# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=109

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

**Page:** 110

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## [Slicer caught an application error](https://discourse.slicer.org/t/slicer-caught-an-application-error/34672)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 3\
**Last updated:** [March 6, 2024, 12:18pm UTC](https://discourse.slicer.org/t/slicer-caught-an-application-error/34672 "2024-03-06T12:18:30Z")

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I am working these two files: https://raw.githubusercontent.com/SlicerMorph/SampleData/master/IMPC\_sample\_data.nrrd and its segmentation https://raw.githubusercontent.com/SlicerMorph/MD/main/IMPC\_sample\_data.seg.nrrd …

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## [Reslice the volume with plane positioned by several reference points](https://discourse.slicer.org/t/reslice-the-volume-with-plane-positioned-by-several-reference-points/34559)

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**Author:** [@UH\_Cho](https://discourse.slicer.org/u/UH_Cho)\
**Replies:** 4\
**Last updated:** [March 6, 2024, 8:32am UTC](https://discourse.slicer.org/t/reslice-the-volume-with-plane-positioned-by-several-reference-points/34559 "2024-03-06T08:32:40Z")

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Is it possible to set several reference points on the volume to form a specific plane, use that plane to reorient the volume, and then reslice and export the result? I am an orthodontist researching the cranio-maxillofa…

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## [UKF exit abnormally](https://discourse.slicer.org/t/ukf-exit-abnormally/34734)

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**Author:** [@Pranali](https://discourse.slicer.org/u/Pranali)\
**Replies:** 0\
**Last updated:** [March 6, 2024, 7:40am UTC](https://discourse.slicer.org/t/ukf-exit-abnormally/34734 "2024-03-06T07:40:20Z")

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Hello, I’m using ubuntu 20.04 , i ran following command with error: ./Slicer --launch UKFTractography --dwiFile /home/inspire\_lab/Downloads/IXI-DATA-nrrd/combine\_conform\_IXI034-HH-1260.nrrd --maskFile /home/inspire\_lab/…

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## [Problem with 3D Slicer start](https://discourse.slicer.org/t/problem-with-3d-slicer-start/34419)

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**Author:** [@soukup.la](https://discourse.slicer.org/u/soukup.la)\
**Replies:** 2\
**Last updated:** [March 6, 2024, 7:38am UTC](https://discourse.slicer.org/t/problem-with-3d-slicer-start/34419 "2024-03-06T07:38:46Z")

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Hello, I am not able to start the Slicer app. It is on Ubuntu 22.04 with these errors in the terminal: Switch to module: “Welcome” QOpenGLWidget: Failed to create context QOpenGLWidget: Failed to create context QOp…

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## [Can we check and rescale pixel intensity values in Slicer?](https://discourse.slicer.org/t/can-we-check-and-rescale-pixel-intensity-values-in-slicer/34709)

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**Author:** [@Windy](https://discourse.slicer.org/u/Windy)\
**Replies:** 5\
**Last updated:** [March 6, 2024, 2:10am UTC](https://discourse.slicer.org/t/can-we-check-and-rescale-pixel-intensity-values-in-slicer/34709 "2024-03-06T02:10:10Z")

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I have a few Micro CT datasets. When I check in Python, I can see some intensity values are between 0 and 255 while some are like between 54 and 223. Since I am working with a machine learning model, I want all of them t…

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## [Unable to open SEG Modality file](https://discourse.slicer.org/t/unable-to-open-seg-modality-file/19881)

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**Author:** [@kaushikdasroy](https://discourse.slicer.org/u/kaushikdasroy)\
**Replies:** 9\
**Last updated:** [March 6, 2024, 12:11am UTC](https://discourse.slicer.org/t/unable-to-open-seg-modality-file/19881 "2024-03-06T00:11:49Z")

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Operating system: Windows 10 Pro Slicer version: 4.11.20210226 r29738 / 7a593c8 Expected behavior: Open the segmentation file Actual behavior: Error message I am trying to open a DICOM SEG file in the slicer and gett…

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## [Bone thickness heatmap along a perpendicular vectors](https://discourse.slicer.org/t/bone-thickness-heatmap-along-a-perpendicular-vectors/34729)

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**Author:** [@coLee](https://discourse.slicer.org/u/coLee)\
**Replies:** 0\
**Last updated:** [March 5, 2024, 11:01pm UTC](https://discourse.slicer.org/t/bone-thickness-heatmap-along-a-perpendicular-vectors/34729 "2024-03-05T23:01:08Z")

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I am trying to create a thickness heatmap model of a segmented pelvis for preop planning of THA. The goal would be to create a heatmap showing the thickness where a screw could be placed. For this I figure I would need s…

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## [Paths under Slicer python](https://discourse.slicer.org/t/paths-under-slicer-python/34671)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 7\
**Last updated:** [March 5, 2024, 10:10pm UTC](https://discourse.slicer.org/t/paths-under-slicer-python/34671 "2024-03-05T22:10:47Z")

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Why does the first segmentation load fail, even though the file is clearly found? Do files always have to be referred with their full path? \>\>\> os.getcwd() '/Users/amaga' \>\>\> os.path.isfile("MD/"+segmentation) True \>\>\> …

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## [How to measure the CT number (HU) from all image series?](https://discourse.slicer.org/t/how-to-measure-the-ct-number-hu-from-all-image-series/34722)

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**Author:** [@siksincs](https://discourse.slicer.org/u/siksincs)\
**Replies:** 0\
**Last updated:** [March 5, 2024, 8:24pm UTC](https://discourse.slicer.org/t/how-to-measure-the-ct-number-hu-from-all-image-series/34722 "2024-03-05T20:24:42Z")

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After I used ‘segment cross-section area’ to measure the area (mm^2) from each slice, how can I measure the CT number from each slice?

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## [Convert .mhd dose volume to RTDose file and export](https://discourse.slicer.org/t/convert-mhd-dose-volume-to-rtdose-file-and-export/15696)

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**Author:** [@p4perz](https://discourse.slicer.org/u/p4perz)\
**Replies:** 2\
**Last updated:** [March 4, 2024, 11:07pm UTC](https://discourse.slicer.org/t/convert-mhd-dose-volume-to-rtdose-file-and-export/15696 "2024-03-04T23:07:09Z")

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The output of my Monte Carlo simulations for the dose distributions are multiple .mha dose volumes. I would aim to compare them to other dose distributions and overlap them with CT DICOMs. There are many tools availabl…

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## [I want to set the IJK to RAS direction matrix for all my scans I upload. ](https://discourse.slicer.org/t/i-want-to-set-the-ijk-to-ras-direction-matrix-for-all-my-scans-i-upload/34696)

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**Author:** [@Bartdh](https://discourse.slicer.org/u/Bartdh)\
**Replies:** 1\
**Last updated:** [March 4, 2024, 8:27pm UTC](https://discourse.slicer.org/t/i-want-to-set-the-ijk-to-ras-direction-matrix-for-all-my-scans-i-upload/34696 "2024-03-04T20:27:14Z")

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I want to set the IJK to RAS direction matrix for all my scans I upload. The current matrix gives me a mirrored volume after segmentation. I believe the “IJK to RAS direction matrix” should be (1 0 0, 0 1 0, 0 0 1). How …

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## [While running segment app in slicer, showing wrong url](https://discourse.slicer.org/t/while-running-segment-app-in-slicer-showing-wrong-url/34703)

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**Author:** [@Ajay\_Kumar](https://discourse.slicer.org/u/Ajay_Kumar)\
**Replies:** 1\
**Last updated:** [March 4, 2024, 7:18pm UTC](https://discourse.slicer.org/t/while-running-segment-app-in-slicer-showing-wrong-url/34703 "2024-03-04T19:18:46Z")

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\--------After downloading this below dataset monailabel datasets --download --name Task07\_Pancreas --output . ------and after runnig below the command to run the app monailabel start\_server --app apps/radiology --stud…

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## [paint tool can't not used properly](https://discourse.slicer.org/t/paint-tool-cant-not-used-properly/34698)

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**Author:** [@yujunlin](https://discourse.slicer.org/u/yujunlin)\
**Replies:** 1\
**Last updated:** [March 4, 2024, 5:03pm UTC](https://discourse.slicer.org/t/paint-tool-cant-not-used-properly/34698 "2024-03-04T17:03:13Z")

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Problem: I am trying to edit an CT using the segment editor and the paint feature in the editor. But when I go to paint, I can’t paint my wanted content on image. no trace was showed in the image. it can’t allowed me to …

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## [Show segmentation in 3d only](https://discourse.slicer.org/t/show-segmentation-in-3d-only/34597)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 5\
**Last updated:** [March 4, 2024, 2:53pm UTC](https://discourse.slicer.org/t/show-segmentation-in-3d-only/34597 "2024-03-04T14:53:17Z")

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Is it posssible to Show segmentation in 3d only . I like to screenshot a view showing slices ( no segmentation ) and 3d segmentation . Thanks

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## [ITK library FactoryRegistration not found](https://discourse.slicer.org/t/itk-library-factoryregistration-not-found/34685)

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**Author:** [@Pranali](https://discourse.slicer.org/u/Pranali)\
**Replies:** 1\
**Last updated:** [March 4, 2024, 1:44pm UTC](https://discourse.slicer.org/t/itk-library-factoryregistration-not-found/34685 "2024-03-04T13:44:41Z")

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Hi, I’m trying to convert 200 Nifti volumes to Nrrd using Python script for DWI Convert. I’m getting the following error “while loading shared libraries: libITKFactoryRegistration.so: cannot open shared object file: No s…

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## [The ROI doesn't work in Film Dosimetry](https://discourse.slicer.org/t/the-roi-doesnt-work-in-film-dosimetry/34669)

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**Author:** [@Erfan\_Mollai](https://discourse.slicer.org/u/Erfan_Mollai)\
**Replies:** 1\
**Last updated:** [March 4, 2024, 1:11pm UTC](https://discourse.slicer.org/t/the-roi-doesnt-work-in-film-dosimetry/34669 "2024-03-04T13:11:50Z")

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The ROI key in “perform calibration” in dosimetry analysis didn’t work :frowning: what should i do please help me

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## [Issues with smoothening effect for all visible segments](https://discourse.slicer.org/t/issues-with-smoothening-effect-for-all-visible-segments/34688)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 0\
**Last updated:** [March 4, 2024, 9:53am UTC](https://discourse.slicer.org/t/issues-with-smoothening-effect-for-all-visible-segments/34688 "2024-03-04T09:53:07Z")

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im trying to median smooth segments with all visible segments selected. however upon smoothening. one segment gets replaced by another as in the pic. It is not a big deal issue just wanted to report it

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## [Python script for Diffusion module](https://discourse.slicer.org/t/python-script-for-diffusion-module/34683)

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**Author:** [@Pranali](https://discourse.slicer.org/u/Pranali)\
**Replies:** 0\
**Last updated:** [March 4, 2024, 5:21am UTC](https://discourse.slicer.org/t/python-script-for-diffusion-module/34683 "2024-03-04T05:21:45Z")

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I want to convert 200 Nifti files to .nrrd using Python script in 3dslicer(DWI Convert). And the followed by UKF TRactography.can someone let me know if is there an automated way to do this?

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## [Volumetric measurement of the root canal space before and after root canal treatment](https://discourse.slicer.org/t/volumetric-measurement-of-the-root-canal-space-before-and-after-root-canal-treatment/34681)

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**Author:** [@Jacek\_S](https://discourse.slicer.org/u/Jacek_S)\
**Replies:** 0\
**Last updated:** [March 4, 2024, 2:38am UTC](https://discourse.slicer.org/t/volumetric-measurement-of-the-root-canal-space-before-and-after-root-canal-treatment/34681 "2024-03-04T02:38:49Z")

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Operating system: MacOS 14.3.1 Slicer version:5.6.1 Expected behavior: defined volume of root canal space Actual behavior: sliced model of the tooth , but no separation for pulp space Hi everyone, I am very new to t…

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## [Markups plane: placement process is confusing](https://discourse.slicer.org/t/markups-plane-placement-process-is-confusing/34675)

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**Author:** [@chir.set](https://discourse.slicer.org/u/chir.set)\
**Replies:** 1\
**Last updated:** [March 3, 2024, 7:50pm UTC](https://discourse.slicer.org/t/markups-plane-placement-process-is-confusing/34675 "2024-03-03T19:50:05Z")

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I’m using 5.7.0-2024-02-29 r32739 / c7fe865 from your repository on Linux. When placing a markups plane, the mouse cursor remains in placement mode. Clicking in a slice view creates a second plane and releases the mouse …

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## [Get histograms multiple single images.](https://discourse.slicer.org/t/get-histograms-multiple-single-images/34670)

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**Author:** [@Fabio](https://discourse.slicer.org/u/Fabio)\
**Replies:** 0\
**Last updated:** [March 3, 2024, 3:19am UTC](https://discourse.slicer.org/t/get-histograms-multiple-single-images/34670 "2024-03-03T03:19:10Z")

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Hi, I have hundreds of dicom images which I am looking to get their individual histograms and getting all the results (for every image) in a single file. Is it possible? Thaks for your help.

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## [SPHARM-PDM runtime](https://discourse.slicer.org/t/spharm-pdm-runtime/34666)

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**Author:** [@samia](https://discourse.slicer.org/u/samia)\
**Replies:** 0\
**Last updated:** [March 3, 2024, 3:16am UTC](https://discourse.slicer.org/t/spharm-pdm-runtime/34666 "2024-03-03T03:16:45Z")

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Hello , i’m using SPHARM-PDM module in slicerSalt to represent the tooth using spherical harmonics but the run time for the parametrization part is taking to much time (one hour and sometimes more ) for only one tooth. I…

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## [Free VTK Courses?](https://discourse.slicer.org/t/free-vtk-courses/34650)

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**Author:** [@kiki](https://discourse.slicer.org/u/kiki)\
**Replies:** 2\
**Last updated:** [March 2, 2024, 7:08am UTC](https://discourse.slicer.org/t/free-vtk-courses/34650 "2024-03-02T07:08:12Z")

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Hello everyone, i want to learn VTK in C++ but i found mostly outdated tutorial videos on the internet. Are there any free courses available for this? I am a student and due to my some financial issues it is not possib…

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## [Segmenting GE Voluson ultrasound image](https://discourse.slicer.org/t/segmenting-ge-voluson-ultrasound-image/13971)

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**Author:** [@Davide](https://discourse.slicer.org/u/Davide)\
**Replies:** 5\
**Last updated:** [March 2, 2024, 1:48am UTC](https://discourse.slicer.org/t/segmenting-ge-voluson-ultrasound-image/13971 "2024-03-02T01:48:02Z")

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I have loaded a dicom file from a GE Voluson S8 but Im not able to segment the volume. Any suggestion?

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## [str-converted file to labelmap is erroneous](https://discourse.slicer.org/t/str-converted-file-to-labelmap-is-erroneous/34618)

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**Author:** [@richyrich](https://discourse.slicer.org/u/richyrich)\
**Replies:** 3\
**Last updated:** [March 1, 2024, 2:45pm UTC](https://discourse.slicer.org/t/str-converted-file-to-labelmap-is-erroneous/34618 "2024-03-01T14:45:11Z")

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Hi, I have a geometry created by a CFD-solver (StarCCM+). I exported the surface geometry as an .stl file, and then converted it to labelmap (as recommended in the forums). I am getting this weird segmentation below t…

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## [Get the MRML ID of the volume being viewed through a python script](https://discourse.slicer.org/t/get-the-mrml-id-of-the-volume-being-viewed-through-a-python-script/34620)

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**Author:** [@petit223](https://discourse.slicer.org/u/petit223)\
**Replies:** 3\
**Last updated:** [March 1, 2024, 2:21pm UTC](https://discourse.slicer.org/t/get-the-mrml-id-of-the-volume-being-viewed-through-a-python-script/34620 "2024-03-01T14:21:54Z")

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I want to get the MRML ID of the volume being viewed on the interface through a python script For example, now I want to get the MRML ID of “20005: Screen Save” through python code, which is ‘vtkMRMLScalarVolumeNode1…

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## [How to access center view in the 3dwidget using code without pressing the center view option?](https://discourse.slicer.org/t/how-to-access-center-view-in-the-3dwidget-using-code-without-pressing-the-center-view-option/34643)

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**Author:** [@ebin1234](https://discourse.slicer.org/u/ebin1234)\
**Replies:** 4\
**Last updated:** [March 1, 2024, 12:59pm UTC](https://discourse.slicer.org/t/how-to-access-center-view-in-the-3dwidget-using-code-without-pressing-the-center-view-option/34643 "2024-03-01T12:59:45Z")

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How to access center view in the 3dwidget using code without pressing the center view option?.

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## [3d lung vessels](https://discourse.slicer.org/t/3d-lung-vessels/34642)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 0\
**Last updated:** [March 1, 2024, 10:26am UTC](https://discourse.slicer.org/t/3d-lung-vessels/34642 "2024-03-01T10:26:36Z")

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i create lung vessels model but i want to boundary for my model like that image i upload can you please help me . and this is my model i want this model like above on boundary around vessels.

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## [3d lung vessels printing error](https://discourse.slicer.org/t/3d-lung-vessels-printing-error/34637)

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**Author:** [@Vikram](https://discourse.slicer.org/u/Vikram)\
**Replies:** 0\
**Last updated:** [March 1, 2024, 7:04am UTC](https://discourse.slicer.org/t/3d-lung-vessels-printing-error/34637 "2024-03-01T07:04:09Z")

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HI hope all are you doing best , i create 3d lung vessels model by using 3d slicer but the issue is vessels are not connecting to each other , when i print model require support on 3d printer due to not connecting vesse…

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## [Saving/Loading errors - help please](https://discourse.slicer.org/t/saving-loading-errors-help-please/34576)

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**Author:** [@willm1123](https://discourse.slicer.org/u/willm1123)\
**Replies:** 4\
**Last updated:** [February 29, 2024, 10:36pm UTC](https://discourse.slicer.org/t/saving-loading-errors-help-please/34576 "2024-02-29T22:36:00Z")

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Hey y’all, I am an undergraduate student new to the Slicer program. I have been working on continuing a manual segmentation of some CT scan data that was started by another student last semester. After my first day of wo…

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