# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=330

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

**Page:** 331

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## [Extracting muscle cross-sectional area and its centroid locatation from MRI/CT scans](https://discourse.slicer.org/t/extracting-muscle-cross-sectional-area-and-its-centroid-locatation-from-mri-ct-scans/12575)

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**Author:** [@StefSchmidPhD](https://discourse.slicer.org/u/StefSchmidPhD)\
**Replies:** 10\
**Last updated:** [July 17, 2020, 3:08pm UTC](https://discourse.slicer.org/t/extracting-muscle-cross-sectional-area-and-its-centroid-locatation-from-mri-ct-scans/12575 "2020-07-17T15:08:08Z")

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Hi everyone I’m looking for a simple option to extract paraspinal muscle cross-sectional area (CSA) and its centroid location from MRI/CT scans (horizontal vertebral mid-planes). Is there already a feature/an extension …

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## [Slicer opening screen error horizontal green lines](https://discourse.slicer.org/t/slicer-opening-screen-error-horizontal-green-lines/12590)

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**Author:** [@AT3432984](https://discourse.slicer.org/u/AT3432984)\
**Replies:** 0\
**Last updated:** [July 17, 2020, 4:09am UTC](https://discourse.slicer.org/t/slicer-opening-screen-error-horizontal-green-lines/12590 "2020-07-17T04:09:12Z")

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Hi, I am having trouble when opening 3D Slicer. I have had this program for a while and it always works fine, but now when I open it I get a bunch of green lines across the screen. I have looked at the following 2 pa…

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## [Rendered volume doesn't show slices trough ROI](https://discourse.slicer.org/t/rendered-volume-doesnt-show-slices-trough-roi/9215)

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**Author:** [@Carolsv](https://discourse.slicer.org/u/Carolsv)\
**Replies:** 6\
**Last updated:** [July 1, 2020, 1:47pm UTC](https://discourse.slicer.org/t/rendered-volume-doesnt-show-slices-trough-roi/9215 "2020-07-01T13:47:01Z")

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Dear all, I have been trying to see patterns of variation in bone structures. For that, I am rendering a volume by using the Segment Editor module and applying ‘Threshold’ in a new added segment. After that, I am able t…

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## [Viewing Side by Side](https://discourse.slicer.org/t/viewing-side-by-side/12563)

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**Author:** [@vertebrae](https://discourse.slicer.org/u/vertebrae)\
**Replies:** 8\
**Last updated:** [July 16, 2020, 3:30pm UTC](https://discourse.slicer.org/t/viewing-side-by-side/12563 "2020-07-16T15:30:41Z")

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Is there python code to switch the viewing panes? Before I do my segmentation, I need to set the code to display only the Coronal and Sagittal view before the segmentation and then display the 3D view along with the coro…

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## [Newbie quick question - delete a mesh??](https://discourse.slicer.org/t/newbie-quick-question-delete-a-mesh/12555)

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**Author:** [@H\_Smith](https://discourse.slicer.org/u/H_Smith)\
**Replies:** 4\
**Last updated:** [July 16, 2020, 1:13pm UTC](https://discourse.slicer.org/t/newbie-quick-question-delete-a-mesh/12555 "2020-07-16T13:13:36Z")

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I feel apologetic to ask such a simple question but I can’t find an answer! Every time I’ve made a mesh in the Editor module, I can’t see how to delete it, if I want to try again. Every time I’m using Close Scene to sta…

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## [Extend SlicerRT](https://discourse.slicer.org/t/extend-slicerrt/12569)

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**Author:** [@toyama](https://discourse.slicer.org/u/toyama)\
**Replies:** 1\
**Last updated:** [July 16, 2020, 9:28am UTC](https://discourse.slicer.org/t/extend-slicerrt/12569 "2020-07-16T09:28:46Z")

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↑I want to do CMake to extend SlicerRT, but I cannot specify “where is source code” in the downloaded file. What should I specify for “where is source code”? Please answer.

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## [Cannot edit outside a segmentation bounding box](https://discourse.slicer.org/t/cannot-edit-outside-a-segmentation-bounding-box/2451)

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**Author:** [@bobread](https://discourse.slicer.org/u/bobread)\
**Replies:** 8\
**Last updated:** [July 16, 2020, 3:48am UTC](https://discourse.slicer.org/t/cannot-edit-outside-a-segmentation-bounding-box/2451 "2020-07-16T03:48:05Z")

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Hi, I have a segmentation which I am trying to edit but when I try to add or delete points outside of a bounding box nothing happens. I imported the segmentation from a label map and the bounding box encloses the non-bac…

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## [Selecting and interacting with points in plot](https://discourse.slicer.org/t/selecting-and-interacting-with-points-in-plot/12564)

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**Author:** [@sthirumal](https://discourse.slicer.org/u/sthirumal)\
**Replies:** 1\
**Last updated:** [July 16, 2020, 2:54am UTC](https://discourse.slicer.org/t/selecting-and-interacting-with-points-in-plot/12564 "2020-07-16T02:54:14Z")

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For my scatter plots in Slicer, I am using the interaction mode “select points” in order to select specific points on the plot. Once I’ve selected my points, however, I’m unsure how exactly to use my selection. I’ve used…

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## [Importing PACs anonymised data into 3D Slicer](https://discourse.slicer.org/t/importing-pacs-anonymised-data-into-3d-slicer/12560)

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**Author:** [@David\_Nahabedian](https://discourse.slicer.org/u/David_Nahabedian)\
**Replies:** 3\
**Last updated:** [July 15, 2020, 7:29pm UTC](https://discourse.slicer.org/t/importing-pacs-anonymised-data-into-3d-slicer/12560 "2020-07-15T19:29:27Z")

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Hello slicer community. I am trying to import MRI’s and CT scans from a client into 3D sclicer form a PACs based system. I am familiar with importing DICOM data but this is very new to me. THe PACs system can be viewed i…

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## [Slicer App Store (extensions) down?](https://discourse.slicer.org/t/slicer-app-store-extensions-down/12554)

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**Author:** [@hherhold](https://discourse.slicer.org/u/hherhold)\
**Replies:** 2\
**Last updated:** [July 15, 2020, 5:18pm UTC](https://discourse.slicer.org/t/slicer-app-store-extensions-down/12554 "2020-07-15T17:18:09Z")

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I get the following error when I try to go to @KitwareMedical/slicer-extensions-webapp The system has encountered the following error: Uncaught exception ‘PDOException’ with message ‘SQLSTATE\[HY000\] \[1040\] Too many con…

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## [Remove atifacts background after registration](https://discourse.slicer.org/t/remove-atifacts-background-after-registration/12551)

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**Author:** [@1116](https://discourse.slicer.org/u/1116)\
**Replies:** 3\
**Last updated:** [July 15, 2020, 12:45pm UTC](https://discourse.slicer.org/t/remove-atifacts-background-after-registration/12551 "2020-07-15T12:45:27Z")

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After rigid registration using Elastix, I got CT data with artifacts at background is there any way to remove background remaining only head volume?

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## [Fiducial RAS Coordinates to MATLAB](https://discourse.slicer.org/t/fiducial-ras-coordinates-to-matlab/12530)

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**Author:** [@gaurav\_bhide](https://discourse.slicer.org/u/gaurav_bhide)\
**Replies:** 2\
**Last updated:** [July 15, 2020, 9:38am UTC](https://discourse.slicer.org/t/fiducial-ras-coordinates-to-matlab/12530 "2020-07-15T09:38:30Z")

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Hello, OS - Windows 10 Slicer Version - 4.10.2 I have the slicer installed with the MATLAB Bridge extension. I have my own DICOM Image that I load on the 3D slicer. Then I have placed a few fiducials. I want to trans…

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## [DICOM data import error: patients are read as others](https://discourse.slicer.org/t/dicom-data-import-error-patients-are-read-as-others/12041)

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**Author:** [@Alexandre\_Huat](https://discourse.slicer.org/u/Alexandre_Huat)\
**Replies:** 9\
**Last updated:** [July 15, 2020, 9:14am UTC](https://discourse.slicer.org/t/dicom-data-import-error-patients-are-read-as-others/12041 "2020-07-15T09:14:18Z")

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Operating system: macOS 10.14.6 / Ubuntu 18.04 LTS Slicer version: 10.4.2 Slicer extension used: SlicerRT Expected behavior: I have a DICOM RT database: each folder is the RT image set of a specific patient, that is, …

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## [The current 3D slicer version of Windows is unresponsive](https://discourse.slicer.org/t/the-current-3d-slicer-version-of-windows-is-unresponsive/12546)

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**Author:** [@KIM\_TY](https://discourse.slicer.org/u/KIM_TY)\
**Replies:** 2\
**Last updated:** [July 15, 2020, 5:43am UTC](https://discourse.slicer.org/t/the-current-3d-slicer-version-of-windows-is-unresponsive/12546 "2020-07-15T05:43:09Z")

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Thank you all for your answers, Steve Piper, Sam Horvath, James Butler, and lassoan. I don’t think the mac version has a problem. There are overwhelmingly many versions of Windows in Asia. Currently, the 4.11 (29216) …

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## [How to change the label value of binary labelmap volume?](https://discourse.slicer.org/t/how-to-change-the-label-value-of-binary-labelmap-volume/12511)

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**Author:** [@N.Arjmandi](https://discourse.slicer.org/u/N.Arjmandi)\
**Replies:** 8\
**Last updated:** [July 15, 2020, 3:55am UTC](https://discourse.slicer.org/t/how-to-change-the-label-value-of-binary-labelmap-volume/12511 "2020-07-15T03:55:06Z")

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I imported CT images and radiotherapy structures (segmented organ shuch as bladder , rectum, and … ) into the 3D Slicer , then created a binary labelmap of the structures. The software assigned a label value (index) for …

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## [How does Label Statistics Calculate Volume w/ regards to Slice Thickness/Spacing](https://discourse.slicer.org/t/how-does-label-statistics-calculate-volume-w-regards-to-slice-thickness-spacing/12541)

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**Author:** [@ebear](https://discourse.slicer.org/u/ebear)\
**Replies:** 2\
**Last updated:** [July 14, 2020, 7:33pm UTC](https://discourse.slicer.org/t/how-does-label-statistics-calculate-volume-w-regards-to-slice-thickness-spacing/12541 "2020-07-14T19:33:38Z")

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We used the Editor module to delineate tumor volumes slice-by-slice for an MRI series with slice thickness of 0.5mm and slice spacing of 1mm. When using Label Statistics to convert these slice-by-slice labels into a Lab…

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## [Registration of MRI Scans](https://discourse.slicer.org/t/registration-of-mri-scans/12536)

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**Author:** [@bernland](https://discourse.slicer.org/u/bernland)\
**Replies:** 1\
**Last updated:** [July 14, 2020, 7:26pm UTC](https://discourse.slicer.org/t/registration-of-mri-scans/12536 "2020-07-14T19:26:34Z")

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As you can see on the below screenshots, there is an offset between two abdominal MRIs (anywhere between 0 and 6 mm). What would be the best way to register the volumes in Silcer? Any help is greatly appreciated!

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## [Measurement of vessel diameter](https://discourse.slicer.org/t/measurement-of-vessel-diameter/12535)

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**Author:** [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Replies:** 1\
**Last updated:** [July 14, 2020, 3:55pm UTC](https://discourse.slicer.org/t/measurement-of-vessel-diameter/12535 "2020-07-14T15:55:37Z")

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Hello, I want to determine the diameter of a vessel and use the ‘ruler’ tool for this. How can I make a vertical cut through the vessel? To do this with the curser, it’s a matter of luck. Usually there is an oblique cu…

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## [Composition of MRI Slabs](https://discourse.slicer.org/t/composition-of-mri-slabs/12534)

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**Author:** [@bernland](https://discourse.slicer.org/u/bernland)\
**Replies:** 0\
**Last updated:** [July 14, 2020, 2:57pm UTC](https://discourse.slicer.org/t/composition-of-mri-slabs/12534 "2020-07-14T14:57:42Z")

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The abdominal MRI under review is composed of three slabs of around 100 slices each. The slabs are acquired in hold-breath supine position taking around 20 seconds. Naturally, a step between two such slabs may occur due …

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## [Generating an opaque volume using volume rendering](https://discourse.slicer.org/t/generating-an-opaque-volume-using-volume-rendering/12528)

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**Author:** [@mwyburd](https://discourse.slicer.org/u/mwyburd)\
**Replies:** 1\
**Last updated:** [July 14, 2020, 1:55pm UTC](https://discourse.slicer.org/t/generating-an-opaque-volume-using-volume-rendering/12528 "2020-07-14T13:55:03Z")

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I have a volume which contains continuous measures of depth and I want an opaque 3D volume rendering. I have thresholded the volume (in the volume module), to remove the background and have used “synchronize with volumes…

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## [Simplified web based core application](https://discourse.slicer.org/t/simplified-web-based-core-application/12487)

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**Author:** [@tobiedesgreniers](https://discourse.slicer.org/u/tobiedesgreniers)\
**Replies:** 3\
**Last updated:** [July 14, 2020, 4:32am UTC](https://discourse.slicer.org/t/simplified-web-based-core-application/12487 "2020-07-14T04:32:01Z")

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Hi 3DSlicer community! I’m a student in computer engineering and i’m working on a bachelor end project aiming to develop a commercial service prototype for surgeons to print biomimetic models of human parts to practice …

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## [Paint brush behaviour in Classic Editor versus Segmentation Editor](https://discourse.slicer.org/t/paint-brush-behaviour-in-classic-editor-versus-segmentation-editor/12518)

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**Author:** [@Jaswant](https://discourse.slicer.org/u/Jaswant)\
**Replies:** 1\
**Last updated:** [July 14, 2020, 3:44am UTC](https://discourse.slicer.org/t/paint-brush-behaviour-in-classic-editor-versus-segmentation-editor/12518 "2020-07-14T03:44:01Z")

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I am a novice, so please re-direct to the feature that I would like to use. I am working with whole body contrast CT data set from a dog for teaching and 3D printing purspose. Previously, I used classical editor to Thre…

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## [Post-processing of brain vessel models](https://discourse.slicer.org/t/post-processing-of-brain-vessel-models/12045)

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**Author:** [@Andreas](https://discourse.slicer.org/u/Andreas)\
**Replies:** 6\
**Last updated:** [July 13, 2020, 6:58pm UTC](https://discourse.slicer.org/t/post-processing-of-brain-vessel-models/12045 "2020-07-13T18:58:08Z")

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I still have questions about post-processing of brain vessel models: 1.) Is it more advantageous to use first the smoothing function for post-processing the vessel models in order to improve the vessel lumen and thus th…

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## [.STL file to stack of images](https://discourse.slicer.org/t/stl-file-to-stack-of-images/12498)

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**Author:** [@Violaine\_Barrois](https://discourse.slicer.org/u/Violaine_Barrois)\
**Replies:** 1\
**Last updated:** [July 13, 2020, 6:09pm UTC](https://discourse.slicer.org/t/stl-file-to-stack-of-images/12498 "2020-07-13T18:09:48Z")

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Hi, is there any way to create a series of (JPG/TIFF or. any other) images from a .STL file? I am a graphic designer & want to print a book with each layer on one page, Can anyone help me with this please? I work on …

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## [There are some problems with the Windows version](https://discourse.slicer.org/t/there-are-some-problems-with-the-windows-version/12484)

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**Author:** [@KIM\_TY](https://discourse.slicer.org/u/KIM_TY)\
**Replies:** 3\
**Last updated:** [July 13, 2020, 2:19pm UTC](https://discourse.slicer.org/t/there-are-some-problems-with-the-windows-version/12484 "2020-07-13T14:19:15Z")

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Thank you for providing us with a great program called 3D slicer for free. There are some problems with the Windows version. This is the same problem with MSI, ASUS gaming laptop, and high-performance PC.(window 10 pro…

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## [How the definition of tortuosity in VMTK?](https://discourse.slicer.org/t/how-the-definition-of-tortuosity-in-vmtk/12503)

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**Author:** [@wwx992881](https://discourse.slicer.org/u/wwx992881)\
**Replies:** 2\
**Last updated:** [July 13, 2020, 1:54pm UTC](https://discourse.slicer.org/t/how-the-definition-of-tortuosity-in-vmtk/12503 "2020-07-13T13:54:25Z")

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HI,All I’ve extracted the center line,and I don’t know the definition of tortuosity in 3D table. I see a definition of tortuosity in the literature:Tortuosity was defined as L/D–1, where L is the length of the centre…

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## [Calculate ICE and jacobian of displacement vector field](https://discourse.slicer.org/t/calculate-ice-and-jacobian-of-displacement-vector-field/12507)

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**Author:** [@toyama](https://discourse.slicer.org/u/toyama)\
**Replies:** 0\
**Last updated:** [July 13, 2020, 1:14pm UTC](https://discourse.slicer.org/t/calculate-ice-and-jacobian-of-displacement-vector-field/12507 "2020-07-13T13:14:04Z")

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I am using 3D Slicer 4.10.2. I read “Slicer Registration QA”, but I don’t know how to download the module for calculating ICE and Jacobian. How can I download it?

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## [Calculate ICE and jacobian of displacement vector field](https://discourse.slicer.org/t/calculate-ice-and-jacobian-of-displacement-vector-field/12508)

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**Author:** [@toyama](https://discourse.slicer.org/u/toyama)\
**Replies:** 1\
**Last updated:** [July 13, 2020, 1:14pm UTC](https://discourse.slicer.org/t/calculate-ice-and-jacobian-of-displacement-vector-field/12508 "2020-07-13T13:14:31Z")

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I am using 3DSlicer 4.10.2. I want to calculate ICE and Jacobian with this tool, but I cannot do it like “SlicerRegistrationQA”. I do not know the cause. Please tell me more detailed materials such as downloading RegQA …

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## [Is it possible to apply visually crop of the 3D model to see it's internal surface?](https://discourse.slicer.org/t/is-it-possible-to-apply-visually-crop-of-the-3d-model-to-see-its-internal-surface/12409)

<div class="topic-metadata">

**Author:** [@jarrik](https://discourse.slicer.org/u/jarrik)\
**Replies:** 9\
**Last updated:** [July 13, 2020, 2:05am UTC](https://discourse.slicer.org/t/is-it-possible-to-apply-visually-crop-of-the-3d-model-to-see-its-internal-surface/12409 "2020-07-13T02:05:40Z")

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Operating system: win10 Slicer version: 4.10.2 Expected behavior: Actual behavior:

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## [How to choose the optimized number of quantization levels and the voxel size of the images in CT texture analysis?](https://discourse.slicer.org/t/how-to-choose-the-optimized-number-of-quantization-levels-and-the-voxel-size-of-the-images-in-ct-texture-analysis/12495)

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**Author:** [@danceward](https://discourse.slicer.org/u/danceward)\
**Replies:** 0\
**Last updated:** [July 12, 2020, 2:11pm UTC](https://discourse.slicer.org/t/how-to-choose-the-optimized-number-of-quantization-levels-and-the-voxel-size-of-the-images-in-ct-texture-analysis/12495 "2020-07-12T14:11:46Z")

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Dear experts, I want to do texture analysis with chest CT images by 3d-slicer.but how to choose the optimized number of quantization greylevels and the voxel size of the images in CT texture analysis? Thanks!

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