# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=285

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

**Page:** 286

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## [Crop volume broken in Linux](https://discourse.slicer.org/t/crop-volume-broken-in-linux/17228)

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**Author:** [@manjula](https://discourse.slicer.org/u/manjula)\
**Replies:** 5\
**Last updated:** [April 22, 2021, 12:58pm UTC](https://discourse.slicer.org/t/crop-volume-broken-in-linux/17228 "2021-04-22T12:58:40Z")

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Slicer version - 4.13.0-2021-04-03 r29809 / 057dea2 and 4.13.0-2021-04-18 r29854 OS - Linux - Garuda Linux The crop volume seems to not work and I just tried the latest preview release as well and there also it is not …

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## [Depth map of 3D environment](https://discourse.slicer.org/t/depth-map-of-3d-environment/17238)

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**Author:** [@ifried01](https://discourse.slicer.org/u/ifried01)\
**Replies:** 2\
**Last updated:** [April 21, 2021, 8:56pm UTC](https://discourse.slicer.org/t/depth-map-of-3d-environment/17238 "2021-04-21T20:56:09Z")

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Hi All, Is it possible to generate a depth map of the 3D environment in Slicer? I have looked around a bit and don’t believe this exists. Thanks!

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## [I downloaded SlicerIGT to run LumpNav but it I cannot open slicelets](https://discourse.slicer.org/t/i-downloaded-slicerigt-to-run-lumpnav-but-it-i-cannot-open-slicelets/17237)

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**Author:** [@will\_kim](https://discourse.slicer.org/u/will_kim)\
**Replies:** 1\
**Last updated:** [April 21, 2021, 7:22pm UTC](https://discourse.slicer.org/t/i-downloaded-slicerigt-to-run-lumpnav-but-it-i-cannot-open-slicelets/17237 "2021-04-21T19:22:41Z")

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I am getting an error and cannot seem to open LumpNav slicelets even after I installed the SlicerIGT. It says could not find the Plus Remote module and I cannot find it within the SlicerIGT. How should I resolve this pro…

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## [Help with orientation marker and ruler](https://discourse.slicer.org/t/help-with-orientation-marker-and-ruler/13454)

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**Author:** [@rohan\_n](https://discourse.slicer.org/u/rohan_n)\
**Replies:** 25\
**Last updated:** [April 21, 2021, 7:55pm UTC](https://discourse.slicer.org/t/help-with-orientation-marker-and-ruler/13454 "2021-04-21T19:55:56Z")

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Hello, I need help with the following. Is there a line of Python code that I can add to my scripted module to make the Axes Orientation Marker show up on the red and yellow slices automatically, without navigating to…

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## [CT to optical image registration](https://discourse.slicer.org/t/ct-to-optical-image-registration/514)

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**Author:** [@Niousha\_Aflatouni](https://discourse.slicer.org/u/Niousha_Aflatouni)\
**Replies:** 22\
**Last updated:** [April 21, 2021, 6:37pm UTC](https://discourse.slicer.org/t/ct-to-optical-image-registration/514 "2021-04-21T18:37:46Z")

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Hi there, I have 2 image sets: one is a high resolution CT from a small specimen with 0.15, 0.15, 0.15 millimeter spacing in each of the X, Y and Z axis, the other one is an optical stack of the same specimen taken usi…

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## [Screen capture problem with FFmpeg version](https://discourse.slicer.org/t/screen-capture-problem-with-ffmpeg-version/17234)

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**Author:** [@HodaGH](https://discourse.slicer.org/u/HodaGH)\
**Replies:** 0\
**Last updated:** [April 21, 2021, 5:49pm UTC](https://discourse.slicer.org/t/screen-capture-problem-with-ffmpeg-version/17234 "2021-04-21T17:49:58Z")

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Hi all, I want to use screen capture to make a video of fading between my fixed and registered images but before that I get an error while installing FFmpeg. I’m on MacOS Mojave and I installed FFmpeg with : brew instal…

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## [Issue on Slicer UI in Windows10 - green stripes](https://discourse.slicer.org/t/issue-on-slicer-ui-in-windows10-green-stripes/17232)

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**Author:** [@om-ganesh](https://discourse.slicer.org/u/om-ganesh)\
**Replies:** 1\
**Last updated:** [April 21, 2021, 4:51pm UTC](https://discourse.slicer.org/t/issue-on-slicer-ui-in-windows10-green-stripes/17232 "2021-04-21T16:51:23Z")

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I am not able to load the Slicer3D in Windows10. I am having the weird UI issues as shown in snapshot. I tried fresh installation with both versions 4.10.2 and the latest stable 4.11.2. Any community members have this…

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## [How to export segmentation as masks (.jpgs?)](https://discourse.slicer.org/t/how-to-export-segmentation-as-masks-jpgs/5656)

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**Author:** [@Arcsecond](https://discourse.slicer.org/u/Arcsecond)\
**Replies:** 12\
**Last updated:** [April 21, 2021, 4:49pm UTC](https://discourse.slicer.org/t/how-to-export-segmentation-as-masks-jpgs/5656 "2021-04-21T16:49:00Z")

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Operating system: Linux Slicer version: 4.10.1 I have as input DICOM files and I want to export the segmentations on those files in the form of a mask. The intended use is to load the masks into a numpy array for furth…

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## [Merge multiple models while preserving the internal cavity](https://discourse.slicer.org/t/merge-multiple-models-while-preserving-the-internal-cavity/17203)

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**Author:** [@lazymark2](https://discourse.slicer.org/u/lazymark2)\
**Replies:** 2\
**Last updated:** [April 21, 2021, 4:18pm UTC](https://discourse.slicer.org/t/merge-multiple-models-while-preserving-the-internal-cavity/17203 "2021-04-21T16:18:49Z")

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Hi everyone, new to slicer 3D here. Recently I want to prepare a mandible model for 3D printing. Now I have a mandibular dentition model with root canal system existed as internal cavity (hollow): and a mandible mo…

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## [Bulild 3D Slicer - step: python failed](https://discourse.slicer.org/t/bulild-3d-slicer-step-python-failed/17224)

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**Author:** [@wlixism](https://discourse.slicer.org/u/wlixism)\
**Replies:** 0\
**Last updated:** [April 21, 2021, 2:50pm UTC](https://discourse.slicer.org/t/bulild-3d-slicer-step-python-failed/17224 "2021-04-21T14:50:56Z")

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Dear all, I was asked to create a 3D slicer module at work. I ran cmake according to the build instructions, but I got some errors in python step. I guess the cause was that my env PYTHONHOME was used. In that case, …

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## [How does 3dslicer read external marker coordinates](https://discourse.slicer.org/t/how-does-3dslicer-read-external-marker-coordinates/17192)

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**Author:** [@wujie](https://discourse.slicer.org/u/wujie)\
**Replies:** 3\
**Last updated:** [April 21, 2021, 2:22pm UTC](https://discourse.slicer.org/t/how-does-3dslicer-read-external-marker-coordinates/17192 "2021-04-21T14:22:53Z")

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How does 3dslicer read external marker coordinates

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## [Scaling slider for LinearTransform](https://discourse.slicer.org/t/scaling-slider-for-lineartransform/17204)

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**Author:** [@FriedrichKretschmer](https://discourse.slicer.org/u/FriedrichKretschmer)\
**Replies:** 3\
**Last updated:** [April 21, 2021, 12:27pm UTC](https://discourse.slicer.org/t/scaling-slider-for-lineartransform/17204 "2021-04-21T12:27:40Z")

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Dear community, I am trying to register multiple 2D in-situ images to a 3D CT brain scan. For this purpose I do an initial coarse alignment by a manual linear transform. In a second step I apply landmark registration. I…

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## [Only part of segmention is visible when I load the segmentation first time](https://discourse.slicer.org/t/only-part-of-segmention-is-visible-when-i-load-the-segmentation-first-time/17218)

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**Author:** [@Ge\_Tang](https://discourse.slicer.org/u/Ge_Tang)\
**Replies:** 1\
**Last updated:** [April 21, 2021, 10:36am UTC](https://discourse.slicer.org/t/only-part-of-segmention-is-visible-when-i-load-the-segmentation-first-time/17218 "2021-04-21T10:36:53Z")

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Operating system:Windows 10 Slicer version:4.11 Expected behavior: All the segmentation should be visible Hi, all, I changed my script to have some logging information during looping over all the subjects. After this…

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## [Module executable file](https://discourse.slicer.org/t/module-executable-file/17128)

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**Author:** [@marianaslicer](https://discourse.slicer.org/u/marianaslicer)\
**Replies:** 11\
**Last updated:** [April 21, 2021, 9:34am UTC](https://discourse.slicer.org/t/module-executable-file/17128 "2021-04-21T09:34:39Z")

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Hi everyone, I developed a python scriped module using the Extension Wizard module in 3D Slicer (4.13.0) which takes as inputs the PatientID and a 3D volume. The module is running when the user clicks on the “Run” butto…

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## [How to Calculate/appear Bq/ml using 3D Slicer](https://discourse.slicer.org/t/how-to-calculate-appear-bq-ml-using-3d-slicer/16884)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 4\
**Last updated:** [April 20, 2021, 10:28pm UTC](https://discourse.slicer.org/t/how-to-calculate-appear-bq-ml-using-3d-slicer/16884 "2021-04-20T22:28:58Z")

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Operating system: windows Slicer version: 4.11 Expected behavior: Actual behavior: Anyone knows how to calculate the Bq/ml using a 3D Slicer? Just now only can calculate SUV max, SUV min, SUV mean.

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## [Installation Error](https://discourse.slicer.org/t/installation-error/17205)

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**Author:** [@Shalini](https://discourse.slicer.org/u/Shalini)\
**Replies:** 1\
**Last updated:** [April 20, 2021, 8:17pm UTC](https://discourse.slicer.org/t/installation-error/17205 "2021-04-20T20:17:13Z")

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Hello , I have installed 3D Slicer on Linux but unable to find Radiomics in Extension manager.

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## [Pip installing and using nipype](https://discourse.slicer.org/t/pip-installing-and-using-nipype/17215)

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**Author:** [@mangotee](https://discourse.slicer.org/u/mangotee)\
**Replies:** 1\
**Last updated:** [April 20, 2021, 8:06pm UTC](https://discourse.slicer.org/t/pip-installing-and-using-nipype/17215 "2021-04-20T20:06:53Z")

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Hi, I’m trying to install and use nipype inside Slicer. I can install via pip\_install('nipype') However, when I try to import nipype, I get the following error message(s): Traceback (most recent call last): File "\<c…

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## [Edited segmentation mask has different transformation matrix to original segmentation](https://discourse.slicer.org/t/edited-segmentation-mask-has-different-transformation-matrix-to-original-segmentation/17154)

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**Author:** [@yizhwan](https://discourse.slicer.org/u/yizhwan)\
**Replies:** 2\
**Last updated:** [April 20, 2021, 2:39pm UTC](https://discourse.slicer.org/t/edited-segmentation-mask-has-different-transformation-matrix-to-original-segmentation/17154 "2021-04-20T14:39:37Z")

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Hi all, I have a segmentation (brain tumour) derived from a deep learning pipeline. It shares the same transformation matrix as the T1/T2/FLAIR scans for the subject. I imported the segmentation into Slicer as a label …

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## [Cannot load large Ultrasound DICOM file](https://discourse.slicer.org/t/cannot-load-large-ultrasound-dicom-file/17194)

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**Author:** [@ZHENZC](https://discourse.slicer.org/u/ZHENZC)\
**Replies:** 3\
**Last updated:** [April 20, 2021, 12:57pm UTC](https://discourse.slicer.org/t/cannot-load-large-ultrasound-dicom-file/17194 "2021-04-20T12:57:19Z")

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Cannon Ultrasound DICOM small file can be loaded(approximately 5Mb for a 30s video) However larger file cannot be loaded(approximately 100Mb for a 3min video). The error is showed in the attached screenshot. How to…

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## [Pet Tumor Segmentation](https://discourse.slicer.org/t/pet-tumor-segmentation/17190)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 1\
**Last updated:** [April 20, 2021, 10:59am UTC](https://discourse.slicer.org/t/pet-tumor-segmentation/17190 "2021-04-20T10:59:14Z")

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Hi Everyone, Does anyone know what is the method that used in PET Tumor Segmentation tool? is it gradientwieght method? or otsu method? or adaptive method? or Fourier Surface method?

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## [2021.04.19 Transitioning Discourse plan: Expect 15 minutes of read-only time](https://discourse.slicer.org/t/2021-04-19-transitioning-discourse-plan-expect-15-minutes-of-read-only-time/17188)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 0\
**Last updated:** [April 19, 2021, 9:38pm UTC](https://discourse.slicer.org/t/2021-04-19-transitioning-discourse-plan-expect-15-minutes-of-read-only-time/17188 "2021-04-19T21:38:08Z")

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Later this evening, we will be switching the plan associated with our discourse instance. The move usually results in less than 15 minutes of read-only time.

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## [how to get a high resolution of modified 3d models?](https://discourse.slicer.org/t/how-to-get-a-high-resolution-of-modified-3d-models/17185)

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**Author:** [@Michele\_Atzori](https://discourse.slicer.org/u/Michele_Atzori)\
**Replies:** 1\
**Last updated:** [April 19, 2021, 8:21pm UTC](https://discourse.slicer.org/t/how-to-get-a-high-resolution-of-modified-3d-models/17185 "2021-04-19T20:21:41Z")

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Goodmorning everyone. I recently discovered this beautiful 3d slicer software. I wanted to ask why the images I drag onto the 3d screen are much more defined than those obtained from the thresold-show 3d editor; they are…

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## [How to define camera perspective of 3D view window](https://discourse.slicer.org/t/how-to-define-camera-perspective-of-3d-view-window/17136)

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**Author:** [@deferd](https://discourse.slicer.org/u/deferd)\
**Replies:** 3\
**Last updated:** [April 19, 2021, 7:57pm UTC](https://discourse.slicer.org/t/how-to-define-camera-perspective-of-3d-view-window/17136 "2021-04-19T19:57:28Z")

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Hello I am trying to control the perspective of an X-ray-like image generated from CT data. E.g., I would like to define the distance between the focal point and a specific anatomical feature and control the viewing ang…

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## [STL with gaps after segmentation](https://discourse.slicer.org/t/stl-with-gaps-after-segmentation/17180)

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**Author:** [@Marknagel](https://discourse.slicer.org/u/Marknagel)\
**Replies:** 6\
**Last updated:** [April 19, 2021, 6:58pm UTC](https://discourse.slicer.org/t/stl-with-gaps-after-segmentation/17180 "2021-04-19T18:58:06Z")

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Hey everybody! I’m pretty new to 3D Slicer, basically using it to 3d print bones out of CT-data. Managed to print a femur once, but i’m now having a hard time to print a humerus: I seperated the humuers from the rest …

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## [Module Qt Designer Check Box](https://discourse.slicer.org/t/module-qt-designer-check-box/17172)

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**Author:** [@Gabriel](https://discourse.slicer.org/u/Gabriel)\
**Replies:** 3\
**Last updated:** [April 19, 2021, 6:57pm UTC](https://discourse.slicer.org/t/module-qt-designer-check-box/17172 "2021-04-19T18:57:34Z")

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I am creating a module and have used Qt Designer to add in a checkbox. For now I have just added a print function to test the checkbox, later I want it to carry out a function when clicked on. In the main PY file, unde…

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## [Brain volume MRI](https://discourse.slicer.org/t/brain-volume-mri/17169)

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**Author:** [@amjadibr](https://discourse.slicer.org/u/amjadibr)\
**Replies:** 1\
**Last updated:** [April 19, 2021, 4:11pm UTC](https://discourse.slicer.org/t/brain-volume-mri/17169 "2021-04-19T16:11:44Z")

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Hi everyone, I am trying to measure the whole brain volume in MRI. I don’t know if the Slicer is the right tool to do it. The result would be numbers representing the volume of the whole brain Thank you in advance

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## [Problem with Radiomics when Bin Width set to 0.01](https://discourse.slicer.org/t/problem-with-radiomics-when-bin-width-set-to-0-01/17173)

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**Author:** [@Marg](https://discourse.slicer.org/u/Marg)\
**Replies:** 1\
**Last updated:** [April 19, 2021, 3:46pm UTC](https://discourse.slicer.org/t/problem-with-radiomics-when-bin-width-set-to-0-01/17173 "2021-04-19T15:46:23Z")

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Hi. I am using 3D Slicer version 4.11.2020930. Last week I was able to perform Radiomics extraction with bin width 0.01 with no issues. Today on the same data set I get a blank table when Bin Width is set to 0.01. It see…

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## [Alter Individual Image Slice Origins in a Node](https://discourse.slicer.org/t/alter-individual-image-slice-origins-in-a-node/16905)

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**Author:** [@Gabriel](https://discourse.slicer.org/u/Gabriel)\
**Replies:** 6\
**Last updated:** [April 19, 2021, 2:40pm UTC](https://discourse.slicer.org/t/alter-individual-image-slice-origins-in-a-node/16905 "2021-04-19T14:40:00Z")

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Hello Everyone, I am working on a project where I will receive UltraSound images (in TIFF format). However the US images are taken from a robotic arm so will not all have the same origin or spacing between images. The or…

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## [Align 3D ultrasound image and surface model](https://discourse.slicer.org/t/align-3d-ultrasound-image-and-surface-model/17158)

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**Author:** [@sulaimanvesal](https://discourse.slicer.org/u/sulaimanvesal)\
**Replies:** 8\
**Last updated:** [April 18, 2021, 7:47pm UTC](https://discourse.slicer.org/t/align-3d-ultrasound-image-and-surface-model/17158 "2021-04-18T19:47:00Z")

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Hi @lassoan, It’s been a week that I am struggling with the new dataset that I received including ultrasound/MRI and their corresponding STL files. As I have mentioned earlier, I wrote the code and successfully combined…

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## [Saved surface model is not aligned with volume when viewed in external software](https://discourse.slicer.org/t/saved-surface-model-is-not-aligned-with-volume-when-viewed-in-external-software/821)

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**Author:** [@fmaule](https://discourse.slicer.org/u/fmaule)\
**Replies:** 1\
**Last updated:** [August 4, 2017, 1:11pm UTC](https://discourse.slicer.org/t/saved-surface-model-is-not-aligned-with-volume-when-viewed-in-external-software/821 "2017-08-04T13:11:03Z")

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Operating system: Windows 7 enterprise 64bit Slicer version:4.6.2 Expected behavior: I expect to visualize in 3D space the files .stl or .ply surfaces correctly alligned with the nifti anatomical image (on which I ha…

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