# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=243

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

**Page:** 244

---

## [Working between datasets/slices and reanalyzing saved data](https://discourse.slicer.org/t/working-between-datasets-slices-and-reanalyzing-saved-data/21457)

<div class="topic-metadata">

**Author:** [@enismullaj1992](https://discourse.slicer.org/u/enismullaj1992)\
**Replies:** 0\
**Last updated:** [January 14, 2022, 3:30am UTC](https://discourse.slicer.org/t/working-between-datasets-slices-and-reanalyzing-saved-data/21457 "2022-01-14T03:30:15Z")

</div>

Hey everyone! I am a student from Rush University and we are working on a project which analyzes muscle area and hounsefield units on CT scans of the L3 region in hospitalized patients. The major issues that occur are …

---

## [DICOM Export Issue to Treatment Planning System](https://discourse.slicer.org/t/dicom-export-issue-to-treatment-planning-system/21453)

<div class="topic-metadata">

**Author:** [@sdomal](https://discourse.slicer.org/u/sdomal)\
**Replies:** 3\
**Last updated:** [January 14, 2022, 3:04am UTC](https://discourse.slicer.org/t/dicom-export-issue-to-treatment-planning-system/21453 "2022-01-14T03:04:24Z")

</div>

Operating system: Windows Slicer version: 4.11.20200930 Expected behavior: I am trying to export a virtual phantom as a DICOM image set as to be read in by a treatment planning system, specifically RayStation. I am exp…

---

## [Convert fcsv files into nts files](https://discourse.slicer.org/t/convert-fcsv-files-into-nts-files/21451)

<div class="topic-metadata">

**Author:** [@jusopar](https://discourse.slicer.org/u/jusopar)\
**Replies:** 4\
**Last updated:** [January 13, 2022, 10:59pm UTC](https://discourse.slicer.org/t/convert-fcsv-files-into-nts-files/21451 "2022-01-13T22:59:35Z")

</div>

Is it possible to export landmarks as nts files? If not, is there a way to convert fcsv files into nts files? Operating system: Windows Slicer version: 4.11.20210226 Expected behavior: Actual behavior:

---

## [Loading Annotation Ruler as Markups Line](https://discourse.slicer.org/t/loading-annotation-ruler-as-markups-line/21426)

<div class="topic-metadata">

**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 1\
**Last updated:** [January 13, 2022, 5:23pm UTC](https://discourse.slicer.org/t/loading-annotation-ruler-as-markups-line/21426 "2022-01-13T17:23:46Z")

</div>

If I have a bunch of annotation ruler node objects saved to disk as .acsv files, what is the correct way to load these into Slicer as Markups Line node objects? I would like to use the improved display node capabilities …

---

## [\[qSlicerScalarVolumeDisplayWidget\] Adding user-defined histogram to this](https://discourse.slicer.org/t/qslicerscalarvolumedisplaywidget-adding-user-defined-histogram-to-this/21448)

<div class="topic-metadata">

**Author:** [@strider\_hunter](https://discourse.slicer.org/u/strider_hunter)\
**Replies:** 0\
**Last updated:** [January 13, 2022, 4:29pm UTC](https://discourse.slicer.org/t/qslicerscalarvolumedisplaywidget-adding-user-defined-histogram-to-this/21448 "2022-01-13T16:29:02Z")

</div>

Hi, I wish to add a user-defined histogram in ScalarVolumeDisplayWidget. Is it possible to do so? I have seen solutions that display histograms using slicer.util.plot(), but I have a very specific user-defined layout th…

---

## [Change default color palette for segmentation](https://discourse.slicer.org/t/change-default-color-palette-for-segmentation/20288)

<div class="topic-metadata">

**Author:** [@sronen71](https://discourse.slicer.org/u/sronen71)\
**Replies:** 3\
**Last updated:** [January 13, 2022, 1:10pm UTC](https://discourse.slicer.org/t/change-default-color-palette-for-segmentation/20288 "2022-01-13T13:10:26Z")

</div>

When I start a new segmentation in segment editor, and add segments, the default color palette (Color node) is GenericAnatomyColors. How can I tell 3D Slicer to use a different palette (Color node) as default? For exampl…

---

## [Replace voxel values with probabilities](https://discourse.slicer.org/t/replace-voxel-values-with-probabilities/21442)

<div class="topic-metadata">

**Author:** [@smcch](https://discourse.slicer.org/u/smcch)\
**Replies:** 0\
**Last updated:** [January 13, 2022, 12:35pm UTC](https://discourse.slicer.org/t/replace-voxel-values-with-probabilities/21442 "2022-01-13T12:35:59Z")

</div>

Hi ! I would like to know how to replace the intensity values from the voxels of an image (nifti) by probability values (0-1) to generate a plot in colors. I have two files, the original image in nifti and the probabili…

---

## [Saving Markups Scalar values to a file](https://discourse.slicer.org/t/saving-markups-scalar-values-to-a-file/21287)

<div class="topic-metadata">

**Author:** [@Shambhavi\_Malik](https://discourse.slicer.org/u/Shambhavi_Malik)\
**Replies:** 18\
**Last updated:** [January 13, 2022, 6:15am UTC](https://discourse.slicer.org/t/saving-markups-scalar-values-to-a-file/21287 "2022-01-13T06:15:07Z")

</div>

I am using the Markups and VMTK module for blood vessel centerline extraction. In the markups module, is there a method to save the blood vessel radius at each node to a file such as JSON or fcsv? In the scalars section,…

---

## [Issues when calling another python environment in a CLI module](https://discourse.slicer.org/t/issues-when-calling-another-python-environment-in-a-cli-module/21430)

<div class="topic-metadata">

**Author:** [@Mathieu\_Leclercq](https://discourse.slicer.org/u/Mathieu_Leclercq)\
**Replies:** 1\
**Last updated:** [January 13, 2022, 12:46am UTC](https://discourse.slicer.org/t/issues-when-calling-another-python-environment-in-a-cli-module/21430 "2022-01-13T00:46:36Z")

</div>

Hello, I am developing an extension for Slicer that offers a GUI for runnning 3D surface segmentation. The GUI and the segmentation algorithm both work fine separately, but I need to call my own python environment in th…

---

## [How do I get volume dimensions from section of 3D render out of DICOM files? ](https://discourse.slicer.org/t/how-do-i-get-volume-dimensions-from-section-of-3d-render-out-of-dicom-files/21429)

<div class="topic-metadata">

**Author:** [@Anzor\_Aslanukov](https://discourse.slicer.org/u/Anzor_Aslanukov)\
**Replies:** 1\
**Last updated:** [January 12, 2022, 11:54pm UTC](https://discourse.slicer.org/t/how-do-i-get-volume-dimensions-from-section-of-3d-render-out-of-dicom-files/21429 "2022-01-12T23:54:42Z")

</div>

I’ve got the DICOM files of a mouse head. Using the grow from seeds method in Segment Editor, one tooth from the jaw has been selected and rendered into a 3D volume. Is it possible to get volume dimensions from about the…

---

## [Volume Rendering : displaying ROI leads to a crash on self built Slicer](https://discourse.slicer.org/t/volume-rendering-displaying-roi-leads-to-a-crash-on-self-built-slicer/21389)

<div class="topic-metadata">

**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 7\
**Last updated:** [January 12, 2022, 3:32pm UTC](https://discourse.slicer.org/t/volume-rendering-displaying-roi-leads-to-a-crash-on-self-built-slicer/21389 "2022-01-12T15:32:31Z")

</div>

My weekly Slicer build at 4f1e6145ca8 on Arch Linux crashes when showing the ROI in Volume rendering. Factory build Slicer at 4f1e6145ca8 (r30526) does not crash with the same steps. A clean build does not resolve the is…

---

## [No extensions for today's preview build](https://discourse.slicer.org/t/no-extensions-for-todays-preview-build/21417)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 11\
**Last updated:** [January 12, 2022, 2:33pm UTC](https://discourse.slicer.org/t/no-extensions-for-todays-preview-build/21417 "2022-01-12T14:33:32Z")

</div>

I can’t tell if that’s something on my end, but when I open the extension manager in today’s build (windows), there are no extensions listed. Searching them doesn’t find anything. There are no error messages in the log. …

---

## [GPL3 license for Slicer derived app](https://discourse.slicer.org/t/gpl3-license-for-slicer-derived-app/16379)

<div class="topic-metadata">

**Author:** [@keri](https://discourse.slicer.org/u/keri)\
**Replies:** 9\
**Last updated:** [January 12, 2022, 2:03pm UTC](https://discourse.slicer.org/t/gpl3-license-for-slicer-derived-app/16379 "2022-01-12T14:03:09Z")

</div>

I’m starting to develop Slicer based application that is supposed to be used in geoscience field and will be distributed on github under GPL3 license. It will have its own name, mainwindow will be changed, some modules w…

---

## [Saving Linear Transformation Matrix](https://discourse.slicer.org/t/saving-linear-transformation-matrix/1192)

<div class="topic-metadata">

**Author:** [@Anna\_Morelli](https://discourse.slicer.org/u/Anna_Morelli)\
**Replies:** 7\
**Last updated:** [January 12, 2022, 2:35am UTC](https://discourse.slicer.org/t/saving-linear-transformation-matrix/1192 "2022-01-12T02:35:53Z")

</div>

Operating system: Windows 10 Slicer version: 4.6.2 Expected behavior: Matrix in ijk coordinates Actual behavior: Matrix in unknown reference system Hi guys, I’m a beginner in Slicer and I’m in trouble saving the tra…

---

## [Issue with installation of Slicer on Windows](https://discourse.slicer.org/t/issue-with-installation-of-slicer-on-windows/21418)

<div class="topic-metadata">

**Author:** [@HodaJavadi](https://discourse.slicer.org/u/HodaJavadi)\
**Replies:** 1\
**Last updated:** [January 11, 2022, 9:40pm UTC](https://discourse.slicer.org/t/issue-with-installation-of-slicer-on-windows/21418 "2022-01-11T21:40:51Z")

</div>

Hello, I have had Slicer on my desktop (Windows 10) since August 2021 and initially I had no issue. I stopped working with it in past several months and now when I need it again, the software doesn’t open on my desktop.…

---

## [Developer tools for extensions is failing for preview](https://discourse.slicer.org/t/developer-tools-for-extensions-is-failing-for-preview/21324)

<div class="topic-metadata">

**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 2\
**Last updated:** [January 11, 2022, 7:47pm UTC](https://discourse.slicer.org/t/developer-tools-for-extensions-is-failing-for-preview/21324 "2022-01-11T19:47:31Z")

</div>

It is failing on all three platform. Looks like there is a configuraiton issue: https://slicer.cdash.org/build/2539448 @Sam\_Horvath @jcfr

---

## [How cna I save my segmentation seperately?](https://discourse.slicer.org/t/how-cna-i-save-my-segmentation-seperately/21382)

<div class="topic-metadata">

**Author:** [@LIE\_CAI](https://discourse.slicer.org/u/LIE_CAI)\
**Replies:** 6\
**Last updated:** [January 11, 2022, 6:46pm UTC](https://discourse.slicer.org/t/how-cna-i-save-my-segmentation-seperately/21382 "2022-01-11T18:46:28Z")

</div>

For example, now I have two segmentation documents. But when I click the save button I only get one document. How can I save them seperately? Thanks a lot!

---

## [Discrepancy between segmentation threshold and first order radiomics](https://discourse.slicer.org/t/discrepancy-between-segmentation-threshold-and-first-order-radiomics/20374)

<div class="topic-metadata">

**Author:** [@Fabio\_Nunes](https://discourse.slicer.org/u/Fabio_Nunes)\
**Replies:** 2\
**Last updated:** [January 11, 2022, 12:17pm UTC](https://discourse.slicer.org/t/discrepancy-between-segmentation-threshold-and-first-order-radiomics/20374 "2022-01-11T12:17:46Z")

</div>

Hello, Thanks to the advice of Mr. Andras Lasso, I’ve been able to segment the pericardium of the heart (using the Surface Cut option from Slicer). I’ve then applied a threshold to only select the fatty tissue (HU -150 …

---

## [No extensions in extension manager for 4.13.0-2020-11-17](https://discourse.slicer.org/t/no-extensions-in-extension-manager-for-4-13-0-2020-11-17/21405)

<div class="topic-metadata">

**Author:** [@TudorSlicer](https://discourse.slicer.org/u/TudorSlicer)\
**Replies:** 0\
**Last updated:** [January 11, 2022, 9:22am UTC](https://discourse.slicer.org/t/no-extensions-in-extension-manager-for-4-13-0-2020-11-17/21405 "2022-01-11T09:22:41Z")

</div>

Operating system: W10 Slicer version: 4.13.0-2020-11-17 Expected behavior: Find extension called wrap Actual behavior: No extensions listed I am trying to make a bone model. I found advice to use the wrap exten…

---

## [Does Slicer support this kind of PET-CT registration?](https://discourse.slicer.org/t/does-slicer-support-this-kind-of-pet-ct-registration/2354)

<div class="topic-metadata">

**Author:** [@glhfgg1024](https://discourse.slicer.org/u/glhfgg1024)\
**Replies:** 11\
**Last updated:** [January 11, 2022, 2:43am UTC](https://discourse.slicer.org/t/does-slicer-support-this-kind-of-pet-ct-registration/2354 "2022-01-11T02:43:10Z")

</div>

Operating system: Windows 10 Slicer version: 4.8.0 Expected behavior: PET-CT registration Actual behavior: Not sure Hi all, I have a this kind of data. For each case/patient, there are the following images: 1. CT 2…

---

## [how to change the parameters of the reconstruction?](https://discourse.slicer.org/t/how-to-change-the-parameters-of-the-reconstruction/21362)

<div class="topic-metadata">

**Author:** [@yoav\_benhaim](https://discourse.slicer.org/u/yoav_benhaim)\
**Replies:** 1\
**Last updated:** [January 10, 2022, 6:40pm UTC](https://discourse.slicer.org/t/how-to-change-the-parameters-of-the-reconstruction/21362 "2022-01-10T18:40:30Z")

</div>

Operating system: windows Slicer version: 4.11.20210226 I have axiel sections of CT and I want to determine the depth of each section in the reconstruction as well as the distance between each two pixels in length and …

---

## [DICOM, rt structure, uniform extensive of PTV, obtaining overlap volume between PTV and the organ](https://discourse.slicer.org/t/dicom-rt-structure-uniform-extensive-of-ptv-obtaining-overlap-volume-between-ptv-and-the-organ/21373)

<div class="topic-metadata">

**Author:** [@Arash\_Ebrahimi](https://discourse.slicer.org/u/Arash_Ebrahimi)\
**Replies:** 4\
**Last updated:** [January 10, 2022, 1:01pm UTC](https://discourse.slicer.org/t/dicom-rt-structure-uniform-extensive-of-ptv-obtaining-overlap-volume-between-ptv-and-the-organ/21373 "2022-01-10T13:01:07Z")

</div>

Hi to all, I am a medical researcher and my current project is about IMRT and machine learning. To get prepared the input data for Neural network model, I need to enlarge or shorten the PTV volume and calculate overlap…

---

## [Procrustes alignment in SPHARM PDM](https://discourse.slicer.org/t/procrustes-alignment-in-spharm-pdm/20691)

<div class="topic-metadata">

**Author:** [@lili-yu22](https://discourse.slicer.org/u/lili-yu22)\
**Replies:** 1\
**Last updated:** [January 10, 2022, 11:52am UTC](https://discourse.slicer.org/t/procrustes-alignment-in-spharm-pdm/20691 "2022-01-10T11:52:35Z")

</div>

Hi， In the spharm-pdm，alignment of two object using rigid procrustes alignment ，an article mentioned that this rigid procrustes alignment procedure computer an optimal linear geometric transformation that best maps the…

---

## [3D model of only the outer surface of a bone+ 3D model of a bone](https://discourse.slicer.org/t/3d-model-of-only-the-outer-surface-of-a-bone-3d-model-of-a-bone/2714)

<div class="topic-metadata">

**Author:** [@saeed\_mouloodi](https://discourse.slicer.org/u/saeed_mouloodi)\
**Replies:** 16\
**Last updated:** [January 8, 2022, 1:29am UTC](https://discourse.slicer.org/t/3d-model-of-only-the-outer-surface-of-a-bone-3d-model-of-a-bone/2714 "2022-01-08T01:29:33Z")

</div>

Hi, I am very new with the 3D slicer, so my question might be so simple. Still, it is really appreciated if you could help me with it. I have a DCOM data from CT of a bone (to say like femur). I am wondering how can I …

---

## [Volume Rendering Cropping "ON"](https://discourse.slicer.org/t/volume-rendering-cropping-on/21353)

<div class="topic-metadata">

**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 0\
**Last updated:** [January 7, 2022, 2:44pm UTC](https://discourse.slicer.org/t/volume-rendering-cropping-on/21353 "2022-01-07T14:44:08Z")

</div>

I was implementing the volume rendering module using python and I could not get the ROI volume cropping as shown here; displayNode.SetAndObserveROINodeID(roiNode.GetID()) displayNode.CroppingEnabled = True But I did ge…

---

## [How to install python packages using jupyterlab?](https://discourse.slicer.org/t/how-to-install-python-packages-using-jupyterlab/21343)

<div class="topic-metadata">

**Author:** [@user4](https://discourse.slicer.org/u/user4)\
**Replies:** 4\
**Last updated:** [January 7, 2022, 8:31am UTC](https://discourse.slicer.org/t/how-to-install-python-packages-using-jupyterlab/21343 "2022-01-07T08:31:51Z")

</div>

Hi all,I am using the Slicer 4.11 and I am stucked with installing packages. Here is the thing in detail: I was trying to install some packages,say matplotlib in Slicer: Also,I tried to install the package in Pyt…

---

## [How to change view controller slider horizontal to vertical](https://discourse.slicer.org/t/how-to-change-view-controller-slider-horizontal-to-vertical/21350)

<div class="topic-metadata">

**Author:** [@Shahnawaz\_Vora](https://discourse.slicer.org/u/Shahnawaz_Vora)\
**Replies:** 0\
**Last updated:** [January 7, 2022, 5:11am UTC](https://discourse.slicer.org/t/how-to-change-view-controller-slider-horizontal-to-vertical/21350 "2022-01-07T05:11:38Z")

</div>

How i can move slicer viewcontroller slider horizontal to vertical with python script

---

## [Mouse swipe translates view/3D unintentionally -- please help](https://discourse.slicer.org/t/mouse-swipe-translates-view-3d-unintentionally-please-help/21335)

<div class="topic-metadata">

**Author:** [@asdf](https://discourse.slicer.org/u/asdf)\
**Replies:** 4\
**Last updated:** [January 7, 2022, 4:28am UTC](https://discourse.slicer.org/t/mouse-swipe-translates-view-3d-unintentionally-please-help/21335 "2022-01-07T04:28:24Z")

</div>

Brand new to Slicer (4.13, Intel MacOS Catalina) and I’m having the following problem: I have a volume loaded, and I’ve been working mostly in the Segmentation Editor. I’ve found that click+drag rotates the volume (in 2…

---

## [How to segment gray, white and tumor region using NVIDIA clara.](https://discourse.slicer.org/t/how-to-segment-gray-white-and-tumor-region-using-nvidia-clara/21348)

<div class="topic-metadata">

**Author:** [@Akhil\_Ratan\_Mishra](https://discourse.slicer.org/u/Akhil_Ratan_Mishra)\
**Replies:** 0\
**Last updated:** [January 6, 2022, 5:07pm UTC](https://discourse.slicer.org/t/how-to-segment-gray-white-and-tumor-region-using-nvidia-clara/21348 "2022-01-06T17:07:31Z")

</div>

Operating system: Windows 11 Slicer version: 4.11 Expected behavior: Actual behavior:

---

## [Output of calculated specific values of a model for individual ROIs](https://discourse.slicer.org/t/output-of-calculated-specific-values-of-a-model-for-individual-rois/21148)

<div class="topic-metadata">

**Author:** [@MaKe](https://discourse.slicer.org/u/MaKe)\
**Replies:** 4\
**Last updated:** [January 6, 2022, 4:10pm UTC](https://discourse.slicer.org/t/output-of-calculated-specific-values-of-a-model-for-individual-rois/21148 "2022-01-06T16:10:54Z")

</div>

Operating system: Windows 10 Slicer version: 4.11 Hi everyone, I am currently working with 3D Slicer and would like to output specific values within different ROIs of a calculated model as a mean value. For this I hav…

[Previous page](https://discourse.slicer.org/c/support/11.md?page=242)

[Next page](https://discourse.slicer.org/c/support/11.md?page=244)