# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=138

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

**Page:** 139

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## [Correct registration in Slicer output to Freesurfer](https://discourse.slicer.org/t/correct-registration-in-slicer-output-to-freesurfer/31934)

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**Author:** [@Victor\_Zeng](https://discourse.slicer.org/u/Victor_Zeng)\
**Replies:** 1\
**Last updated:** [September 27, 2023, 5:29pm UTC](https://discourse.slicer.org/t/correct-registration-in-slicer-output-to-freesurfer/31934 "2023-09-27T17:29:06Z")

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Hi all, for this project here, I am inputting into Slicer a brain image made in Freesurfer, namely the orig.mgz. Then I am managing manual segmentations done in Slicer using Segment Editor. Then I click on Export visible…

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## [Remove parts of volume outside the segmentation](https://discourse.slicer.org/t/remove-parts-of-volume-outside-the-segmentation/31925)

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**Author:** [@Windy](https://discourse.slicer.org/u/Windy)\
**Replies:** 1\
**Last updated:** [September 27, 2023, 3:35am UTC](https://discourse.slicer.org/t/remove-parts-of-volume-outside-the-segmentation/31925 "2023-09-27T03:35:40Z")

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I have a dataset containing unwanted particles, and I’ve created a segmentation mask to identify and exclude them. Is it possible to utilize this segmentation mask to effectively remove the unwanted particles from the or…

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## [Combine several segmentation VOIs on z axis](https://discourse.slicer.org/t/combine-several-segmentation-vois-on-z-axis/31875)

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**Author:** [@Windy](https://discourse.slicer.org/u/Windy)\
**Replies:** 7\
**Last updated:** [September 26, 2023, 11:12pm UTC](https://discourse.slicer.org/t/combine-several-segmentation-vois-on-z-axis/31875 "2023-09-26T23:12:48Z")

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I have a CT volume of 1500 x 1500 x 3000. To be able to segment them without crashing my laptop while seeing enough details, I follow the following pipeline. I have divided them into 3 VOIs along the z-axis, each VOI h…

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## [Using qMRMLNodeAttributeTableWidget with qMRMLSegmentEditorWidget](https://discourse.slicer.org/t/using-qmrmlnodeattributetablewidget-with-qmrmlsegmenteditorwidget/31904)

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**Author:** [@NguyenVuHoaBinh](https://discourse.slicer.org/u/NguyenVuHoaBinh)\
**Replies:** 5\
**Last updated:** [September 26, 2023, 8:27pm UTC](https://discourse.slicer.org/t/using-qmrmlnodeattributetablewidget-with-qmrmlsegmenteditorwidget/31904 "2023-09-26T20:27:15Z")

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Hello everyone! I am new to 3D Slicer. I am currently creating a sample extension that allow user add additional information about the segmentation when using segment editor, but i got stuck. I dont know how to mapping …

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## [Markups "jump slices" feature changed in Slicer-5.2.2](https://discourse.slicer.org/t/markups-jump-slices-feature-changed-in-slicer-5-2-2/29386)

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**Author:** [@Tobias](https://discourse.slicer.org/u/Tobias)\
**Replies:** 6\
**Last updated:** [September 26, 2023, 7:38pm UTC](https://discourse.slicer.org/t/markups-jump-slices-feature-changed-in-slicer-5-2-2/29386 "2023-09-26T19:38:10Z")

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In my opinion there is a bug in markups in the 5.22 and a few other of the latest versions. Historically if you pressed jump slices you could go between different markups and by selecting one you would automatically go …

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## [Dillation of a specific label, and pushing other label?](https://discourse.slicer.org/t/dillation-of-a-specific-label-and-pushing-other-label/31808)

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**Author:** [@Romain\_Valabregue](https://discourse.slicer.org/u/Romain_Valabregue)\
**Replies:** 8\
**Last updated:** [September 26, 2023, 6:48pm UTC](https://discourse.slicer.org/t/dillation-of-a-specific-label-and-pushing-other-label/31808 "2023-09-26T18:48:35Z")

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Dear all This is my first post, so I would like to first thanks you for this nice community, this forum has already been a great source for me. I am working with full brain segmentation, with tissue label (GM, WM, CSF,…

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## [Exploring VTK-Based 3D Modeling of Floating-Point RTStruct Contours in 3D Slicer](https://discourse.slicer.org/t/exploring-vtk-based-3d-modeling-of-floating-point-rtstruct-contours-in-3d-slicer/31816)

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**Author:** [@ranjan](https://discourse.slicer.org/u/ranjan)\
**Replies:** 3\
**Last updated:** [September 26, 2023, 8:27am UTC](https://discourse.slicer.org/t/exploring-vtk-based-3d-modeling-of-floating-point-rtstruct-contours-in-3d-slicer/31816 "2023-09-26T08:27:19Z")

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We are exploring how 3D Slicer handles the conversion of RTStruct contour data to 3D models, specifically concerning the handling of floating-point coordinates for each slice’s contour. Our primary questions are as follo…

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## [Volume size - labelmap vs closed surface](https://discourse.slicer.org/t/volume-size-labelmap-vs-closed-surface/31889)

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**Author:** [@Inka\_Saraswati](https://discourse.slicer.org/u/Inka_Saraswati)\
**Replies:** 2\
**Last updated:** [September 26, 2023, 2:08am UTC](https://discourse.slicer.org/t/volume-size-labelmap-vs-closed-surface/31889 "2023-09-26T02:08:07Z")

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Hi, I’m using Slicer for research in which I segment and determine volume of a bone defect from a CT image, for the purpose of determining how much graft material is needed. What is the difference between labelmap vs clo…

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## [Slicer not responding when using Auto3dgm](https://discourse.slicer.org/t/slicer-not-responding-when-using-auto3dgm/31883)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 2\
**Last updated:** [September 26, 2023, 2:01am UTC](https://discourse.slicer.org/t/slicer-not-responding-when-using-auto3dgm/31883 "2023-09-26T02:01:39Z")

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Dear researchers, does anyone know why the software is not responding when trying to use 800 landmark points in phase 2 for 8 models of tibial bone in Auto3DGM? I use Intel i7 13th gen and RTX4090; is that not enough?

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## [Segment Editor Paint Issue](https://discourse.slicer.org/t/segment-editor-paint-issue/31899)

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**Author:** [@Hannah\_Osland](https://discourse.slicer.org/u/Hannah_Osland)\
**Replies:** 2\
**Last updated:** [September 26, 2023, 1:18am UTC](https://discourse.slicer.org/t/segment-editor-paint-issue/31899 "2023-09-26T01:18:43Z")

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I am trying to use the segment editor feature to isolate an organ in my animal scans. When I attempt to paint using the segment editor tool, it doesn’t persist. Here were my steps Load .tiff files using ImageStacks on …

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## [How to get original DICOM CT Scan frame number from binary segmentation file?](https://discourse.slicer.org/t/how-to-get-original-dicom-ct-scan-frame-number-from-binary-segmentation-file/31902)

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**Author:** [@HPatel33](https://discourse.slicer.org/u/HPatel33)\
**Replies:** 0\
**Last updated:** [September 26, 2023, 1:13am UTC](https://discourse.slicer.org/t/how-to-get-original-dicom-ct-scan-frame-number-from-binary-segmentation-file/31902 "2023-09-26T01:13:56Z")

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Hi all – I am working on a deep learning framework for liver metastasis. I have the original DICOM CT of the abdomen and pelvis and a binary segmentation mask of the liver alone. I would like to pass axial images of JUST…

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## [Rescaling a segmentation](https://discourse.slicer.org/t/rescaling-a-segmentation/31874)

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**Author:** [@Windy](https://discourse.slicer.org/u/Windy)\
**Replies:** 2\
**Last updated:** [September 26, 2023, 12:55am UTC](https://discourse.slicer.org/t/rescaling-a-segmentation/31874 "2023-09-26T00:55:38Z")

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I have a volume that is 15.44 um isotropic. When I loaded it into the slicer and segmented it, I did not know that the Slicer loaded it as a 1mm volume. Now I figured out the measurements are wrong. When I load the corre…

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## [How does slicer determine when referenced datasets are found?](https://discourse.slicer.org/t/how-does-slicer-determine-when-referenced-datasets-are-found/31885)

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**Author:** [@Justin\_Kirby](https://discourse.slicer.org/u/Justin_Kirby)\
**Replies:** 12\
**Last updated:** [September 25, 2023, 8:11pm UTC](https://discourse.slicer.org/t/how-does-slicer-determine-when-referenced-datasets-are-found/31885 "2023-09-25T20:11:28Z")

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When I load DICOM segmentation data from the Slicer DICOM module I will sometimes be told that it has found referenced datasets, and with other SEG objects I am not. Can someone explain what tags are being evaluated t…

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## [Heart segmentation extension ](https://discourse.slicer.org/t/heart-segmentation-extension/31891)

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**Author:** [@alex\_He](https://discourse.slicer.org/u/alex_He)\
**Replies:** 0\
**Last updated:** [September 25, 2023, 2:50pm UTC](https://discourse.slicer.org/t/heart-segmentation-extension/31891 "2023-09-25T14:50:36Z")

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Hi, i am not able to find the slicerheart extension in extension manager under cardiac category, i m using ver 5.2.2, , please advise.

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## [Anonymised DICOM images are being added to the same patient](https://discourse.slicer.org/t/anonymised-dicom-images-are-being-added-to-the-same-patient/31890)

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**Author:** [@ykl](https://discourse.slicer.org/u/ykl)\
**Replies:** 0\
**Last updated:** [September 25, 2023, 2:50pm UTC](https://discourse.slicer.org/t/anonymised-dicom-images-are-being-added-to-the-same-patient/31890 "2023-09-25T14:50:31Z")

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Hi all, I’m new to Slicer. I have a question regarding DICOM database. I am trying to import MRI/PET scans of several patients from a disk format and all images have been anonymised. On Slicer, all the imaging studies h…

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## [Merge models by maintain the color](https://discourse.slicer.org/t/merge-models-by-maintain-the-color/31869)

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**Author:** [@linda\_varghese](https://discourse.slicer.org/u/linda_varghese)\
**Replies:** 1\
**Last updated:** [September 25, 2023, 2:03pm UTC](https://discourse.slicer.org/t/merge-models-by-maintain-the-color/31869 "2023-09-25T14:03:49Z")

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I wanted to merge different nodes(models) together and also maintain the color of each structure and export it in .obj I tried to merge the models by ‘merge models’ and even by ‘logical operators’ but the color of all s…

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## [How to convert the result of GPA into 3D model?](https://discourse.slicer.org/t/how-to-convert-the-result-of-gpa-into-3d-model/31873)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 2\
**Last updated:** [September 25, 2023, 12:20pm UTC](https://discourse.slicer.org/t/how-to-convert-the-result-of-gpa-into-3d-model/31873 "2023-09-25T12:20:27Z")

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Hi, please give some advice. I’ve got the point cloud from the GPA module of SlicerMorph, but then get lost about how to turn it into a 3D model in vtk/stl/ply.

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## [Conversion of a complex structure from closed surface to binary labelmap](https://discourse.slicer.org/t/conversion-of-a-complex-structure-from-closed-surface-to-binary-labelmap/31803)

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**Author:** [@Matteboo](https://discourse.slicer.org/u/Matteboo)\
**Replies:** 6\
**Last updated:** [September 25, 2023, 11:25am UTC](https://discourse.slicer.org/t/conversion-of-a-complex-structure-from-closed-surface-to-binary-labelmap/31803 "2023-09-25T11:25:01Z")

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Hello, I import in Slicer a segmentation of bloodvessel in .stl format. However I want to do operation on it in slicer (use the scisor tool for example) and to do that I need to change the master represenation from “C…

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## [The slice views orientation are not aligned with segmentation](https://discourse.slicer.org/t/the-slice-views-orientation-are-not-aligned-with-segmentation/26452)

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**Author:** [@kylin](https://discourse.slicer.org/u/kylin)\
**Replies:** 8\
**Last updated:** [September 25, 2023, 7:23am UTC](https://discourse.slicer.org/t/the-slice-views-orientation-are-not-aligned-with-segmentation/26452 "2023-09-25T07:23:43Z")

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Hi, The mask appeared in adjacent slices when I was drawing a segmentation in one slice, so I can’t draw a segmentation exactly. I know there is a button in the right side of segmentation that can solve the problem. How…

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## [Image preprocessing for texture analysis on MR images](https://discourse.slicer.org/t/image-preprocessing-for-texture-analysis-on-mr-images/10918)

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**Author:** [@Arthinol](https://discourse.slicer.org/u/Arthinol)\
**Replies:** 2\
**Last updated:** [September 24, 2023, 8:38am UTC](https://discourse.slicer.org/t/image-preprocessing-for-texture-analysis-on-mr-images/10918 "2023-09-24T08:38:28Z")

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Hi, I´m wondering if there is a tutorial or recommendations on how to perform preprocessing on MR images for later texture analysis. Which modules should be used for: Interpolation- Especially for 3D segmentation to ob…

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## [Drawing ROI for local threshold is very inefficient?](https://discourse.slicer.org/t/drawing-roi-for-local-threshold-is-very-inefficient/31813)

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**Author:** [@benalb](https://discourse.slicer.org/u/benalb)\
**Replies:** 2\
**Last updated:** [September 24, 2023, 5:28am UTC](https://discourse.slicer.org/t/drawing-roi-for-local-threshold-is-very-inefficient/31813 "2023-09-24T05:28:24Z")

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I’m trying to adapt this methodology performed in AnalyzeDirect to Slicer3D. (Video of methodology in supplementary data) https://link.springer.com/article/10.1007/s00234-016-1720-z#Sec22:~:text=XLSX%2022%20kb)-,ESM%20…

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## [View 3 CT scans that are orthogonal perspectives of the same scan](https://discourse.slicer.org/t/view-3-ct-scans-that-are-orthogonal-perspectives-of-the-same-scan/31814)

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**Author:** [@benalb](https://discourse.slicer.org/u/benalb)\
**Replies:** 2\
**Last updated:** [September 24, 2023, 5:08am UTC](https://discourse.slicer.org/t/view-3-ct-scans-that-are-orthogonal-perspectives-of-the-same-scan/31814 "2023-09-24T05:08:48Z")

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I have figured out a way to do this, but I would appreciate if anyone with experience could tell me if I’ve done it right. The CT scans in my dataset consist of the axial, sagittal, and coronal perspectives in separate …

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## [Carotid Artery Segmentation in tw weighted MRI's](https://discourse.slicer.org/t/carotid-artery-segmentation-in-tw-weighted-mris/31866)

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**Author:** [@Redalligator291](https://discourse.slicer.org/u/Redalligator291)\
**Replies:** 0\
**Last updated:** [September 24, 2023, 2:53am UTC](https://discourse.slicer.org/t/carotid-artery-segmentation-in-tw-weighted-mris/31866 "2023-09-24T02:53:55Z")

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Hi guys, I am very new to 3D slicer and medical images in general. I am trying to segment the carotid arteries in a t2-weighted image. However, I am having trouble doing that. I think fundamentally, I am having trouble k…

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## [How to choose right number of landmark in PseudoLMGenerator?](https://discourse.slicer.org/t/how-to-choose-right-number-of-landmark-in-pseudolmgenerator/31800)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 4\
**Last updated:** [September 23, 2023, 8:52am UTC](https://discourse.slicer.org/t/how-to-choose-right-number-of-landmark-in-pseudolmgenerator/31800 "2023-09-23T08:52:20Z")

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Does lower tolerance spacing and having more landmarks make it easier to get a statistical shape model?

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## [3D volume does not show up in scene created in an old version of Slicer](https://discourse.slicer.org/t/3d-volume-does-not-show-up-in-scene-created-in-an-old-version-of-slicer/31843)

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**Author:** [@thkarag](https://discourse.slicer.org/u/thkarag)\
**Replies:** 3\
**Last updated:** [September 22, 2023, 6:28pm UTC](https://discourse.slicer.org/t/3d-volume-does-not-show-up-in-scene-created-in-an-old-version-of-slicer/31843 "2023-09-22T18:28:39Z")

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Some years ago, I have created a 3D mesh from an .nrrd file, using Volume Rendering using Slicer version 4.11 and saved it into a .mrml file. When I open this .mrml file in Slicer 5.2 the 3D volume does not show up and i…

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## [Wrong volume type when exporting to file](https://discourse.slicer.org/t/wrong-volume-type-when-exporting-to-file/31849)

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**Author:** [@pim](https://discourse.slicer.org/u/pim)\
**Replies:** 2\
**Last updated:** [September 22, 2023, 5:00pm UTC](https://discourse.slicer.org/t/wrong-volume-type-when-exporting-to-file/31849 "2023-09-22T17:00:47Z")

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When performing the Mask Volume operation in the Segment Editor module, using a scalar volume and a segmentation node (converted from a labelmap) as inputs, I correctly obtain a new node as output which is a scalar volum…

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## [3D Slicer MONAILabel Extension](https://discourse.slicer.org/t/3d-slicer-monailabel-extension/31850)

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**Author:** [@akku\_jarwal](https://discourse.slicer.org/u/akku_jarwal)\
**Replies:** 0\
**Last updated:** [September 22, 2023, 4:43pm UTC](https://discourse.slicer.org/t/3d-slicer-monailabel-extension/31850 "2023-09-22T16:43:33Z")

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Hi, I am using MonaiLable for auto segementation of whole body, there is a drop down in the extension “Auto Segmentaion”. So when we connect it to the server of Monai, the pre trained model will display over it. But tod…

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## [3D coordinates from points equidistance along a curved path ](https://discourse.slicer.org/t/3d-coordinates-from-points-equidistance-along-a-curved-path/31770)

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**Author:** [@sjang](https://discourse.slicer.org/u/sjang)\
**Replies:** 4\
**Last updated:** [September 22, 2023, 4:18pm UTC](https://discourse.slicer.org/t/3d-coordinates-from-points-equidistance-along-a-curved-path/31770 "2023-09-22T16:18:08Z")

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Along a curved path, I need the 3D coordinates (x, y, z) every 0.2mm. In this post (Create equidistant points along curve for automated measurements), the solution to getting equidistant points is to resample by selecti…

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## [Obtaining Volume Information for Brain Segmentation Using Closed-Loop Markups in 3D Slicer](https://discourse.slicer.org/t/obtaining-volume-information-for-brain-segmentation-using-closed-loop-markups-in-3d-slicer/31846)

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**Author:** [@sund](https://discourse.slicer.org/u/sund)\
**Replies:** 1\
**Last updated:** [September 22, 2023, 3:36pm UTC](https://discourse.slicer.org/t/obtaining-volume-information-for-brain-segmentation-using-closed-loop-markups-in-3d-slicer/31846 "2023-09-22T15:36:35Z")

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Hello everyone, I have been using the closed-loop markup module in 3D Slicer to segment the brain on individual MRI slices. Now, I am trying to obtain volume information for the entire brain by considering the closed-lo…

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## [Cannot find module TotalSegmentator](https://discourse.slicer.org/t/cannot-find-module-totalsegmentator/31845)

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**Author:** [@alex\_He](https://discourse.slicer.org/u/alex_He)\
**Replies:** 1\
**Last updated:** [September 22, 2023, 1:42pm UTC](https://discourse.slicer.org/t/cannot-find-module-totalsegmentator/31845 "2023-09-22T13:42:16Z")

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Hi i am using windows11 and install slicer 5.2.2 and totalsegmentator 1.5.3 installed from module extention manager, but when i click the apply button, it takes very long time to process and finally shows an error messa…

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