div>

Hi 3DSlicer experts, I am working on a new project. My first goal is to quantify the change of a jaw before and after an orthognathic surgery (therefore comparing the pre and post CBCT). Following the tutorial I found…

---

## [Ultrasonix linear probe calibration matrix](https://discourse.slicer.org/t/ultrasonix-linear-probe-calibration-matrix/11140)

<div class="topic-metadata">

**Author:** [@mta152](https://discourse.slicer.org/u/mta152)\
**Replies:** 0\
**Last updated:** [April 16, 2020, 2:54am UTC](https://discourse.slicer.org/t/ultrasonix-linear-probe-calibration-matrix/11140 "2020-04-16T02:54:51Z")

</div>

Hi, I have a little confusion about the calibration matrix (referred to as C matrix) for the linear probe. As written in this website: GPS Data Collection - WikiSonix, C is a 3x3 matrix and based on this website Plus ap…

---

## [Segment Comparison module - error](https://discourse.slicer.org/t/segment-comparison-module-error/14428)

<div class="topic-metadata">

**Author:** [@janneke\_slicer](https://discourse.slicer.org/u/janneke_slicer)\
**Replies:** 0\
**Last updated:** [November 4, 2020, 1:47pm UTC](https://discourse.slicer.org/t/segment-comparison-module-error/14428 "2020-11-04T13:47:28Z")

</div>

Hello, I am using Slicer 4.11.20200930. I want to use the Segment Comparison module to compute the Dice score of segmentations, which worked fine in older versions of Slicer. However, now I get the following error: “Er…

---

## [How to read DVF from dicom and save in another compact format](https://discourse.slicer.org/t/how-to-read-dvf-from-dicom-and-save-in-another-compact-format/14673)

<div class="topic-metadata">

**Author:** [@MachadoL](https://discourse.slicer.org/u/MachadoL)\
**Replies:** 0\
**Last updated:** [November 18, 2020, 3:26pm UTC](https://discourse.slicer.org/t/how-to-read-dvf-from-dicom-and-save-in-another-compact-format/14673 "2020-11-18T15:26:44Z")

</div>

Hello, Guys. I am working with a public image dataset. (Image + DVF in dicom format). I’d like to know how to interpret and export the DVF in a compact format. The image + DVF im using are available here. Thanks.

---

## [Convert Unstructured Grid to Volume](https://discourse.slicer.org/t/convert-unstructured-grid-to-volume/14748)

<div class="topic-metadata">

**Author:** [@Asees\_Kaur](https://discourse.slicer.org/u/Asees_Kaur)\
**Replies:** 0\
**Last updated:** [November 23, 2020, 8:51pm UTC](https://discourse.slicer.org/t/convert-unstructured-grid-to-volume/14748 "2020-11-23T20:51:41Z")

</div>

Hi @lassoan, I am currently trying to convert my unstructured grid to a volume. So I can import it into Slicer and export it as DICOM images. The process I’m following is: Create my input file: Convert UnstructuredGr…

---

## [How would I go about modifying the ROSMED tutorial robot with my own robot?](https://discourse.slicer.org/t/how-would-i-go-about-modifying-the-rosmed-tutorial-robot-with-my-own-robot/13379)

<div class="topic-metadata">

**Author:** [@CHRIS\_HUYNH](https://discourse.slicer.org/u/CHRIS_HUYNH)\
**Replies:** 0\
**Last updated:** [September 7, 2020, 6:48pm UTC](https://discourse.slicer.org/t/how-would-i-go-about-modifying-the-rosmed-tutorial-robot-with-my-own-robot/13379 "2020-09-07T18:48:48Z")

</div>

I’ve gone through the ROSMED tutorials and it’s very similar to what I’m trying to achieve with my project. My goal is to recreate the tutorials using my own robot and from the tutorial, I can see that I’d have to set up…

---

## [Automatically have slice view oriented a specific way](https://discourse.slicer.org/t/automatically-have-slice-view-oriented-a-specific-way/17355)

<div class="topic-metadata">

**Author:** [@Jonathan\_Lesage](https://discourse.slicer.org/u/Jonathan_Lesage)\
**Replies:** 0\
**Last updated:** [April 27, 2021, 2:56pm UTC](https://discourse.slicer.org/t/automatically-have-slice-view-oriented-a-specific-way/17355 "2021-04-27T14:56:04Z")

</div>

I am typically loading data from .nrrd files stored as r = x (i), a = y (j), s = z (k). Ideally, I would like to orient the slice views as shown in the attached image. I can manage to accomplish this with the reformat mo…

---

## [Remove deformation](https://discourse.slicer.org/t/remove-deformation/17021)

<div class="topic-metadata">

**Author:** [@Marta\_Fernandez](https://discourse.slicer.org/u/Marta_Fernandez)\
**Replies:** 17\
**Last updated:** [April 27, 2021, 2:24pm UTC](https://discourse.slicer.org/t/remove-deformation/17021 "2021-04-27T14:24:24Z")

</div>

Hello. I have a Skull with deformation in the area of the coronal Suture. How I can remove it, to make the parietals and frontal bone match Thank you in advance.

---

## [Changes to VTK polydata between 4.10 and 4.11](https://discourse.slicer.org/t/changes-to-vtk-polydata-between-4-10-and-4-11/17348)

<div class="topic-metadata">

**Author:** [@codey](https://discourse.slicer.org/u/codey)\
**Replies:** 1\
**Last updated:** [April 27, 2021, 1:30pm UTC](https://discourse.slicer.org/t/changes-to-vtk-polydata-between-4-10-and-4-11/17348 "2021-04-27T13:30:08Z")

</div>

I have noticed that VTK meshes imported in 4.10 and 4.11 differ in their spatial location. Rotation by 180 corrects for this. I presume this is down to a different interpretation of the VTK coordinate system. between the…

---

## [Help me! Update plane from fiducial points...How can I aligne the red plane with Coordinate axis?](https://discourse.slicer.org/t/help-me-update-plane-from-fiducial-points-how-can-i-aligne-the-red-plane-with-coordinate-axis/17344)

<div class="topic-metadata">

**Author:** [@jumbojing](https://discourse.slicer.org/u/jumbojing)\
**Replies:** 0\
**Last updated:** [April 27, 2021, 5:46am UTC](https://discourse.slicer.org/t/help-me-update-plane-from-fiducial-points-how-can-i-aligne-the-red-plane-with-coordinate-axis/17344 "2021-04-27T05:46:49Z")

</div>

\# Update plane from fiducial points def UpdateSlicePlane(data): a = data points = np.array(\[list(zip(\*a))\])\[0\] # b2 = np.array(\[list(zip(\*a))\]) sliceNode = slicer.app.layoutManager().sliceWidget("Red").mrmlSlic…

---

## [SlicerVMTK is not available](https://discourse.slicer.org/t/slicervmtk-is-not-available/17343)

<div class="topic-metadata">

**Author:** [@Romeo\_Guevara](https://discourse.slicer.org/u/Romeo_Guevara)\
**Replies:** 0\
**Last updated:** [April 27, 2021, 3:16am UTC](https://discourse.slicer.org/t/slicervmtk-is-not-available/17343 "2021-04-27T03:16:59Z")

</div>

Good evening, is there a way to get the “slicer VMTK” module in the new version?

[Previous page](https://discourse.slicer.org/c/support/11.md?page=282)

[Next page](https://discourse.slicer.org/c/support/11.md?page=284)