# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=176

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

**Page:** 177

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## [Creation of ROI aligned with freehand ultrasound sweeps -- how to rotate the ROI?](https://discourse.slicer.org/t/creation-of-roi-aligned-with-freehand-ultrasound-sweeps-how-to-rotate-the-roi/18325)

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**Author:** [@AurelieS](https://discourse.slicer.org/u/AurelieS)\
**Replies:** 5\
**Last updated:** [March 2, 2023, 7:29pm UTC](https://discourse.slicer.org/t/creation-of-roi-aligned-with-freehand-ultrasound-sweeps-how-to-rotate-the-roi/18325 "2023-03-02T19:29:32Z")

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Hi, I think my question is quite a beginner question, but since a year now I am doing freehand 3D ultrasound and I just realised that the ROI I am using has a lot of impact on my volume reconstruction. I am therefore t…

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## [Using Paint or Smoothing tool spoils the segment](https://discourse.slicer.org/t/using-paint-or-smoothing-tool-spoils-the-segment/28135)

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**Author:** [@radiodid](https://discourse.slicer.org/u/radiodid)\
**Replies:** 5\
**Last updated:** [March 2, 2023, 5:35pm UTC](https://discourse.slicer.org/t/using-paint-or-smoothing-tool-spoils-the-segment/28135 "2023-03-02T17:35:21Z")

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I recently ran with a problem in Slicer when I try to use Paint to edit a segment and segment immediately spoils on the first contact with the study. Pixels become huge, contours are rough, neighboring structures are lay…

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## [Adapt voxel spacing of segments after changing voxel dimension of master volume](https://discourse.slicer.org/t/adapt-voxel-spacing-of-segments-after-changing-voxel-dimension-of-master-volume/28140)

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**Author:** [@MrMarkus](https://discourse.slicer.org/u/MrMarkus)\
**Replies:** 1\
**Last updated:** [March 2, 2023, 4:30pm UTC](https://discourse.slicer.org/t/adapt-voxel-spacing-of-segments-after-changing-voxel-dimension-of-master-volume/28140 "2023-03-02T16:30:28Z")

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Operating system: Win10 Slicer version: 5.2.1 r31317 / 77da381 Hi, I am encountering the following problem: segments were obtained by using the segment editor the voxel spacing of the master volume was: 1 x 1 x 1 mm…

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## [Global longitudinal strain calculation](https://discourse.slicer.org/t/global-longitudinal-strain-calculation/28139)

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**Author:** [@whu](https://discourse.slicer.org/u/whu)\
**Replies:** 1\
**Last updated:** [March 2, 2023, 3:46pm UTC](https://discourse.slicer.org/t/global-longitudinal-strain-calculation/28139 "2023-03-02T15:46:39Z")

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Dear All, Calculation and analysis of ventricular Global longitudinal strain(GLS) and other strains based on Ultrasound has been research hotspots, is there any extension in Slicer or in the future plan? Or anyone ca…

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## [Generate a model from multiple PNG files](https://discourse.slicer.org/t/generate-a-model-from-multiple-png-files/28116)

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**Author:** [@ConstanzaMor](https://discourse.slicer.org/u/ConstanzaMor)\
**Replies:** 3\
**Last updated:** [March 2, 2023, 1:31pm UTC](https://discourse.slicer.org/t/generate-a-model-from-multiple-png-files/28116 "2023-03-02T13:31:35Z")

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Hello, I’m new to 3D Slicer and I’m working with series of 2D images in PNG or JPEG files. I am trying to arrange them in 3D space since I want to virtually observe the IVD in 360º. So far, I have been able to place the…

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## [Blank Screen after launch when accessing Slicer through remote desktop](https://discourse.slicer.org/t/blank-screen-after-launch-when-accessing-slicer-through-remote-desktop/11066)

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**Author:** [@APern](https://discourse.slicer.org/u/APern)\
**Replies:** 6\
**Last updated:** [March 2, 2023, 12:17pm UTC](https://discourse.slicer.org/t/blank-screen-after-launch-when-accessing-slicer-through-remote-desktop/11066 "2023-03-02T12:17:55Z")

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I’m experiencing difficulty with running 3D Slicer. The program launches but the Slicer window is completely blank, as seen in the attached picture. This has been a consistent and repeatable error without any useful erro…

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## [Error when installing matplotib in Slicer](https://discourse.slicer.org/t/error-when-installing-matplotib-in-slicer/28138)

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**Author:** [@hapkx](https://discourse.slicer.org/u/hapkx)\
**Replies:** 0\
**Last updated:** [March 2, 2023, 8:28am UTC](https://discourse.slicer.org/t/error-when-installing-matplotib-in-slicer/28138 "2023-03-02T08:28:12Z")

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Operating system: Windows11 Slicer version: Slicer 5.0.2 Hi! I’m trying to install matplotlib package in python-interactor in Slicer 5.0.2 with the following commands: from slicer.util import pip\_install pip\_install(…

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## [How can I transfer my custom ultrasound data from python to 3Dslicer through IGT](https://discourse.slicer.org/t/how-can-i-transfer-my-custom-ultrasound-data-from-python-to-3dslicer-through-igt/27336)

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**Author:** [@LV52](https://discourse.slicer.org/u/LV52)\
**Replies:** 4\
**Last updated:** [March 2, 2023, 8:13am UTC](https://discourse.slicer.org/t/how-can-i-transfer-my-custom-ultrasound-data-from-python-to-3dslicer-through-igt/27336 "2023-03-02T08:13:23Z")

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Hi, everyone. I am conducting an academic research and want to use 3DSlicer to reconstruct the ultrasound image from 2D to 3D. I only have offline ultrasound images (both DICOM and .png) and 6-DOF coordinate for each u…

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## [VMTK not found after download](https://discourse.slicer.org/t/vmtk-not-found-after-download/18661)

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**Author:** [@AshvinGupta](https://discourse.slicer.org/u/AshvinGupta)\
**Replies:** 6\
**Last updated:** [March 2, 2023, 6:28am UTC](https://discourse.slicer.org/t/vmtk-not-found-after-download/18661 "2023-03-02T06:28:58Z")

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Hello! After downloading the new preview version of Slicer every time I try to use the VMTK extension I get the same error message: “VMTK library is not found.” This is quite odd as when I go to extensions manager, it sa…

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## [Intensity normalization](https://discourse.slicer.org/t/intensity-normalization/28024)

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**Author:** [@Floren](https://discourse.slicer.org/u/Floren)\
**Replies:** 1\
**Last updated:** [March 2, 2023, 6:24am UTC](https://discourse.slicer.org/t/intensity-normalization/28024 "2023-03-02T06:24:48Z")

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Hello, everyone! I am working with prostate adc maps and trying to measure adc value for prostate tumors in order to demonstrate that there is a correlation between adc value and Gleason score. I understood that i must…

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## [How to calculate the surface area from 3D fetal MRI, then convert to Python](https://discourse.slicer.org/t/how-to-calculate-the-surface-area-from-3d-fetal-mri-then-convert-to-python/27586)

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**Author:** [@Jaleblanc](https://discourse.slicer.org/u/Jaleblanc)\
**Replies:** 31\
**Last updated:** [March 2, 2023, 1:40am UTC](https://discourse.slicer.org/t/how-to-calculate-the-surface-area-from-3d-fetal-mri-then-convert-to-python/27586 "2023-03-02T01:40:41Z")

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Hi all, I’m relatively new to both Python and 3D Slicer, but I am trying to calculate the surface area of the human placenta through 3D Slicer and then convert this into Python code for an automatic calculation of the p…

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## [Save MHA and segmentation into 1 tiff file](https://discourse.slicer.org/t/save-mha-and-segmentation-into-1-tiff-file/28117)

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**Author:** [@Wout\_De\_Wever](https://discourse.slicer.org/u/Wout_De_Wever)\
**Replies:** 1\
**Last updated:** [March 2, 2023, 12:12am UTC](https://discourse.slicer.org/t/save-mha-and-segmentation-into-1-tiff-file/28117 "2023-03-02T00:12:19Z")

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Can I somehow merge my scan with the segmentation I did into one tiff file? With the save option, I’m only able to save the files separately

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## [Python script crashes when running w/o GUI due to smoothing effect](https://discourse.slicer.org/t/python-script-crashes-when-running-w-o-gui-due-to-smoothing-effect/28118)

<div class="topic-metadata">

**Author:** [@Gholl](https://discourse.slicer.org/u/Gholl)\
**Replies:** 3\
**Last updated:** [March 1, 2023, 7:42pm UTC](https://discourse.slicer.org/t/python-script-crashes-when-running-w-o-gui-due-to-smoothing-effect/28118 "2023-03-01T19:42:56Z")

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I try to run a python script via the command ./Slicer --no-splash --no-main-window --python-script ‘customScript.py’. It crashes when executing the following line: segmentEditorWidget.setActiveEffectByName("Smoothing"),…

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## [DICOM data for 4D heart data](https://discourse.slicer.org/t/dicom-data-for-4d-heart-data/28122)

<div class="topic-metadata">

**Author:** [@alireza](https://discourse.slicer.org/u/alireza)\
**Replies:** 2\
**Last updated:** [March 1, 2023, 6:47pm UTC](https://discourse.slicer.org/t/dicom-data-for-4d-heart-data/28122 "2023-03-01T18:47:23Z")

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I’m looking for a 4D dicom data of heart. Slicer seems to have a nice one in the sample data (CT Cardio Sequence) that is inside the welcome message At Cornerstone3D, we have recently added support for 4D data rea…

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## [Extracting data from multiple JSON files.](https://discourse.slicer.org/t/extracting-data-from-multiple-json-files/28115)

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**Author:** [@Paul\_Rothwell](https://discourse.slicer.org/u/Paul_Rothwell)\
**Replies:** 2\
**Last updated:** [March 1, 2023, 6:24pm UTC](https://discourse.slicer.org/t/extracting-data-from-multiple-json-files/28115 "2023-03-01T18:24:57Z")

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I have multiple (14 to be exact) closed curve measurements for each scan (measurement of artery lumen). I ideally would like to extract the length, curvature mean, curvature max and area from each JSON file into excel. I…

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## [Creating DWI from siemens DTI data](https://discourse.slicer.org/t/creating-dwi-from-siemens-dti-data/28099)

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**Author:** [@Shabnam\_R](https://discourse.slicer.org/u/Shabnam_R)\
**Replies:** 6\
**Last updated:** [March 1, 2023, 4:21pm UTC](https://discourse.slicer.org/t/creating-dwi-from-siemens-dti-data/28099 "2023-03-01T16:21:23Z")

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Operating system: Windows 10, Core™ i7 Slicer version: 4.13 Expected behavior: I want to create the DWI from the DTI that I have from siemens scanner, But the files that I have is different from the one that I can find…

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## [segmentation mandible](https://discourse.slicer.org/t/segmentation-mandible/28083)

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**Author:** [@Daria\_999](https://discourse.slicer.org/u/Daria_999)\
**Replies:** 3\
**Last updated:** [March 1, 2023, 4:01pm UTC](https://discourse.slicer.org/t/segmentation-mandible/28083 "2023-03-01T16:01:40Z")

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Hello! Who can please teach me how to segment and apply CT? Like this

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## [Inability to export segmentations as RTStruct File](https://discourse.slicer.org/t/inability-to-export-segmentations-as-rtstruct-file/27745)

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**Author:** [@KSC\_IA](https://discourse.slicer.org/u/KSC_IA)\
**Replies:** 12\
**Last updated:** [March 1, 2023, 3:52am UTC](https://discourse.slicer.org/t/inability-to-export-segmentations-as-rtstruct-file/27745 "2023-03-01T03:52:21Z")

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Slicer Version: 5.2.1 (Stable Release) OS: MacOS Big Sur 11.7.3 (Intel i7) Expected Behaviour: ‘Export as DICOM’ in Export Data converts scene to DICOM files and segmentations to RT Structure file Actual Behaviour: DI…

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## [Linear transforms from SequenceRegistration module?](https://discourse.slicer.org/t/linear-transforms-from-sequenceregistration-module/28102)

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**Author:** [@mikebind](https://discourse.slicer.org/u/mikebind)\
**Replies:** 0\
**Last updated:** [March 1, 2023, 12:08am UTC](https://discourse.slicer.org/t/linear-transforms-from-sequenceregistration-module/28102 "2023-03-01T00:08:44Z")

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Is there a way to have the Sequence Registration module output linear transforms rather than grid transforms? I want to rigidly register a dynamic CT image sequence (to compensate for head turning motion) and SequenceRe…

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## [Ruler and angle measurement in 2D view](https://discourse.slicer.org/t/ruler-and-angle-measurement-in-2d-view/11931)

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**Author:** [@PaoloZaffino](https://discourse.slicer.org/u/PaoloZaffino)\
**Replies:** 4\
**Last updated:** [February 28, 2023, 3:30pm UTC](https://discourse.slicer.org/t/ruler-and-angle-measurement-in-2d-view/11931 "2023-02-28T15:30:03Z")

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Hi all, if I measure a length or an angle with Slicer I can read the value only in the 3D view. Is there any possibility to show it also in the 2D view? Thanks a lot, Paolo

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## [How to segment the tibia using TotalSegmentator?](https://discourse.slicer.org/t/how-to-segment-the-tibia-using-totalsegmentator/28065)

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**Author:** [@zhangliang](https://discourse.slicer.org/u/zhangliang)\
**Replies:** 3\
**Last updated:** [February 28, 2023, 2:04pm UTC](https://discourse.slicer.org/t/how-to-segment-the-tibia-using-totalsegmentator/28065 "2023-02-28T14:04:01Z")

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Hello, I can successfully install totalsegmentator. After trying, we couldn’t segment the tibia and surrounding soft tissue. I don’t know what the problem is.

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## [How can I extract voxel indices of points along a tubular segmentation obtained by Draw Tube?](https://discourse.slicer.org/t/how-can-i-extract-voxel-indices-of-points-along-a-tubular-segmentation-obtained-by-draw-tube/27580)

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**Author:** [@calici](https://discourse.slicer.org/u/calici)\
**Replies:** 2\
**Last updated:** [February 28, 2023, 2:13pm UTC](https://discourse.slicer.org/t/how-can-i-extract-voxel-indices-of-points-along-a-tubular-segmentation-obtained-by-draw-tube/27580 "2023-02-28T14:13:33Z")

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Hi everyone! I am trying to create synthetic Catheter insertion data. First I create synthetic catheter label inside CT via segmentation by Draw Tube as shown below: After that, I convert it to Binary Label Map. I…

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## [Stitcher extension to fuse two series loaded separately](https://discourse.slicer.org/t/stitcher-extension-to-fuse-two-series-loaded-separately/28092)

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**Author:** [@Elmahdy](https://discourse.slicer.org/u/Elmahdy)\
**Replies:** 0\
**Last updated:** [February 28, 2023, 2:13pm UTC](https://discourse.slicer.org/t/stitcher-extension-to-fuse-two-series-loaded-separately/28092 "2023-02-28T14:13:23Z")

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Hello everybody I am trying to stitch CT parts together (two different series to the same patient), unfortunately it does not work.

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## [Extract segment labelmap as 2D slices](https://discourse.slicer.org/t/extract-segment-labelmap-as-2d-slices/28087)

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**Author:** [@Marc-3d](https://discourse.slicer.org/u/Marc-3d)\
**Replies:** 0\
**Last updated:** [February 28, 2023, 9:17am UTC](https://discourse.slicer.org/t/extract-segment-labelmap-as-2d-slices/28087 "2023-02-28T09:17:35Z")

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Hi there, I intend to use 3D slicer to create annotations for training a Detectron2 model. I have found the examples for converting segmentations (labelmaps) into numpy arrays using the Python API. My data is 3D, and th…

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## [Segmenting an image into homogenous compartments](https://discourse.slicer.org/t/segmenting-an-image-into-homogenous-compartments/28051)

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**Author:** [@Zinoviy\_Weinstein](https://discourse.slicer.org/u/Zinoviy_Weinstein)\
**Replies:** 3\
**Last updated:** [February 28, 2023, 7:31am UTC](https://discourse.slicer.org/t/segmenting-an-image-into-homogenous-compartments/28051 "2023-02-28T07:31:04Z")

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Operating system: Ubuntu 22.04 Slicer version: 5.2.2 Hello All. I have an MRI scan that I need to segment into N homogenous compartments for later reconstruction. The challenge here is that it’s not whatever organ, a…

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## [Non-linear transformation is ignored in volume rendering](https://discourse.slicer.org/t/non-linear-transformation-is-ignored-in-volume-rendering/28082)

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**Author:** [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Replies:** 2\
**Last updated:** [February 28, 2023, 2:09am UTC](https://discourse.slicer.org/t/non-linear-transformation-is-ignored-in-volume-rendering/28082 "2023-02-28T02:09:39Z")

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the picture above shows the volume rendering and thresholding result in 3d window and 2d windows,in 2d windows the thresholding match the volume data , but in 3d window,they has a long distance,i don’t know that wrong…

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## [Win11 has problem with Slicer 5.2.1](https://discourse.slicer.org/t/win11-has-problem-with-slicer-5-2-1/27969)

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**Author:** [@jay1987](https://discourse.slicer.org/u/jay1987)\
**Replies:** 2\
**Last updated:** [February 28, 2023, 1:55am UTC](https://discourse.slicer.org/t/win11-has-problem-with-slicer-5-2-1/27969 "2023-02-28T01:55:37Z")

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i have download slicer5.2.1 install package and installed it into win11,the problem is below the screen is totaly white and can’t see any gui except the fist enter dialog ,the computer is a new computer, should i do…

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## [CaseIterator - how to input source data](https://discourse.slicer.org/t/caseiterator-how-to-input-source-data/28079)

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**Author:** [@ummmcam](https://discourse.slicer.org/u/ummmcam)\
**Replies:** 1\
**Last updated:** [February 27, 2023, 11:10pm UTC](https://discourse.slicer.org/t/caseiterator-how-to-input-source-data/28079 "2023-02-27T23:10:51Z")

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Can anyone help me figure out how to create a usable csv for caseiterator? I created a csv with the headers specified in the module. If I import the file into Slicer I can get it to show up in the table list. I added a …

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## [Energy layers in a scanning beam proton treatment plan viewed in SlicerRT](https://discourse.slicer.org/t/energy-layers-in-a-scanning-beam-proton-treatment-plan-viewed-in-slicerrt/27990)

<div class="topic-metadata">

**Author:** [@alema](https://discourse.slicer.org/u/alema)\
**Replies:** 4\
**Last updated:** [February 27, 2023, 5:23pm UTC](https://discourse.slicer.org/t/energy-layers-in-a-scanning-beam-proton-treatment-plan-viewed-in-slicerrt/27990 "2023-02-27T17:23:11Z")

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Hello, Is information about “energy layers” available in SlicerRT? In SlicerRT (version 1.0.0 running as an extension to 3D Slicer 5.2.1 on Linux), I see only one table (corresponding to one energy layer) with x and y p…

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## [Unit of radius an length in VMTK centerline computation](https://discourse.slicer.org/t/unit-of-radius-an-length-in-vmtk-centerline-computation/28072)

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**Author:** [@LeeaLee12345](https://discourse.slicer.org/u/LeeaLee12345)\
**Replies:** 0\
**Last updated:** [February 27, 2023, 9:43am UTC](https://discourse.slicer.org/t/unit-of-radius-an-length-in-vmtk-centerline-computation/28072 "2023-02-27T09:43:01Z")

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Dear all, I am using the VMTK extension to compute centerline and radius of the vessel along the centerline. I would like to ask if the unit of radius and length in this information is px? Thank you very much!

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