# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=150

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

**Page:** 151

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## [Save and import ROI for multiple MRI series](https://discourse.slicer.org/t/save-and-import-roi-for-multiple-mri-series/30814)

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**Author:** [@EduardVerheijen](https://discourse.slicer.org/u/EduardVerheijen)\
**Replies:** 0\
**Last updated:** [July 26, 2023, 8:16pm UTC](https://discourse.slicer.org/t/save-and-import-roi-for-multiple-mri-series/30814 "2023-07-26T20:16:42Z")

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Hi all, I am new to using 3D slicer. For a project I want to crop a 400x400 pixel ROI box from axial MRI scans and export them as DICOM. I managed to do it for one patient’s MRI series, but I need to have the exact same…

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## [VR headset with macOS](https://discourse.slicer.org/t/vr-headset-with-macos/27676)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 5\
**Last updated:** [July 25, 2023, 8:04pm UTC](https://discourse.slicer.org/t/vr-headset-with-macos/27676 "2023-07-25T20:04:06Z")

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I’m interested in buying a VR set to use with slicer3D on mac OS. if anyone would share his experience and recommendation id be very thankful thanks

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## [Problem with files from SlicerMorph in R](https://discourse.slicer.org/t/problem-with-files-from-slicermorph-in-r/30784)

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**Author:** [@Kajper](https://discourse.slicer.org/u/Kajper)\
**Replies:** 1\
**Last updated:** [July 25, 2023, 4:18pm UTC](https://discourse.slicer.org/t/problem-with-files-from-slicermorph-in-r/30784 "2023-07-25T16:18:22Z")

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Dear all, I have started to learn morphometic methods in biology recently. I was using SlicerMorph to place landmarks and samilandmarks on my segementated structures. I have a problem with geomorph (R pacage), I am tryi…

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## [.seg.nrrd file is not the same size as reference volume](https://discourse.slicer.org/t/seg-nrrd-file-is-not-the-same-size-as-reference-volume/30770)

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**Author:** [@Limin](https://discourse.slicer.org/u/Limin)\
**Replies:** 2\
**Last updated:** [July 25, 2023, 3:26pm UTC](https://discourse.slicer.org/t/seg-nrrd-file-is-not-the-same-size-as-reference-volume/30770 "2023-07-25T15:26:16Z")

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Dear all, I am using Slicer-4.11.20210226 on windows system. My segmentations (in seg.nrrd format) were created and linked to their reference volumes (in .nii format) automatically with a python script. The script ran f…

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## [Scripted Module: How to install and import tensorflow-cpu on M2 Mac](https://discourse.slicer.org/t/scripted-module-how-to-install-and-import-tensorflow-cpu-on-m2-mac/30771)

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**Author:** [@Geventh](https://discourse.slicer.org/u/Geventh)\
**Replies:** 2\
**Last updated:** [July 25, 2023, 1:38pm UTC](https://discourse.slicer.org/t/scripted-module-how-to-install-and-import-tensorflow-cpu-on-m2-mac/30771 "2023-07-25T13:38:52Z")

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Hey up until recently I used an Intel Mac and was able to import and use tensorflow and my first ever extension worked fine :slight\_smile: With the M2 Mac Slicer crashes when the module tries to install tensorflow by sl…

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## [OpgenIGTLinkIF: How to use BindMessages](https://discourse.slicer.org/t/opgenigtlinkif-how-to-use-bindmessages/6093)

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**Author:** [@mcfly3001](https://discourse.slicer.org/u/mcfly3001)\
**Replies:** 12\
**Last updated:** [July 25, 2023, 12:48pm UTC](https://discourse.slicer.org/t/opgenigtlinkif-how-to-use-bindmessages/6093 "2023-07-25T12:48:27Z")

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Hi everyone, I am trying to receive some data via OpenIGTLink with additional data added. For example I can already receive a vtkMRMLScalarVolumeNode but in this node I cannot include information about the patient (e.g.…

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## [Color scale for segmentations](https://discourse.slicer.org/t/color-scale-for-segmentations/30760)

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**Author:** [@lvdw](https://discourse.slicer.org/u/lvdw)\
**Replies:** 3\
**Last updated:** [July 25, 2023, 9:40am UTC](https://discourse.slicer.org/t/color-scale-for-segmentations/30760 "2023-07-25T09:40:04Z")

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Operating system: MacOS Slicer version: 5.2.2 I originally had two DICOM series of a CT head: one is the original scan and the second is a processed series that shows some kind of map of hypodensities. I could not make…

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## [\-/+ 3 sigma normalization](https://discourse.slicer.org/t/3-sigma-normalization/28947)

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**Author:** [@mahmood](https://discourse.slicer.org/u/mahmood)\
**Replies:** 3\
**Last updated:** [July 25, 2023, 5:54am UTC](https://discourse.slicer.org/t/3-sigma-normalization/28947 "2023-07-25T05:54:51Z")

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sorry I have a question. How can I apply -/+3 sigma normalization on my dicom files? Thanks

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## [Add full support for custom length units (e.g., microns instead of milimeters)](https://discourse.slicer.org/t/add-full-support-for-custom-length-units-e-g-microns-instead-of-milimeters/30764)

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**Author:** [@swilm](https://discourse.slicer.org/u/swilm)\
**Replies:** 1\
**Last updated:** [July 25, 2023, 5:14am UTC](https://discourse.slicer.org/t/add-full-support-for-custom-length-units-e-g-microns-instead-of-milimeters/30764 "2023-07-25T05:14:14Z")

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Hi I loaded in a nrrd file that was properly scaled and it is showing that the scale of the volume is correct, however when I add a scale bar it is in the wrong units. is there a way to change the units on the scale bar…

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## [tractography single color tract not multi-color tract](https://discourse.slicer.org/t/tractography-single-color-tract-not-multi-color-tract/29952)

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**Author:** [@GunnarE](https://discourse.slicer.org/u/GunnarE)\
**Replies:** 2\
**Last updated:** [July 24, 2023, 10:43pm UTC](https://discourse.slicer.org/t/tractography-single-color-tract-not-multi-color-tract/29952 "2023-07-24T22:43:20Z")

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Hi Slicer community, We have been following multiple tutorials from Dr. Sonia Pujol on diffusion tractography including “Exploring Peritumoral White Matter Fibers for Neurosurgical Planning”, “Diffusion MRI Analsyis”, a…

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## [Virtual reality - recommended equipment?](https://discourse.slicer.org/t/virtual-reality-recommended-equipment/30741)

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**Author:** [@eNable\_Polska](https://discourse.slicer.org/u/eNable_Polska)\
**Replies:** 2\
**Last updated:** [July 24, 2023, 8:05pm UTC](https://discourse.slicer.org/t/virtual-reality-recommended-equipment/30741 "2023-07-24T20:05:26Z")

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What kind of VR is best for Slicer? I tried using google cardboard, the effect is interesting but usability is poor. I’m looking for another solution, good and not too expensive :slight\_smile: Regards Krzysztof Grand…

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## [Renamed extension, but now there's a duplicate in the extensions manager](https://discourse.slicer.org/t/renamed-extension-but-now-theres-a-duplicate-in-the-extensions-manager/30747)

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**Author:** [@jmhuie](https://discourse.slicer.org/u/jmhuie)\
**Replies:** 4\
**Last updated:** [July 24, 2023, 3:48pm UTC](https://discourse.slicer.org/t/renamed-extension-but-now-theres-a-duplicate-in-the-extensions-manager/30747 "2023-07-24T15:48:32Z")

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I recently updated my extension formerly called “SegmentGeometry” and renamed it to “SlicerBiomech”. I updated the .s4ext file in the ExtensionsIndex in the main branch and the 5.2 branch. The change was successful for t…

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## [subregion analysis pyradiomics](https://discourse.slicer.org/t/subregion-analysis-pyradiomics/30758)

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**Author:** [@EdiKEM](https://discourse.slicer.org/u/EdiKEM)\
**Replies:** 0\
**Last updated:** [July 24, 2023, 11:42am UTC](https://discourse.slicer.org/t/subregion-analysis-pyradiomics/30758 "2023-07-24T11:42:57Z")

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Dear community, I have MRI dataset that has been outlined in clinical radiotherapy software to produce RTSS. I have converted the image and contours to NRRD format using the BatchStrutureSetConversion script. I am keen …

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## [Slicer Jupyter Kernel only listening to localhost(127.0.0.1)](https://discourse.slicer.org/t/slicer-jupyter-kernel-only-listening-to-localhost-127-0-0-1/30678)

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**Author:** [@Reshma](https://discourse.slicer.org/u/Reshma)\
**Replies:** 3\
**Last updated:** [July 24, 2023, 11:11am UTC](https://discourse.slicer.org/t/slicer-jupyter-kernel-only-listening-to-localhost-127-0-0-1/30678 "2023-07-24T11:11:40Z")

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I am using fedora linux and I have a 3D Slicer v5.2.2 installed. I am using the JupyterKernel extension and everything works fine locally. When I try to access the same outside from WAN, I am not able to access the jupyt…

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## [Error exporting and importing .vtk](https://discourse.slicer.org/t/error-exporting-and-importing-vtk/30733)

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**Author:** [@gches](https://discourse.slicer.org/u/gches)\
**Replies:** 5\
**Last updated:** [July 24, 2023, 4:12am UTC](https://discourse.slicer.org/t/error-exporting-and-importing-vtk/30733 "2023-07-24T04:12:05Z")

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Hello, I am trying to save the centerline of a model to .vtk. I receive no errors when exporting, however, when importing the centerline into 3D slicer, I receive an error. I received this error on both Slicer versions…

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## [Automation: conversion to .mhd](https://discourse.slicer.org/t/automation-conversion-to-mhd/30681)

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**Author:** [@SterArcher](https://discourse.slicer.org/u/SterArcher)\
**Replies:** 2\
**Last updated:** [July 23, 2023, 2:16pm UTC](https://discourse.slicer.org/t/automation-conversion-to-mhd/30681 "2023-07-23T14:16:59Z")

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Hi! I am using Slicer 3D daily to convert my files into .mhd. Is it possible to automate this, for python script to watch folder and automatically convert anything new to .mhd file? Best and thank you, Luka

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## [bug to calculate dice](https://discourse.slicer.org/t/bug-to-calculate-dice/30293)

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**Author:** [@steph85](https://discourse.slicer.org/u/steph85)\
**Replies:** 6\
**Last updated:** [July 23, 2023, 12:21pm UTC](https://discourse.slicer.org/t/bug-to-calculate-dice/30293 "2023-07-23T12:21:27Z")

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Hi, have you some problem to calculate a dice because for me it takes me too time.

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## [Slicer transformation result is different from my vtk codes](https://discourse.slicer.org/t/slicer-transformation-result-is-different-from-my-vtk-codes/30683)

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**Author:** [@dzzhang](https://discourse.slicer.org/u/dzzhang)\
**Replies:** 8\
**Last updated:** [July 23, 2023, 12:03am UTC](https://discourse.slicer.org/t/slicer-transformation-result-is-different-from-my-vtk-codes/30683 "2023-07-23T00:03:41Z")

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Recently I used the Transform module in Slicer to apply a linear transformation. Let’s say the translation is \[10, 20, 30\]. And the model moved to the correct position. However, when I used my own vtk codes below, the r…

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## [What should I do to activate the list?](https://discourse.slicer.org/t/what-should-i-do-to-activate-the-list/30740)

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**Author:** [@telomere](https://discourse.slicer.org/u/telomere)\
**Replies:** 1\
**Last updated:** [July 22, 2023, 2:17pm UTC](https://discourse.slicer.org/t/what-should-i-do-to-activate-the-list/30740 "2023-07-22T14:17:45Z")

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Hi, I want to move one model to the location of the other model using model registration in SlicerIGT module. But there’s no list in ‘Input fixed(dense) model’ and ‘input moving(sparse) model’. What should I do to m…

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## [4.11 Module panel is too wide and won't resize](https://discourse.slicer.org/t/4-11-module-panel-is-too-wide-and-wont-resize/11394)

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**Author:** [@Melodicpinpon](https://discourse.slicer.org/u/Melodicpinpon)\
**Replies:** 8\
**Last updated:** [July 20, 2023, 1:35pm UTC](https://discourse.slicer.org/t/4-11-module-panel-is-too-wide-and-wont-resize/11394 "2023-07-20T13:35:15Z")

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Hello, My 4.11 version keeps the module panel window at the same size, convering the 2/3 of my screen. I guess I should use the 4.10 instead…

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## [Distance between slices ](https://discourse.slicer.org/t/distance-between-slices/30730)

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**Author:** [@Lindee\_Wilson](https://discourse.slicer.org/u/Lindee_Wilson)\
**Replies:** 13\
**Last updated:** [July 22, 2023, 12:51am UTC](https://discourse.slicer.org/t/distance-between-slices/30730 "2023-07-22T00:51:11Z")

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Hi, I am currently segmenting something from a screenshot. Therefore, it is a 2D image. I am wanting to make it into a 2D surface mesh. I was told since 3D slicer will only export as 3D .stl files, to duplicate the segm…

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## [MONAILabel cannot connect: ConnectionRefusedError: \[WinError 10061\] No connection could be made because the target machine actively refused it](https://discourse.slicer.org/t/monailabel-cannot-connect-connectionrefusederror-winerror-10061-no-connection-could-be-made-because-the-target-machine-actively-refused-it/24021)

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**Author:** [@hourglassnam](https://discourse.slicer.org/u/hourglassnam)\
**Replies:** 20\
**Last updated:** [July 21, 2023, 8:46pm UTC](https://discourse.slicer.org/t/monailabel-cannot-connect-connectionrefusederror-winerror-10061-no-connection-could-be-made-because-the-target-machine-actively-refused-it/24021 "2023-07-21T20:46:24Z")

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Hello, I have tried running the MONAILabel module but keep getting a connection refused error. At first, I suspected the firewall to be the reason and allowed the slicer.exe app through the window firewall on the co…

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## [Fail to launch FiberTractMeasurements CLI module on Windows](https://discourse.slicer.org/t/fail-to-launch-fibertractmeasurements-cli-module-on-windows/30708)

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**Author:** [@Kening\_Zhang](https://discourse.slicer.org/u/Kening_Zhang)\
**Replies:** 3\
**Last updated:** [July 21, 2023, 2:58pm UTC](https://discourse.slicer.org/t/fail-to-launch-fibertractmeasurements-cli-module-on-windows/30708 "2023-07-21T14:58:30Z")

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Dear developers, When I type this command to use cli FiberTractMeasurements on my windows computer, some errors jumped, which says, can’t find xxx.dll, and cannot run the code, reinstalling the program may resolve …

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## [Muscle Fat Segmentation](https://discourse.slicer.org/t/muscle-fat-segmentation/30726)

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**Author:** [@jmathew](https://discourse.slicer.org/u/jmathew)\
**Replies:** 1\
**Last updated:** [July 21, 2023, 2:49pm UTC](https://discourse.slicer.org/t/muscle-fat-segmentation/30726 "2023-07-21T14:49:35Z")

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Hello, I am trying to separate fat and muscle on an MRI, and would like to be able to have a count of pixel/voxel of any muscle that I would outline. Currently I am measuring the CSA of various muscles on an Axial MRI. …

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## [Cannot open TopCon OCT (.fda) file on Slicer](https://discourse.slicer.org/t/cannot-open-topcon-oct-fda-file-on-slicer/30718)

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**Author:** [@mburaozkan.mz](https://discourse.slicer.org/u/mburaozkan.mz)\
**Replies:** 2\
**Last updated:** [July 21, 2023, 2:21pm UTC](https://discourse.slicer.org/t/cannot-open-topcon-oct-fda-file-on-slicer/30718 "2023-07-21T14:21:06Z")

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I am trying to open Topcon .fda file but I just can’t cause it gives me no error at all just: …/192784.fda - load failed Is there anything I need to do before upload the file? other than that I just followed the docu…

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## [About convert jpg to nrrd](https://discourse.slicer.org/t/about-convert-jpg-to-nrrd/30702)

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**Author:** [@Matt8268](https://discourse.slicer.org/u/Matt8268)\
**Replies:** 1\
**Last updated:** [July 21, 2023, 2:15pm UTC](https://discourse.slicer.org/t/about-convert-jpg-to-nrrd/30702 "2023-07-21T14:15:45Z")

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Dear PyRadiomics / 3DSlicer community, When importing JPEG images into 3D Slicer and converting them to the NRRD format, they may not be recognized by the Radiomics module. However, by converting them to a scalar volume…

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## [Segmenting ischemic stroke lesions based on ADC threshold](https://discourse.slicer.org/t/segmenting-ischemic-stroke-lesions-based-on-adc-threshold/30680)

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**Author:** [@lvdw](https://discourse.slicer.org/u/lvdw)\
**Replies:** 1\
**Last updated:** [July 21, 2023, 2:13pm UTC](https://discourse.slicer.org/t/segmenting-ischemic-stroke-lesions-based-on-adc-threshold/30680 "2023-07-21T14:13:40Z")

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Operating system: MacOS Slicer version: 5,2,2 I’m not sure if this issue isn’t solved elsewhere but I couldn’t find it. I’m rather new to Slicer. I would like to segment ischemic strokes based on sb1000 and ADC, but I …

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## [Rotating and resampling volumes with Python](https://discourse.slicer.org/t/rotating-and-resampling-volumes-with-python/9089)

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**Author:** [@Prashant\_Pandey](https://discourse.slicer.org/u/Prashant_Pandey)\
**Replies:** 3\
**Last updated:** [July 21, 2023, 2:02pm UTC](https://discourse.slicer.org/t/rotating-and-resampling-volumes-with-python/9089 "2023-07-21T14:02:42Z")

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I’ve written a very simple python scrited module which sums a CT image’s along one of the 3 given axes to create a DRR-like image. However I want to extend this module to sum along an abitrary axis through the image inst…

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## [Measure image intensity profile along markups curve](https://discourse.slicer.org/t/measure-image-intensity-profile-along-markups-curve/10663)

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**Author:** [@kmalexander](https://discourse.slicer.org/u/kmalexander)\
**Replies:** 6\
**Last updated:** [July 20, 2023, 10:22pm UTC](https://discourse.slicer.org/t/measure-image-intensity-profile-along-markups-curve/10663 "2023-07-20T22:22:34Z")

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I’m looking to get a curved line profile from a volume, however it seems that the Line Profile tool does not work when using a MarkupsCurve input line - only the MarkupsLine works. When a MarkupsCurve input line is sele…

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## [How to slice along a curve and display it in 2D view in real time](https://discourse.slicer.org/t/how-to-slice-along-a-curve-and-display-it-in-2d-view-in-real-time/30711)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [July 20, 2023, 7:42pm UTC](https://discourse.slicer.org/t/how-to-slice-along-a-curve-and-display-it-in-2d-view-in-real-time/30711 "2023-07-20T19:42:42Z")

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In the video, I need to constantly rotate the yellow line to make sure that the yellow line is basically perpendicular to the curve, and then I can see the result I want in the sagittal view. Is there any way to automat…

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