# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=168

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

**Page:** 169

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## [Negative values in nrrd field 'Segmentation\_ReferenceImageExtentOffset' ](https://discourse.slicer.org/t/negative-values-in-nrrd-field-segmentation-referenceimageextentoffset/28931)

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**Author:** [@Megan](https://discourse.slicer.org/u/Megan)\
**Replies:** 1\
**Last updated:** [April 15, 2023, 4:10pm UTC](https://discourse.slicer.org/t/negative-values-in-nrrd-field-segmentation-referenceimageextentoffset/28931 "2023-04-15T16:10:32Z")

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When reading in a .seg.nrrd file in python using pynrrd, I get a negative value in the ‘Segmentation\_ReferenceImageExtentOffset’ field (‘35 86 -1’). Are negative values relative to the end of the volume e.g. work backwa…

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## [New text engrave/emboss effect in Segment Editor](https://discourse.slicer.org/t/new-text-engrave-emboss-effect-in-segment-editor/12013)

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**Author:** [@lassoan](https://discourse.slicer.org/u/lassoan)\
**Replies:** 8\
**Last updated:** [July 6, 2020, 11:38pm UTC](https://discourse.slicer.org/t/new-text-engrave-emboss-effect-in-segment-editor/12013 "2020-07-06T23:38:05Z")

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A new tool added to Segment Editor for drawing text on segments. Both engrave and emboss modes are available. Text can be placed by defining a plane using 3 points, and then position can be adjusted in 3D, along with tex…

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## [Logical operators intersect function causes selected segment to disappear](https://discourse.slicer.org/t/logical-operators-intersect-function-causes-selected-segment-to-disappear/28896)

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**Author:** [@Shreya\_Kashyap](https://discourse.slicer.org/u/Shreya_Kashyap)\
**Replies:** 1\
**Last updated:** [April 15, 2023, 3:08am UTC](https://discourse.slicer.org/t/logical-operators-intersect-function-causes-selected-segment-to-disappear/28896 "2023-04-15T03:08:35Z")

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Hi everyone, I am trying to use the Intersect function to remove portions of segment1 (yellow) that are not inside segment2 (green). When I click intersect all of segment1 disappears, even portions that should be in seg…

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## [One of the studies as background? How to do it?](https://discourse.slicer.org/t/one-of-the-studies-as-background-how-to-do-it/28921)

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**Author:** [@eNable\_Polska](https://discourse.slicer.org/u/eNable_Polska)\
**Replies:** 0\
**Last updated:** [April 14, 2023, 4:35pm UTC](https://discourse.slicer.org/t/one-of-the-studies-as-background-how-to-do-it/28921 "2023-04-14T16:35:57Z")

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Problem: I have two exams of the same patient, CT, same equipment, same parameters. I want to see study 1 as foreground and background study 2, how to do it? When I import both studies, no matter how I set the order, I…

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## [TotalSegmentator installation problem due to Zenodo connection error](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705)

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**Author:** [@zhangliang](https://discourse.slicer.org/u/zhangliang)\
**Replies:** 9\
**Last updated:** [April 14, 2023, 2:57pm UTC](https://discourse.slicer.org/t/totalsegmentator-installation-problem-due-to-zenodo-connection-error/27705 "2023-04-14T14:57:41Z")

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I have some problems installing TotalSegmentator. Let me try to describe it clearly. I hope to get your help. My device：DELL windows 10 NVIDIA GeForceRTX3060 ,Display Memory: 28386 MB pyTorch :version 1.13+cu117 NVidi…

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## [Anyone Know How to coregistering four images](https://discourse.slicer.org/t/anyone-know-how-to-coregistering-four-images/28899)

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**Author:** [@akmal871026](https://discourse.slicer.org/u/akmal871026)\
**Replies:** 1\
**Last updated:** [April 14, 2023, 2:19pm UTC](https://discourse.slicer.org/t/anyone-know-how-to-coregistering-four-images/28899 "2023-04-14T14:19:26Z")

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Anyone know, how to do coregistering using four images. That I want to know is like the metric alignment for four images,

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## [Embedding the text in 3D model](https://discourse.slicer.org/t/embedding-the-text-in-3d-model/28789)

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**Author:** [@kopachini](https://discourse.slicer.org/u/kopachini)\
**Replies:** 2\
**Last updated:** [April 14, 2023, 12:04pm UTC](https://discourse.slicer.org/t/embedding-the-text-in-3d-model/28789 "2023-04-14T12:04:17Z")

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That feature would be cool, so we don’t have to use another 3D modeling software :slight\_smile:

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## [Export stl issue with meshmixer or other softwares](https://discourse.slicer.org/t/export-stl-issue-with-meshmixer-or-other-softwares/28881)

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**Author:** [@ortho3d](https://discourse.slicer.org/u/ortho3d)\
**Replies:** 2\
**Last updated:** [April 14, 2023, 8:57am UTC](https://discourse.slicer.org/t/export-stl-issue-with-meshmixer-or-other-softwares/28881 "2023-04-14T08:57:58Z")

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Operating system: Slicer version:503 why the export in stl is not done as before see pictures thank you should I reinstall 3Dslicer

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## [Can not download SlicerRT tutorial documents](https://discourse.slicer.org/t/can-not-download-slicerrt-tutorial-documents/28862)

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**Author:** [@Dex2046](https://discourse.slicer.org/u/Dex2046)\
**Replies:** 6\
**Last updated:** [April 14, 2023, 2:55am UTC](https://discourse.slicer.org/t/can-not-download-slicerrt-tutorial-documents/28862 "2023-04-14T02:55:05Z")

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I’m new in 3d slicer , so I want some documents in slicerRT, but I could not download from github. How could I get them? thank you all

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## [3D slicer doesn't work on ubuntu 20.04](https://discourse.slicer.org/t/3d-slicer-doesnt-work-on-ubuntu-20-04/28826)

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**Author:** [@EddardaaBL](https://discourse.slicer.org/u/EddardaaBL)\
**Replies:** 2\
**Last updated:** [April 13, 2023, 3:03pm UTC](https://discourse.slicer.org/t/3d-slicer-doesnt-work-on-ubuntu-20-04/28826 "2023-04-13T15:03:09Z")

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I’ve downloaded the last stable release of 3d Slicer (version 5.2.2) for Linux systems but it seems that it’s not working whenever I try to initialize 3d Slicer, this latter couldn’t be working

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## [what algorithm is 3Dslicer's Add Scalar Volumes module based on for image fusion?](https://discourse.slicer.org/t/what-algorithm-is-3dslicers-add-scalar-volumes-module-based-on-for-image-fusion/28888)

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**Author:** [@ending](https://discourse.slicer.org/u/ending)\
**Replies:** 4\
**Last updated:** [April 13, 2023, 2:34pm UTC](https://discourse.slicer.org/t/what-algorithm-is-3dslicers-add-scalar-volumes-module-based-on-for-image-fusion/28888 "2023-04-13T14:34:18Z")

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I have a question for everyone what algorithm is 3Dslicer’s Add Scalar Volumes module based on for image fusion?

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## [How to stop a process without "Force Quit"](https://discourse.slicer.org/t/how-to-stop-a-process-without-force-quit/8415)

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**Author:** [@dfafalis](https://discourse.slicer.org/u/dfafalis)\
**Replies:** 7\
**Last updated:** [April 12, 2023, 11:04pm UTC](https://discourse.slicer.org/t/how-to-stop-a-process-without-force-quit/8415 "2023-04-12T23:04:40Z")

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While using effects (any effects available) I very frequently encounter this problem: a window pops up stating that the system is running out of memory and recommends to Force Quit Slicer This happens a lot, either wit…

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## [Issue displaying color legend in other slice views](https://discourse.slicer.org/t/issue-displaying-color-legend-in-other-slice-views/27784)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 10\
**Last updated:** [April 12, 2023, 2:34pm UTC](https://discourse.slicer.org/t/issue-displaying-color-legend-in-other-slice-views/27784 "2023-04-12T14:34:40Z")

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I was trying to display a color legend in some custom slice views when I noticed that it was not showing as I expected. Is there a certain set of conditions to make sure the color legend shows in the other non-standard s…

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## [3D MRI / histology / optical image registration of cardiac images for tissue thickness analysis](https://discourse.slicer.org/t/3d-mri-histology-optical-image-registration-of-cardiac-images-for-tissue-thickness-analysis/28733)

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**Author:** [@MichaelF](https://discourse.slicer.org/u/MichaelF)\
**Replies:** 3\
**Last updated:** [April 12, 2023, 9:35am UTC](https://discourse.slicer.org/t/3d-mri-histology-optical-image-registration-of-cardiac-images-for-tissue-thickness-analysis/28733 "2023-04-12T09:35:34Z")

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Dear Slicer Community, I am looking for help with the co-registration and analysis of 3 different types of data. I have started to develop a pipeline for analysis, but my approach so far has been limited by my experienc…

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## ['ColocZStats' extension install error on Windows](https://discourse.slicer.org/t/coloczstats-extension-install-error-on-windows/28581)

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**Author:** [@CharlesChen](https://discourse.slicer.org/u/CharlesChen)\
**Replies:** 2\
**Last updated:** [April 12, 2023, 3:31am UTC](https://discourse.slicer.org/t/coloczstats-extension-install-error-on-windows/28581 "2023-04-12T03:31:51Z")

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OS: Win 10 Version: 3D Slicer Stable 5.2.2 Hi there, I downloaded and installed the 3D Slicer stable version 5.2.2 on my windows for the first time. After installing the ‘ColocZStats’ extension through its built-in ‘…

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## [Run a 3D Slicer module multiple times on different scans](https://discourse.slicer.org/t/run-a-3d-slicer-module-multiple-times-on-different-scans/28726)

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**Author:** [@rahulhere](https://discourse.slicer.org/u/rahulhere)\
**Replies:** 2\
**Last updated:** [April 11, 2023, 2:38pm UTC](https://discourse.slicer.org/t/run-a-3d-slicer-module-multiple-times-on-different-scans/28726 "2023-04-11T14:38:10Z")

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Hi Team, I need to use the N4ITK MRI Bias correction module of 3D slicer. I have multiple scans on which I want to use the Module. Is there a way to automate running the module on multiple scans (looping basically) and …

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## [Local DICOM folder query](https://discourse.slicer.org/t/local-dicom-folder-query/28840)

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**Author:** [@docmaniac](https://discourse.slicer.org/u/docmaniac)\
**Replies:** 1\
**Last updated:** [April 11, 2023, 2:03pm UTC](https://discourse.slicer.org/t/local-dicom-folder-query/28840 "2023-04-11T14:03:23Z")

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Hi there! Can you tell me if it’s possible to set up the slicer to automatically check a folder for new DICOM files and add them to its database? And, do you know if there are any plugins that can help with this?

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## [Anyone know how to reconstruct thin-slice CT into thick-slice CT with 3D-slicer.](https://discourse.slicer.org/t/anyone-know-how-to-reconstruct-thin-slice-ct-into-thick-slice-ct-with-3d-slicer/28828)

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**Author:** [@guokjdaks](https://discourse.slicer.org/u/guokjdaks)\
**Replies:** 2\
**Last updated:** [April 11, 2023, 4:56am UTC](https://discourse.slicer.org/t/anyone-know-how-to-reconstruct-thin-slice-ct-into-thick-slice-ct-with-3d-slicer/28828 "2023-04-11T04:56:33Z")

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Operating system:windows10 Slicer version:5.0.3 Expected behavior: Actual behavior:

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## [How to import markup control points as nodes?](https://discourse.slicer.org/t/how-to-import-markup-control-points-as-nodes/28806)

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**Author:** [@Vathsan](https://discourse.slicer.org/u/Vathsan)\
**Replies:** 3\
**Last updated:** [April 10, 2023, 8:33pm UTC](https://discourse.slicer.org/t/how-to-import-markup-control-points-as-nodes/28806 "2023-04-10T20:33:29Z")

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I’ve exported a set of markup control points as a table (.csv format). When I import the table, the control points do not appear under nodes section of the markup module. I need to apply a set of transformations to these…

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## [Install the Slicer-deep seg extension](https://discourse.slicer.org/t/install-the-slicer-deep-seg-extension/28756)

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**Author:** [@curtis\_sohn](https://discourse.slicer.org/u/curtis_sohn)\
**Replies:** 1\
**Last updated:** [April 10, 2023, 8:36am UTC](https://discourse.slicer.org/t/install-the-slicer-deep-seg-extension/28756 "2023-04-10T08:36:56Z")

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Hello! Slicer version : 5.2.1 I’m trying to download the Slicer-DeepSeg extension via the 3D Slicer Extension Manager. However, I can’t find the Slicer-Deepseg in the manager. How can I manually install or find a way…

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## [Shape variation analyzer](https://discourse.slicer.org/t/shape-variation-analyzer/23836)

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**Author:** [@lili-yu22](https://discourse.slicer.org/u/lili-yu22)\
**Replies:** 12\
**Last updated:** [April 9, 2023, 6:20pm UTC](https://discourse.slicer.org/t/shape-variation-analyzer/23836 "2023-04-09T18:20:34Z")

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Systerm：win10，slicer5.1.0 l have installed the extension shape variation analyzer，but it shows not loaded，the python interactor shows module not found error：no module named joblib，can you give me some guidelines?

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## [Save transform as .mat](https://discourse.slicer.org/t/save-transform-as-mat/28792)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 1\
**Last updated:** [April 9, 2023, 1:52am UTC](https://discourse.slicer.org/t/save-transform-as-mat/28792 "2023-04-09T01:52:39Z")

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Hi Could some please help me to save a LinearTransform as .mat file using commandline pls. I have checked script repository , and tried chat GPT , Could find anything. I generate 50-100 linear transforms (after model…

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## [Gate bindings for Slicer](https://discourse.slicer.org/t/gate-bindings-for-slicer/28794)

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**Author:** [@Alex\_Vergara](https://discourse.slicer.org/u/Alex_Vergara)\
**Replies:** 2\
**Last updated:** [April 8, 2023, 8:39pm UTC](https://discourse.slicer.org/t/gate-bindings-for-slicer/28794 "2023-04-08T20:39:50Z")

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I’m trying to use Gate inside Slicer within my module OpenDose3D. However, it’s being a bit difficult to install gate as a pip package. slicer.util.pip\_install("opengate") Traceback (most recent call last): File "\<co…

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## [Volume rendering property lock](https://discourse.slicer.org/t/volume-rendering-property-lock/28761)

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**Author:** [@muratmaga](https://discourse.slicer.org/u/muratmaga)\
**Replies:** 12\
**Last updated:** [April 8, 2023, 6:19pm UTC](https://discourse.slicer.org/t/volume-rendering-property-lock/28761 "2023-04-08T18:19:46Z")

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Here is a use case, which comes up often for us, where the current volume rendering interface is quite clunky. I am looking for suggestions on how to implement in data module that will streamline this use case. Basicall…

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## [TotalSegmentator - Missing humerus distal part](https://discourse.slicer.org/t/totalsegmentator-missing-humerus-distal-part/28803)

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**Author:** [@Augusto](https://discourse.slicer.org/u/Augusto)\
**Replies:** 4\
**Last updated:** [April 8, 2023, 12:57pm UTC](https://discourse.slicer.org/t/totalsegmentator-missing-humerus-distal-part/28803 "2023-04-08T12:57:21Z")

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Hello, I am using TotalSegmentator for 3DSlicer version 1.5.5 (which is the most recent one right?) for the segmentation of the clavicle, humerus and scapula bones, using CPU and full resolution mode, in Slicer 5.2.1. T…

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## [Kidney tumor segmentation](https://discourse.slicer.org/t/kidney-tumor-segmentation/28808)

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**Author:** [@zaher\_bahouth](https://discourse.slicer.org/u/zaher_bahouth)\
**Replies:** 2\
**Last updated:** [April 8, 2023, 6:35am UTC](https://discourse.slicer.org/t/kidney-tumor-segmentation/28808 "2023-04-08T06:35:33Z")

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I’m a kidney surgeon, trying to find the best way to do segmentation for kidney and kidney tumors on DICOM ct scans Is there any extension that could be helpful?

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## [How can I fill a hollow area present in a femur head?](https://discourse.slicer.org/t/how-can-i-fill-a-hollow-area-present-in-a-femur-head/28804)

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**Author:** [@JESUS](https://discourse.slicer.org/u/JESUS)\
**Replies:** 1\
**Last updated:** [April 7, 2023, 10:09pm UTC](https://discourse.slicer.org/t/how-can-i-fill-a-hollow-area-present-in-a-femur-head/28804 "2023-04-07T22:09:41Z")

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Hello my name is Jesus, I am doing a project in which I must do a 3D modeling, using DCOM images. But I have a small problem, some areas present in the head of the femur are not completely filled, and I do not know what …

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## [TotalSegmentator will not run in High Res on CPU since updating to 5.2.2](https://discourse.slicer.org/t/totalsegmentator-will-not-run-in-high-res-on-cpu-since-updating-to-5-2-2/28355)

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**Author:** [@Ds44](https://discourse.slicer.org/u/Ds44)\
**Replies:** 3\
**Last updated:** [April 7, 2023, 6:17pm UTC](https://discourse.slicer.org/t/totalsegmentator-will-not-run-in-high-res-on-cpu-since-updating-to-5-2-2/28355 "2023-04-07T18:17:30Z")

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Hi all, Since updating to 5.2.2, I have had trouble with TotalSegmenator. Currently, it will only segment in fast mode even if I click full resolution when prompted to choose. Before I updated it would segment in High…

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## [How can I correct this "Wrap solidify failed: Input segment closed surface representation is empty"?](https://discourse.slicer.org/t/how-can-i-correct-this-wrap-solidify-failed-input-segment-closed-surface-representation-is-empty/28777)

<div class="topic-metadata">

**Author:** [@TOSBABA](https://discourse.slicer.org/u/TOSBABA)\
**Replies:** 3\
**Last updated:** [April 7, 2023, 10:52am UTC](https://discourse.slicer.org/t/how-can-i-correct-this-wrap-solidify-failed-input-segment-closed-surface-representation-is-empty/28777 "2023-04-07T10:52:02Z")

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Hi I am DR Murat, Will appreciate yor help to solve: How can I correct this :Wrap solidify failed: Input segment closed surface representation is empty .?

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## [Save transforms and models as batch](https://discourse.slicer.org/t/save-transforms-and-models-as-batch/28706)

<div class="topic-metadata">

**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 4\
**Last updated:** [April 7, 2023, 10:45am UTC](https://discourse.slicer.org/t/save-transforms-and-models-as-batch/28706 "2023-04-07T10:45:39Z")

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Hi I have a series of models, indexed from 1 to 10. I use the model registration module to register model 1 to all the subsequent models. Then I want to save the transformation matrices as .mat files from 1-10. Could…

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