# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=196

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

**Page:** 197

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## [Calculating RMSE in Landmarks Registration](https://discourse.slicer.org/t/calculating-rmse-in-landmarks-registration/26049)

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**Author:** [@domP](https://discourse.slicer.org/u/domP)\
**Replies:** 1\
**Last updated:** [November 3, 2022, 3:56pm UTC](https://discourse.slicer.org/t/calculating-rmse-in-landmarks-registration/26049 "2022-11-03T15:56:20Z")

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Hi, Could I ask if anyone has a code to calculate RMSE obtained from “Fiducial Registration Wizard” module? I have read the repository’s code linked below: but when I have tried to replicate it on Matlab I have got …

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## [Flip orientation in the axial viewport?](https://discourse.slicer.org/t/flip-orientation-in-the-axial-viewport/2759)

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**Author:** [@drusmanbashir](https://discourse.slicer.org/u/drusmanbashir)\
**Replies:** 7\
**Last updated:** [November 3, 2022, 3:23pm UTC](https://discourse.slicer.org/t/flip-orientation-in-the-axial-viewport/2759 "2022-11-03T15:23:39Z")

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Hi, While viewing axial slices, I wish to be able to flip the view so that the right side becomes left and vice-versa like in every DICOM viewer. Is this function there / a plugin that allows it? Thanks Usman.

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## [Incorporate Gmsh in 3d Slicer](https://discourse.slicer.org/t/incorporate-gmsh-in-3d-slicer/26037)

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**Author:** [@ZSoltani](https://discourse.slicer.org/u/ZSoltani)\
**Replies:** 3\
**Last updated:** [November 3, 2022, 2:54pm UTC](https://discourse.slicer.org/t/incorporate-gmsh-in-3d-slicer/26037 "2022-11-03T14:54:12Z")

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Dear 3D Slicer community, Is it possible to incorporate Gmsh in 3D Slicer? Thank you in advance for your help, Zahra

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## [Incorporate CGAL in 3D Slicer](https://discourse.slicer.org/t/incorporate-cgal-in-3d-slicer/25963)

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**Author:** [@ZSoltani](https://discourse.slicer.org/u/ZSoltani)\
**Replies:** 2\
**Last updated:** [October 30, 2022, 3:26pm UTC](https://discourse.slicer.org/t/incorporate-cgal-in-3d-slicer/25963 "2022-10-30T15:26:58Z")

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Hi, I need to incorporate CGAL in 3D Slicer for generating mesh. Any advise please? Thank you.

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## [Does image registration require equal number of slices of images?](https://discourse.slicer.org/t/does-image-registration-require-equal-number-of-slices-of-images/25930)

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**Author:** [@gaurav\_patel](https://discourse.slicer.org/u/gaurav_patel)\
**Replies:** 5\
**Last updated:** [November 3, 2022, 12:33pm UTC](https://discourse.slicer.org/t/does-image-registration-require-equal-number-of-slices-of-images/25930 "2022-11-03T12:33:36Z")

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How is registration hadled in multimodal case wherein there are unequal number of slice eg. whole body CT with partial MR like abdomen Operating system:Windows 7 Slicer version: Expected behavior: Actual behavior:

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## [HIPPOCOMPUS, WM. GM & CSF AUTO/SEMI AUTO SEGMENTATION](https://discourse.slicer.org/t/hippocompus-wm-gm-csf-auto-semi-auto-segmentation/26030)

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**Author:** [@D.Prasad](https://discourse.slicer.org/u/D.Prasad)\
**Replies:** 1\
**Last updated:** [November 2, 2022, 11:58pm UTC](https://discourse.slicer.org/t/hippocompus-wm-gm-csf-auto-semi-auto-segmentation/26030 "2022-11-02T23:58:09Z")

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Operating system: WINDOWS Slicer version: 5. 0.3 Expected behavior: na Actual behavior:na HELLO EVERY ONE. I WANT TO EXTRACT/SEGMENT HIPPOCOMPUS TISSUE, GRAY MATTER, WHITE MATTER AND CSF FROM THE BRAIN MRI IMAGE(S…

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## [Which module can export the relevant data of the fiber bundle，which created using UKF tractography](https://discourse.slicer.org/t/which-module-can-export-the-relevant-data-of-the-fiber-bundle-which-created-using-ukf-tractography/26031)

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**Author:** [@Joshuazzzs](https://discourse.slicer.org/u/Joshuazzzs)\
**Replies:** 1\
**Last updated:** [November 2, 2022, 11:57pm UTC](https://discourse.slicer.org/t/which-module-can-export-the-relevant-data-of-the-fiber-bundle-which-created-using-ukf-tractography/26031 "2022-11-02T23:57:04Z")

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Hi! We use the UKF tractography module to creat the neural fibers. Which module can export the relevant data of the fiber bundle, as in the following image, generate a table directly…

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## [Different result using same transformation](https://discourse.slicer.org/t/different-result-using-same-transformation/26038)

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**Author:** [@alan6690](https://discourse.slicer.org/u/alan6690)\
**Replies:** 0\
**Last updated:** [November 2, 2022, 2:44pm UTC](https://discourse.slicer.org/t/different-result-using-same-transformation/26038 "2022-11-02T14:44:53Z")

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I have registered two lung CT images using elastix deformable registration module and saved the transformation matrix as a h5 file. I realize if I apply the transformation matrix into an identical copy of the same moving…

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## [Feature maps with MRI sequence in the background](https://discourse.slicer.org/t/feature-maps-with-mri-sequence-in-the-background/26033)

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**Author:** [@asmaharry](https://discourse.slicer.org/u/asmaharry)\
**Replies:** 0\
**Last updated:** [November 2, 2022, 11:53am UTC](https://discourse.slicer.org/t/feature-maps-with-mri-sequence-in-the-background/26033 "2022-11-02T11:53:21Z")

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Hello, I am new user here. How to create a feature map of any pyradiomics features in 3D slicer? how we can show it like an image given in the example? Here an example image is uploaded (The top image shows the orig…

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## [How to apply this matix in slicer for a modelNode](https://discourse.slicer.org/t/how-to-apply-this-matix-in-slicer-for-a-modelnode/26025)

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**Author:** [@timeanddoctor](https://discourse.slicer.org/u/timeanddoctor)\
**Replies:** 1\
**Last updated:** [November 2, 2022, 9:36am UTC](https://discourse.slicer.org/t/how-to-apply-this-matix-in-slicer-for-a-modelnode/26025 "2022-11-02T09:36:54Z")

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np.Mtrix(Transform4\*4): K, R position(x,y,z): X(position), Y(target) (R\[2,:\]X)Y=KRX Can I change upper equation to such format : Y=Mat\*X. So if X is a Node , I could use it in slicer. Thanks

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## [Improving manual segmentation of the aorta](https://discourse.slicer.org/t/improving-manual-segmentation-of-the-aorta/25972)

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**Author:** [@chendong9416](https://discourse.slicer.org/u/chendong9416)\
**Replies:** 7\
**Last updated:** [November 2, 2022, 9:37am UTC](https://discourse.slicer.org/t/improving-manual-segmentation-of-the-aorta/25972 "2022-11-02T09:37:10Z")

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For aortic dissection, the measurement of aortic diameter (outer wall to outwall) in several levels is clinical relevent. Automatic segmentation works well for the aortic lumen but will miss the aotic wall and intimal f…

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## [A very dumb question: how do I implement a voxel-based feature extraction?](https://discourse.slicer.org/t/a-very-dumb-question-how-do-i-implement-a-voxel-based-feature-extraction/26018)

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**Author:** [@blaze\_cipher](https://discourse.slicer.org/u/blaze_cipher)\
**Replies:** 0\
**Last updated:** [November 2, 2022, 3:21am UTC](https://discourse.slicer.org/t/a-very-dumb-question-how-do-i-implement-a-voxel-based-feature-extraction/26018 "2022-11-02T03:21:53Z")

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To anyone who can help: I’ve learnt that voxel based feature extraction would generate a .nrrd file, but I can only generate a generic csv file, though in the file it showd dimensionality was 3D and voxel numbers, so ho…

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## [Problems with Python console tab completion](https://discourse.slicer.org/t/problems-with-python-console-tab-completion/25965)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 3\
**Last updated:** [November 2, 2022, 3:13am UTC](https://discourse.slicer.org/t/problems-with-python-console-tab-completion/25965 "2022-11-02T03:13:08Z")

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With recent python console changes I’m having difficulties using \[TAB\] to inspect available methods from the python console. I’m getting output upon pressing \[TAB\] which then breaks things up that I’m trying to type. It …

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## [Flip normal / primitive](https://discourse.slicer.org/t/flip-normal-primitive/26007)

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**Author:** [@mohammed\_alshakhas](https://discourse.slicer.org/u/mohammed_alshakhas)\
**Replies:** 1\
**Last updated:** [November 1, 2022, 7:13pm UTC](https://discourse.slicer.org/t/flip-normal-primitive/26007 "2022-11-01T19:13:27Z")

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i often segment and export scan models . after exporting the software I’m using for surgical simulation often get the models dark . i need to export to mesh mixer and do a flip to normal . is there a way to avoid or cor…

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## [Elastix returned non-zero exit status 4294967294](https://discourse.slicer.org/t/elastix-returned-non-zero-exit-status-4294967294/25888)

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**Author:** [@oliverhalaseh](https://discourse.slicer.org/u/oliverhalaseh)\
**Replies:** 1\
**Last updated:** [November 1, 2022, 6:36pm UTC](https://discourse.slicer.org/t/elastix-returned-non-zero-exit-status-4294967294/25888 "2022-11-01T18:36:32Z")

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Dear All, I started work on \[SlicerSegmentationRecipes/VesselSegmentationBySubtraction at master · lassoan/SlicerSegmentationRecipes · GitHub\] (SlicerSegmentationRecipes/VesselSegmentationBySubtraction at master · lass…

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## [Multi-raw image loading using RawImageGuess extension](https://discourse.slicer.org/t/multi-raw-image-loading-using-rawimageguess-extension/26126)

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**Author:** [@seyang](https://discourse.slicer.org/u/seyang)\
**Replies:** 7\
**Last updated:** [November 15, 2022, 1:09am UTC](https://discourse.slicer.org/t/multi-raw-image-loading-using-rawimageguess-extension/26126 "2022-11-15T01:09:17Z")

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Can someone help us to import multi-raw images? Our system is remaining each slice image. Ex) 240 Slice = Slice0001,0002,0003, 0004… As I confirm the RawImageGuess extension module, only supports one raw image. We re…

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## [Master volume is not set as either the foreground or background](https://discourse.slicer.org/t/master-volume-is-not-set-as-either-the-foreground-or-background/26009)

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**Author:** [@Mmirzaa1](https://discourse.slicer.org/u/Mmirzaa1)\
**Replies:** 0\
**Last updated:** [November 1, 2022, 6:04pm UTC](https://discourse.slicer.org/t/master-volume-is-not-set-as-either-the-foreground-or-background/26009 "2022-11-01T18:04:49Z")

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Hello everyone. I am using the latest stable version of 3Dslicer and I came across a problem: I want to open DICOM images as a single series and be able to view them consequently, however the software recognizes each o…

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## [Processing of a large number of MRIs](https://discourse.slicer.org/t/processing-of-a-large-number-of-mris/26006)

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**Author:** [@tsinesh](https://discourse.slicer.org/u/tsinesh)\
**Replies:** 0\
**Last updated:** [November 1, 2022, 5:09pm UTC](https://discourse.slicer.org/t/processing-of-a-large-number-of-mris/26006 "2022-11-01T17:09:35Z")

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How can I perform an analysis on a large data set with e.g. 800 MRIs? I imagine to process all images uniformly as far as possible automatically in a loop: e.g. N4 homogenization algorithm for MRI Bias Field Correction …

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## [High resolution screenshot](https://discourse.slicer.org/t/high-resolution-screenshot/25995)

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**Author:** [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Replies:** 0\
**Last updated:** [November 1, 2022, 3:37am UTC](https://discourse.slicer.org/t/high-resolution-screenshot/25995 "2022-11-01T03:37:09Z")

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How can I get the high resolution screenshot. The default quality is not good!

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## [How to edit an STL file using Segment Editor](https://discourse.slicer.org/t/how-to-edit-an-stl-file-using-segment-editor/17559)

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**Author:** [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Replies:** 13\
**Last updated:** [November 1, 2022, 3:32am UTC](https://discourse.slicer.org/t/how-to-edit-an-stl-file-using-segment-editor/17559 "2022-11-01T03:32:21Z")

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I want to do some modifications on my stl file. when I open it from file as a data the “Segment Editor” is NOT active. How may I do that?

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## [Vertebral Foramen Segmentation with Fill between Slices](https://discourse.slicer.org/t/vertebral-foramen-segmentation-with-fill-between-slices/25994)

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**Author:** [@dav](https://discourse.slicer.org/u/dav)\
**Replies:** 0\
**Last updated:** [November 1, 2022, 1:39am UTC](https://discourse.slicer.org/t/vertebral-foramen-segmentation-with-fill-between-slices/25994 "2022-11-01T01:39:43Z")

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Trying to segment the vertebral space in this image where I’ve already segmented out the lumbar spine. I found that fill between slices works moderately well, (see image) however upon initializing you can see how th…

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## [CLI modules ignore parent transform](https://discourse.slicer.org/t/cli-modules-ignore-parent-transform/25987)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 1\
**Last updated:** [October 31, 2022, 7:47pm UTC](https://discourse.slicer.org/t/cli-modules-ignore-parent-transform/25987 "2022-10-31T19:47:35Z")

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It seems confusing that CLI modules ignore the parent transform and users need to harden the transform to get the results that they expect. See this discussion for a recent example: Does anyone know the reason why CL…

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## [Generate 3D visualization by Stacking 2D RGB H&E Images](https://discourse.slicer.org/t/generate-3d-visualization-by-stacking-2d-rgb-h-e-images/25956)

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**Author:** [@chokevin8](https://discourse.slicer.org/u/chokevin8)\
**Replies:** 7\
**Last updated:** [October 30, 2022, 12:39pm UTC](https://discourse.slicer.org/t/generate-3d-visualization-by-stacking-2d-rgb-h-e-images/25956 "2022-10-30T12:39:42Z")

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Operating system: Windows 11 Slicer version: 3D Slicer 5.0.3 Expected behavior: N/A Actual behavior: N/A Hi, I have 34 H&E (histology) 2-D RGB Images that are in .png file format and I want to stack them to visualize…

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## [Slicer doesn't load](https://discourse.slicer.org/t/slicer-doesnt-load/25968)

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**Author:** [@scorpo\_901](https://discourse.slicer.org/u/scorpo_901)\
**Replies:** 1\
**Last updated:** [October 29, 2022, 8:21pm UTC](https://discourse.slicer.org/t/slicer-doesnt-load/25968 "2022-10-29T20:21:03Z")

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Hello, my slicer was working very well with blender, now I double click on the slicer.exe and it isn’t working. I tried to uninstall and reinstall it, it worked for a day, then the same problem recurred. Did any one fa…

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## [Change shell thickness](https://discourse.slicer.org/t/change-shell-thickness/15081)

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**Author:** [@Hamid](https://discourse.slicer.org/u/Hamid)\
**Replies:** 12\
**Last updated:** [October 30, 2022, 2:16am UTC](https://discourse.slicer.org/t/change-shell-thickness/15081 "2022-10-30T02:16:01Z")

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I made a thick shell with t=2mm using “Hollow”. How can I add thickness to the shell for example I want to get the 5 mm thick(add 3 mm to the exist shell)? There are some limitation to get back to the original lumen so I…

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## [Fill or extract cavities in segmentations using the new "Wrap Solidify" effect](https://discourse.slicer.org/t/fill-or-extract-cavities-in-segmentations-using-the-new-wrap-solidify-effect/11248)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 12\
**Last updated:** [October 25, 2022, 2:35pm UTC](https://discourse.slicer.org/t/fill-or-extract-cavities-in-segmentations-using-the-new-wrap-solidify-effect/11248 "2022-10-25T14:35:45Z")

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Making a segment that has fractured, discontinuous boundary and holes inside to be a simple solid object is a quite common task for segmentation. For example it is needed for creating simple solid bone models from CT ima…

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## [Hi, I have problems solving the "couldn't not load.....scalar volume" problem](https://discourse.slicer.org/t/hi-i-have-problems-solving-the-couldnt-not-load-scalar-volume-problem/2840)

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**Author:** [@felipec\_34](https://discourse.slicer.org/u/felipec_34)\
**Replies:** 10\
**Last updated:** [October 28, 2022, 11:11pm UTC](https://discourse.slicer.org/t/hi-i-have-problems-solving-the-couldnt-not-load-scalar-volume-problem/2840 "2022-10-28T23:11:17Z")

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Operating system: windows 8.1 Slicer version: 4.8.1 Expected behavior: loading the dicom data Actual behavior: not loading Please help me with this. I tried to change the dicom information with dicomcleaner but it di…

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## [The sagittal and coronal scales are wrong and segmentation does not work](https://discourse.slicer.org/t/the-sagittal-and-coronal-scales-are-wrong-and-segmentation-does-not-work/25922)

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**Author:** [@Eiichi](https://discourse.slicer.org/u/Eiichi)\
**Replies:** 5\
**Last updated:** [October 28, 2022, 3:30pm UTC](https://discourse.slicer.org/t/the-sagittal-and-coronal-scales-are-wrong-and-segmentation-does-not-work/25922 "2022-10-28T15:30:35Z")

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Hi, I’m Eiichi, a Japanese plastic surgeon and researcher. I am studying the evaluation of the healing process of cranial bone defects in rats. For this purpose, the cranial crowns of rats are collected and imaged with…

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## [Scan time relation to slice number and voxel size](https://discourse.slicer.org/t/scan-time-relation-to-slice-number-and-voxel-size/25947)

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**Author:** [@juliangallaun](https://discourse.slicer.org/u/juliangallaun)\
**Replies:** 4\
**Last updated:** [October 28, 2022, 3:27pm UTC](https://discourse.slicer.org/t/scan-time-relation-to-slice-number-and-voxel-size/25947 "2022-10-28T15:27:19Z")

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Hello everyone, I have a more logical question to people which are working with CT-Scanners in general. For example I have a volume which consist of 100 slices (the voxel size is 10 → 10x10x10), to decrease the GPU pow…

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## [Get rotation angles from transform matrix](https://discourse.slicer.org/t/get-rotation-angles-from-transform-matrix/25935)

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**Author:** [@domP](https://discourse.slicer.org/u/domP)\
**Replies:** 4\
**Last updated:** [October 28, 2022, 12:42pm UTC](https://discourse.slicer.org/t/get-rotation-angles-from-transform-matrix/25935 "2022-10-28T12:42:34Z")

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Operating system: Windows 11 Home Slicer version: 5.0.2 Expected behavior: Actual behavior: Hello everybody, I’m in trouble with the module ‘Transforms’ in 3D Slicer. My goal is to compare the transform matrix obtai…

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