# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=288

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

**Page:** 289

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## [Slicer will change the shape of the model?](https://discourse.slicer.org/t/slicer-will-change-the-shape-of-the-model/16962)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [April 6, 2021, 12:59pm UTC](https://discourse.slicer.org/t/slicer-will-change-the-shape-of-the-model/16962 "2021-04-06T12:59:50Z")

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Dear friends! win slicer v4.11 0226 I imported a blood vessel model into the software, and then imported it into the segmentation editor,do nothing, show 3D directly,the model as you see.It is not clear. The red is th…

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## [Some segmentations are very large](https://discourse.slicer.org/t/some-segmentations-are-very-large/16935)

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**Author:** [@Daniel\_Byrne](https://discourse.slicer.org/u/Daniel_Byrne)\
**Replies:** 4\
**Last updated:** [April 5, 2021, 7:38pm UTC](https://discourse.slicer.org/t/some-segmentations-are-very-large/16935 "2021-04-05T19:38:13Z")

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So I have created 7 segmentation a from a knee MRI, and 3 of these segmentation seem to be on a different scale because there huge? Even though they were all exported at the same time

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## [How can I crop some CT data into same region?](https://discourse.slicer.org/t/how-can-i-crop-some-ct-data-into-same-region/16863)

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**Author:** [@hir](https://discourse.slicer.org/u/hir)\
**Replies:** 5\
**Last updated:** [April 5, 2021, 12:56am UTC](https://discourse.slicer.org/t/how-can-i-crop-some-ct-data-into-same-region/16863 "2021-04-05T00:56:15Z")

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Hi, I’m new to 3D slicer. I have several series of CT data, like day0,1,… for each mouse. I want to compare bone volume change over time. I use “Expert Automated Registration” to align the orientations. Then, I want …

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## [Changing slice thickness for epicardial adipose tissue analysis](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928)

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**Author:** [@Mark\_Brahier](https://discourse.slicer.org/u/Mark_Brahier)\
**Replies:** 6\
**Last updated:** [April 3, 2021, 9:37pm UTC](https://discourse.slicer.org/t/changing-slice-thickness-for-epicardial-adipose-tissue-analysis/16928 "2021-04-03T21:37:27Z")

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I’m currently using 3D Slicer for manual segmentation of cardiac CTs to quantify epicardial adipose tissue. The CTs that I have are high resolution at a slice thickness of 0.5mm or less (some as small as 0.15mm). Within …

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## [Read performance between json and fcsv](https://discourse.slicer.org/t/read-performance-between-json-and-fcsv/16879)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 6\
**Last updated:** [April 3, 2021, 3:12pm UTC](https://discourse.slicer.org/t/read-performance-between-json-and-fcsv/16879 "2021-04-03T15:12:23Z")

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I have the same markups file with many points saved as fcsv and json. Reading the same file via JSON is instantenous, whereas fcsv takes minutes. This replicates all the time in the windows table. Files are here: https:…

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## [Compute the transformation based on selected local coordinate system](https://discourse.slicer.org/t/compute-the-transformation-based-on-selected-local-coordinate-system/16802)

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**Author:** [@Tekk\_ya](https://discourse.slicer.org/u/Tekk_ya)\
**Replies:** 3\
**Last updated:** [April 3, 2021, 12:40pm UTC](https://discourse.slicer.org/t/compute-the-transformation-based-on-selected-local-coordinate-system/16802 "2021-04-03T12:40:53Z")

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Hi 3DSlicer community, I have a question about computing the transformation matrix for a desired local coordinate system. To be more specific, I have two 3D models, one is a 3D model in its original position, the second…

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## [Segmentation tool, Deep learning, Auditory ossicles](https://discourse.slicer.org/t/segmentation-tool-deep-learning-auditory-ossicles/16852)

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**Author:** [@j.v.d](https://discourse.slicer.org/u/j.v.d)\
**Replies:** 1\
**Last updated:** [April 3, 2021, 3:14am UTC](https://discourse.slicer.org/t/segmentation-tool-deep-learning-auditory-ossicles/16852 "2021-04-03T03:14:09Z")

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Operating system: macOS Big Sur 11.2.1 Slicer version: 4.11.20210226 Expected behavior: Automatic segmentation of the auditory ossicles Actual behavior: Segmentation via thresholding and no segmentation for the stapes …

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## [Reducing opacity of individual sections of a 3D model](https://discourse.slicer.org/t/reducing-opacity-of-individual-sections-of-a-3d-model/16840)

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**Author:** [@Pseudoceros](https://discourse.slicer.org/u/Pseudoceros)\
**Replies:** 2\
**Last updated:** [April 3, 2021, 3:06am UTC](https://discourse.slicer.org/t/reducing-opacity-of-individual-sections-of-a-3d-model/16840 "2021-04-03T03:06:52Z")

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Hi all, I managed to create a 3D reconstruction out of 2D histology slices but I’m having trouble with transparency. Basically, the organs that I want to visualised are “inside” the 3D object, meaning that there are sli…

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## [how to superimpose and colour amp digital dental models in STL files](https://discourse.slicer.org/t/how-to-superimpose-and-colour-amp-digital-dental-models-in-stl-files/16841)

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**Author:** [@drjyotsna](https://discourse.slicer.org/u/drjyotsna)\
**Replies:** 1\
**Last updated:** [April 3, 2021, 3:04am UTC](https://discourse.slicer.org/t/how-to-superimpose-and-colour-amp-digital-dental-models-in-stl-files/16841 "2021-04-03T03:04:13Z")

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Operating system: Slicer version: Expected behavior: Actual behavior:

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## [Resolving DICOM image resolution](https://discourse.slicer.org/t/resolving-dicom-image-resolution/16830)

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**Author:** [@Krista\_Asoluka](https://discourse.slicer.org/u/Krista_Asoluka)\
**Replies:** 1\
**Last updated:** [April 3, 2021, 2:51am UTC](https://discourse.slicer.org/t/resolving-dicom-image-resolution/16830 "2021-04-03T02:51:11Z")

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Hello everyone, I need help with understanding why and how to improve resolution. I’m carrying out some basic segmentation on bone models for my research. When I threshold and generate the model, there are a lot of gaps…

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## [Crop Volume reports error when input is a color volume](https://discourse.slicer.org/t/crop-volume-reports-error-when-input-is-a-color-volume/16857)

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**Author:** [@giovform](https://discourse.slicer.org/u/giovform)\
**Replies:** 2\
**Last updated:** [April 3, 2021, 2:22am UTC](https://discourse.slicer.org/t/crop-volume-reports-error-when-input-is-a-color-volume/16857 "2021-04-03T02:22:07Z")

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Steps to reproduce: Load any 2D image using “Add Data”; Go to “Crop Volume” module; On “Input ROI” select “Create new AnnotationROI”; Change the ROI to any subregion of the image on the red slice view; On “Output volum…

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## [Apply a linear transformation to a segmentation](https://discourse.slicer.org/t/apply-a-linear-transformation-to-a-segmentation/16365)

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**Author:** [@michela.destito](https://discourse.slicer.org/u/michela.destito)\
**Replies:** 3\
**Last updated:** [April 3, 2021, 2:03am UTC](https://discourse.slicer.org/t/apply-a-linear-transformation-to-a-segmentation/16365 "2021-04-03T02:03:56Z")

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Hi, I have a question. I would like to apply a linear transformation to a segmentation via command line and always save it as a segmentation, so I don’t want to refer it to any volume. it’s possible? Thank you very much…

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## [Breach Warning ScriptRepository](https://discourse.slicer.org/t/breach-warning-scriptrepository/16767)

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**Author:** [@Raj\_Kumar\_Ranabhat](https://discourse.slicer.org/u/Raj_Kumar_Ranabhat)\
**Replies:** 3\
**Last updated:** [April 3, 2021, 1:54am UTC](https://discourse.slicer.org/t/breach-warning-scriptrepository/16767 "2021-04-03T01:54:24Z")

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Hi, I am trying to use Breach Warning function from IGT extension in our project which seems to be very useful. Are there any resources / Python scripting for developer regarding this Breach Warning Module ? I am using …

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## [Building slicer on the NVIDIA Jetsontx2 not working](https://discourse.slicer.org/t/building-slicer-on-the-nvidia-jetsontx2-not-working/16913)

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**Author:** [@ryleyreid](https://discourse.slicer.org/u/ryleyreid)\
**Replies:** 3\
**Last updated:** [April 3, 2021, 1:26am UTC](https://discourse.slicer.org/t/building-slicer-on-the-nvidia-jetsontx2-not-working/16913 "2021-04-03T01:26:41Z")

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I am trying to build 3D slicer on a single board computer, specifically the Jetsontx2 for a case study. The goal is to run 3Dslicer on the computer with a trained neural net to do local calibrations. The build hasn’t bee…

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## [Extensions manager errors in 4/1 MacOS nightly](https://discourse.slicer.org/t/extensions-manager-errors-in-4-1-macos-nightly/16910)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 2\
**Last updated:** [April 3, 2021, 1:03am UTC](https://discourse.slicer.org/t/extensions-manager-errors-in-4-1-macos-nightly/16910 "2021-04-03T01:03:42Z")

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MacOS latest nightly 4/1, downloaded moments ago after extremely cool images with ambient shadows. Extensions manager very slow to come up, and I get the following in the console: DevTools listening on ws://127.0.0.1:1…

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## [Slicer wiki edit permissions reset](https://discourse.slicer.org/t/slicer-wiki-edit-permissions-reset/9236)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 8\
**Last updated:** [April 2, 2021, 9:00pm UTC](https://discourse.slicer.org/t/slicer-wiki-edit-permissions-reset/9236 "2021-04-02T21:00:39Z")

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I tried to edit, and discovered that my permissions to edit Slicer wiki content are gone. Is this expected? Is Slicer wiki in “read only” mode? @mhalle do you know what is going on?

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## [Isotropic Volume with B-Spline Interpolation](https://discourse.slicer.org/t/isotropic-volume-with-b-spline-interpolation/16933)

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**Author:** [@Fluvio\_Lobo](https://discourse.slicer.org/u/Fluvio_Lobo)\
**Replies:** 1\
**Last updated:** [April 2, 2021, 8:30pm UTC](https://discourse.slicer.org/t/isotropic-volume-with-b-spline-interpolation/16933 "2021-04-02T20:30:32Z")

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Hello, I am trying to understand what is exactly happening when I use the crop volume function with the isotropic spacing and B-spline interpolation flags on. This is mostly for a discussion section on a publication and…

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## [Save DICOM as a coronal](https://discourse.slicer.org/t/save-dicom-as-a-coronal/16932)

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**Author:** [@Rouba1987](https://discourse.slicer.org/u/Rouba1987)\
**Replies:** 1\
**Last updated:** [April 2, 2021, 7:53pm UTC](https://discourse.slicer.org/t/save-dicom-as-a-coronal/16932 "2021-04-02T19:53:57Z")

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Hi, I am trying to save a DICOM dataset (MRI) in slicer however it is changing the orientation from coronal to axial in the DICOM header. I need to import these scans into software to register to another MRI and its cau…

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## [Ridgeline Artifacts from Wrap Solidify Effect (Segment Editor Module)](https://discourse.slicer.org/t/ridgeline-artifacts-from-wrap-solidify-effect-segment-editor-module/16886)

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**Author:** [@davidboerma](https://discourse.slicer.org/u/davidboerma)\
**Replies:** 1\
**Last updated:** [April 2, 2021, 7:29pm UTC](https://discourse.slicer.org/t/ridgeline-artifacts-from-wrap-solidify-effect-segment-editor-module/16886 "2021-04-02T19:29:26Z")

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Hi folks, the “Wrap Solidify” effect intermittently introduces thin raised lines onto the models it produces from my segmentations. It tends to occur on a specimen-by-specimen basis and hasn’t responded to increasing the…

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## [Is centerline extraction from volume rendering possible?](https://discourse.slicer.org/t/is-centerline-extraction-from-volume-rendering-possible/16922)

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**Author:** [@chendong9416](https://discourse.slicer.org/u/chendong9416)\
**Replies:** 1\
**Last updated:** [April 2, 2021, 1:06pm UTC](https://discourse.slicer.org/t/is-centerline-extraction-from-volume-rendering-possible/16922 "2021-04-02T13:06:04Z")

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since segmentation will be difficult sometomes from CTA with poor quality, but they can still be well displayed in volume rendering, thus I wonder if centerline extraction directly from volume rendering possible?

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## [Run Freesurfer command from Slicer extension](https://discourse.slicer.org/t/run-freesurfer-command-from-slicer-extension/13504)

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**Author:** [@ezemikulan](https://discourse.slicer.org/u/ezemikulan)\
**Replies:** 5\
**Last updated:** [April 2, 2021, 9:41am UTC](https://discourse.slicer.org/t/run-freesurfer-command-from-slicer-extension/13504 "2021-04-02T09:41:15Z")

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Hi, I’m developing an Extension in python to anonymize MRIs and I need to use some Freesurfer commands (mri\_info, mris\_convert and mri\_watershed). Is there a way to run Freesurfer commands from inside a Slicer Extension…

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## [Multivolume data load](https://discourse.slicer.org/t/multivolume-data-load/16890)

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**Author:** [@selmanca](https://discourse.slicer.org/u/selmanca)\
**Replies:** 1\
**Last updated:** [April 2, 2021, 12:12am UTC](https://discourse.slicer.org/t/multivolume-data-load/16890 "2021-04-02T00:12:13Z")

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Operating system: Win 10 Slicer version: 4.13.0 (Latest) Expected behavior: Loading multivolume data Actual behavior: Hi developers, I am trying to load my t2 images map with different TEs and python interactor give…

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## [3DSlicer GUI all bugged and with green stripes on Windows 10](https://discourse.slicer.org/t/3dslicer-gui-all-bugged-and-with-green-stripes-on-windows-10/16914)

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**Author:** [@Gustavo\_S\_N](https://discourse.slicer.org/u/Gustavo_S_N)\
**Replies:** 1\
**Last updated:** [April 2, 2021, 12:01am UTC](https://discourse.slicer.org/t/3dslicer-gui-all-bugged-and-with-green-stripes-on-windows-10/16914 "2021-04-02T00:01:50Z")

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Hello all, I’ve installed 3DSlicer for the first time for the purpose of viewing a DICOM folder for planing dental implants. The installation process went ok but now when I start 3DSlicer I get this GUI: This issue…

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## [Mutli texture rendering with obj + mlt + multiple jpgs](https://discourse.slicer.org/t/mutli-texture-rendering-with-obj-mlt-multiple-jpgs/14773)

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**Author:** [@ezgimercan](https://discourse.slicer.org/u/ezgimercan)\
**Replies:** 4\
**Last updated:** [April 1, 2021, 5:37pm UTC](https://discourse.slicer.org/t/mutli-texture-rendering-with-obj-mlt-multiple-jpgs/14773 "2021-04-01T17:37:51Z")

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I have a 3D mesh in OBJ format created by a commercial stereophotogrammetry setup. It has an associated .mtl file and a couple JPGs for texture. My collaborators need to use texture to annotate some curves/points on thes…

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## [New feature: Surface rendering with ambient shadows for improved depth perception](https://discourse.slicer.org/t/new-feature-surface-rendering-with-ambient-shadows-for-improved-depth-perception/16903)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 3\
**Last updated:** [April 1, 2021, 5:32pm UTC](https://discourse.slicer.org/t/new-feature-surface-rendering-with-ambient-shadows-for-improved-depth-perception/16903 "2021-04-01T17:32:53Z")

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Slicer Preview Release uses an upgraded version of the VTK rendering library, which has many new rendering features that can make renderings in Slicer more realistic. We exposed one of these new features: ambient shadow…

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## [How to set this option as the default option](https://discourse.slicer.org/t/how-to-set-this-option-as-the-default-option/16892)

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**Author:** [@slicer365](https://discourse.slicer.org/u/slicer365)\
**Replies:** 1\
**Last updated:** [April 1, 2021, 4:18pm UTC](https://discourse.slicer.org/t/how-to-set-this-option-as-the-default-option/16892 "2021-04-01T16:18:43Z")

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How to set this option as the default option so that you do not need to set it every time you open the software, because this mode is more commonly used more often

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## [How to load MRI DCM files as multiple dimensions?](https://discourse.slicer.org/t/how-to-load-mri-dcm-files-as-multiple-dimensions/16908)

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**Author:** [@AlexRichardson2001](https://discourse.slicer.org/u/AlexRichardson2001)\
**Replies:** 1\
**Last updated:** [April 1, 2021, 1:24pm UTC](https://discourse.slicer.org/t/how-to-load-mri-dcm-files-as-multiple-dimensions/16908 "2021-04-01T13:24:33Z")

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I have loaded all of my DCM files but they only show in one dimension, not multiple like they should. Is there any way I can manually label them by dimension, or is this a faulty question because the data itself if fault…

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## [Where is "DWI to DTI Estimation"](https://discourse.slicer.org/t/where-is-dwi-to-dti-estimation/16887)

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**Author:** [@nknt](https://discourse.slicer.org/u/nknt)\
**Replies:** 1\
**Last updated:** [April 1, 2021, 12:00pm UTC](https://discourse.slicer.org/t/where-is-dwi-to-dti-estimation/16887 "2021-04-01T12:00:49Z")

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Operating system: Win 10 Slicer version: 4.11.20210226 Hello everyone, I’ m reading a tutorial on 3DSlicer version 4.1 to learn how to use it. And it says to select the module “DWI to DTI Estimation”. But I didn’t fi…

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## [How can I crop some DICOM data into same shape?](https://discourse.slicer.org/t/how-can-i-crop-some-dicom-data-into-same-shape/16888)

<div class="topic-metadata">

**Author:** [@hir](https://discourse.slicer.org/u/hir)\
**Replies:** 1\
**Last updated:** [April 1, 2021, 5:28am UTC](https://discourse.slicer.org/t/how-can-i-crop-some-dicom-data-into-same-shape/16888 "2021-04-01T05:28:41Z")

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Hi I’m new to 3D slicer. I have several series of DICOM data, day0,1… for each mouse. Now I can use “Expert Automated Registration” to align them. Then I want to crop each DICOM data with same region to calculate the …

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## [Scripting Slicer - What is possible?](https://discourse.slicer.org/t/scripting-slicer-what-is-possible/16873)

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**Author:** [@Hball99](https://discourse.slicer.org/u/Hball99)\
**Replies:** 1\
**Last updated:** [March 31, 2021, 5:17pm UTC](https://discourse.slicer.org/t/scripting-slicer-what-is-possible/16873 "2021-03-31T17:17:06Z")

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Hello there! I am quite new to Slicer and I am having difficulties to understand what is actually possible with Slicer Scripting and what not. So my problem is the following: I know that I can script modules that I can…

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