# Support

**URL:** https://discourse.slicer.org/c/support/11.md?page=136

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

**Page:** 137

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## [How to clean up temp file after cropping volume](https://discourse.slicer.org/t/how-to-clean-up-temp-file-after-cropping-volume/12939)

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**Author:** [@ungi](https://discourse.slicer.org/u/ungi)\
**Replies:** 4\
**Last updated:** [August 11, 2020, 4:44am UTC](https://discourse.slicer.org/t/how-to-clean-up-temp-file-after-cropping-volume/12939 "2020-08-11T04:44:12Z")

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Hi, I have a script that automatically crops (and resamples) my volumes in Slicer. It works fine, but every time it runs, it leaves a copy of the original volume in the temp folder. In my case, here: c:\\Users\\tamas\\App…

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## [Downloading a dicom folder](https://discourse.slicer.org/t/downloading-a-dicom-folder/32111)

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**Author:** [@bharat](https://discourse.slicer.org/u/bharat)\
**Replies:** 1\
**Last updated:** [October 9, 2023, 4:22pm UTC](https://discourse.slicer.org/t/downloading-a-dicom-folder/32111 "2023-10-09T16:22:36Z")

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greetings I have Slicer 3d 5.40 version. when I try to download a folder, individual slices get loaded as per the images attached. what am I doing wrong?. bharat m. mody

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## [to open the RDSR of clinical images](https://discourse.slicer.org/t/to-open-the-rdsr-of-clinical-images/32107)

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**Author:** [@atorresin](https://discourse.slicer.org/u/atorresin)\
**Replies:** 1\
**Last updated:** [October 9, 2023, 4:21pm UTC](https://discourse.slicer.org/t/to-open-the-rdsr-of-clinical-images/32107 "2023-10-09T16:21:28Z")

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Operating system: macOS 14.0 Slicer version: 5.2.2 Expected behavior: Actual behavior: I need to open and to read the RDSR SOP class. Is it possible using Slicer? thanks alberto

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## [Segmentating bone in Total Segmentator](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399)

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**Author:** [@KEF](https://discourse.slicer.org/u/KEF)\
**Replies:** 10\
**Last updated:** [October 9, 2023, 2:43pm UTC](https://discourse.slicer.org/t/segmentating-bone-in-total-segmentator/29399 "2023-10-09T14:43:23Z")

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Hello I am new to 3D slicer and I am currently testing it to segment bone. I just downloaded the Total segmentator extention and tried to apply it to a CT of two legs. When the prosess finished it curiously only chose t…

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## [More precision of TotalSegmentator?](https://discourse.slicer.org/t/more-precision-of-totalsegmentator/32036)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 6\
**Last updated:** [October 9, 2023, 2:08pm UTC](https://discourse.slicer.org/t/more-precision-of-totalsegmentator/32036 "2023-10-09T14:08:10Z")

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Hi, Is there some way to get better resolution when using TotalSegmentator (less than the default resolution of 1.5mm)? Or is there any other program?

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## [How to quickly and automatically divide kidneys](https://discourse.slicer.org/t/how-to-quickly-and-automatically-divide-kidneys/32077)

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**Author:** [@wl301](https://discourse.slicer.org/u/wl301)\
**Replies:** 1\
**Last updated:** [October 8, 2023, 10:48pm UTC](https://discourse.slicer.org/t/how-to-quickly-and-automatically-divide-kidneys/32077 "2023-10-08T22:48:10Z")

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Operating system:window10 Slicer version:slicer5.4.0 Expected behavior:automatically divide kidneys Actual behavior:

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## [What is the best way to smoothing TotalSegmentator result?](https://discourse.slicer.org/t/what-is-the-best-way-to-smoothing-totalsegmentator-result/32096)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 2\
**Last updated:** [October 8, 2023, 10:45pm UTC](https://discourse.slicer.org/t/what-is-the-best-way-to-smoothing-totalsegmentator-result/32096 "2023-10-08T22:45:37Z")

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Hi, i used TotalSegmentator to segment tibial bone, but the result is not as smooth as using seed and growth, even after configure the smoothing factor into 1. Is there some procedure to make it smoother?

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## [Text annotations in multiple 3D viewers](https://discourse.slicer.org/t/text-annotations-in-multiple-3d-viewers/32093)

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**Author:** [@S\_Motch\_Perrine](https://discourse.slicer.org/u/S_Motch_Perrine)\
**Replies:** 1\
**Last updated:** [October 8, 2023, 12:29am UTC](https://discourse.slicer.org/t/text-annotations-in-multiple-3d-viewers/32093 "2023-10-08T00:29:39Z")

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Overview of the issue: I want text data associated with scans to show as annotations in the 3D viewer or viewers in which the specific scan is being visualized. The ultimate goal is to be able to have multiple lines of t…

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## [VMTK Module - extract center line makes the model invisible / erased!](https://discourse.slicer.org/t/vmtk-module-extract-center-line-makes-the-model-invisible-erased/32084)

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**Author:** [@Henry\_Lopes](https://discourse.slicer.org/u/Henry_Lopes)\
**Replies:** 0\
**Last updated:** [October 7, 2023, 5:33am UTC](https://discourse.slicer.org/t/vmtk-module-extract-center-line-makes-the-model-invisible-erased/32084 "2023-10-07T05:33:14Z")

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So many times (almost always) when I use the “extract center line” function of the VMTK module, the model I used as input surface is blanked (it still appears in DATA, but invisible in any view even with visibility marke…

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## [Registration on intersecting volumes](https://discourse.slicer.org/t/registration-on-intersecting-volumes/32083)

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**Author:** [@wesselk](https://discourse.slicer.org/u/wesselk)\
**Replies:** 1\
**Last updated:** [October 6, 2023, 10:27pm UTC](https://discourse.slicer.org/t/registration-on-intersecting-volumes/32083 "2023-10-06T22:27:18Z")

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Hello, I am trying to concatenate 2 CT volumes into 1 continuous volume. I realize that registration is generally intended for 2 scans with nearly identical captured anatomy, but I was hoping to essentially stitch toget…

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## [CMake error in SlicerExtensionCPack.cmake while configuring extension](https://discourse.slicer.org/t/cmake-error-in-slicerextensioncpack-cmake-while-configuring-extension/32080)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 1\
**Last updated:** [October 6, 2023, 9:42pm UTC](https://discourse.slicer.org/t/cmake-error-in-slicerextensioncpack-cmake-while-configuring-extension/32080 "2023-10-06T21:42:50Z")

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I am getting the error below while trying to configure the build for the SlicerIDCBrowser extension. The error seems to be unrelated to the extension. Does anyone know how to work around it? I am using the latest, and t…

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## [Slicer window is blank](https://discourse.slicer.org/t/slicer-window-is-blank/32081)

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**Author:** [@Priyanka](https://discourse.slicer.org/u/Priyanka)\
**Replies:** 0\
**Last updated:** [October 6, 2023, 7:55pm UTC](https://discourse.slicer.org/t/slicer-window-is-blank/32081 "2023-10-06T19:55:12Z")

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Hello, I have been using 3D slicer for a bit, and 3D window now appears blank. I have attached the screenshot, how can I fix that? Thanks, Priyanka

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## [Segmenting Canon Ultrasound volumes ](https://discourse.slicer.org/t/segmenting-canon-ultrasound-volumes/31240)

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**Author:** [@Ladnewg](https://discourse.slicer.org/u/Ladnewg)\
**Replies:** 2\
**Last updated:** [October 6, 2023, 6:15pm UTC](https://discourse.slicer.org/t/segmenting-canon-ultrasound-volumes/31240 "2023-10-06T18:15:27Z")

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Hi ! I am currently working on an ultrasound project. I use the equipment: following Aplio I700 Canon with Smart Sensor 3D mode: Magnetic tracking system. I acquired a series of images of a ghost in order to calculate…

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## [Empty segmentation saved to file, but after reload cannot modify](https://discourse.slicer.org/t/empty-segmentation-saved-to-file-but-after-reload-cannot-modify/32078)

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**Author:** [@Tamisu](https://discourse.slicer.org/u/Tamisu)\
**Replies:** 0\
**Last updated:** [October 6, 2023, 5:53pm UTC](https://discourse.slicer.org/t/empty-segmentation-saved-to-file-but-after-reload-cannot-modify/32078 "2023-10-06T17:53:00Z")

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Hello! I have a problem. I do this: Load a 2D image Create a segmentation in Segment editor (no click on Add) Then save it to file. (A seg.nrrd is created) Close the scene Reload the 2D image, reload the segmentation C…

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## [Reopening file with linear transformation](https://discourse.slicer.org/t/reopening-file-with-linear-transformation/32076)

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**Author:** [@megmgast](https://discourse.slicer.org/u/megmgast)\
**Replies:** 0\
**Last updated:** [October 6, 2023, 5:52pm UTC](https://discourse.slicer.org/t/reopening-file-with-linear-transformation/32076 "2023-10-06T17:52:55Z")

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Operating system: Mac OS Ventura 13.5.2 Slicer version: 5.4.0 Expected behavior: Open saved mrml file, or combination of nrrd, transformation and 3d image files with transformation Actual behavior: When reopening file…

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## [MarkupsToModel generic error warning for surface generation](https://discourse.slicer.org/t/markupstomodel-generic-error-warning-for-surface-generation/32071)

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**Author:** [@helenawill95](https://discourse.slicer.org/u/helenawill95)\
**Replies:** 0\
**Last updated:** [October 6, 2023, 2:50pm UTC](https://discourse.slicer.org/t/markupstomodel-generic-error-warning-for-surface-generation/32071 "2023-10-06T14:50:55Z")

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I’m currently having a generic warning using MarkUpsToModel to produce a model from fiducial nodes. I have this error (but can’t find the source of the problem): \[VTK\] Generic Warning: In D:\\D\\S\\S-0-E-b\\MarkupsToModel\\M…

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## [Vagina segmentation and reconstruction from MRI image](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989)

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**Author:** [@Miri\_Trope](https://discourse.slicer.org/u/Miri_Trope)\
**Replies:** 5\
**Last updated:** [October 6, 2023, 2:00pm UTC](https://discourse.slicer.org/t/vagina-segmentation-and-reconstruction-from-mri-image/31989 "2023-10-06T14:00:52Z")

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Dear community, I am currently in the process of segmenting the vagina from MRI images. I came across a research paper where they used OsiriX to delineate the vaginal contour (vagina\_sed\_1). I’m curious if Slicer, offer…

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## [Skin segmentation in 3D slicer](https://discourse.slicer.org/t/skin-segmentation-in-3d-slicer/32066)

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**Author:** [@Chuan](https://discourse.slicer.org/u/Chuan)\
**Replies:** 0\
**Last updated:** [October 6, 2023, 8:59am UTC](https://discourse.slicer.org/t/skin-segmentation-in-3d-slicer/32066 "2023-10-06T08:59:29Z")

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Hi, Basically my task is to extract skin surface of infant whole body from CT image, but the limitation is my CT image comes from a dead baby with sunken skin in some areas, as you can see in the figure. The figure is …

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## [I need help: Encountered "Could not load ... as a scalar volume" when loading MRI sequence](https://discourse.slicer.org/t/i-need-help-encountered-could-not-load-as-a-scalar-volume-when-loading-mri-sequence/32038)

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**Author:** [@IrisFang](https://discourse.slicer.org/u/IrisFang)\
**Replies:** 4\
**Last updated:** [October 6, 2023, 7:43am UTC](https://discourse.slicer.org/t/i-need-help-encountered-could-not-load-as-a-scalar-volume-when-loading-mri-sequence/32038 "2023-10-06T07:43:46Z")

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Dear developer, Hello~ When I loaded the MRI image sequence today, the software kept reporting errors, “Could not load: 23: t1\_quick3d\_tra\_fs\_bh\_P\_MPRTRA as a Scalar Volume”, but there was no problem when loading CT im…

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## [Sample data post-processing](https://discourse.slicer.org/t/sample-data-post-processing/32059)

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**Author:** [@zhang](https://discourse.slicer.org/u/zhang)\
**Replies:** 1\
**Last updated:** [October 6, 2023, 4:55am UTC](https://discourse.slicer.org/t/sample-data-post-processing/32059 "2023-10-06T04:55:00Z")

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I am a neurosurgeon. Can I use 3D Slicer software for sample data post-processing and publish related papers aimed at conducting brain anatomy learning research, without involving commercial purposes? Is it related to in…

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## [Need help understanding how Slicer DICOM database is initialized](https://discourse.slicer.org/t/need-help-understanding-how-slicer-dicom-database-is-initialized/32056)

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**Author:** [@fedorov](https://discourse.slicer.org/u/fedorov)\
**Replies:** 2\
**Last updated:** [October 5, 2023, 9:51pm UTC](https://discourse.slicer.org/t/need-help-understanding-how-slicer-dicom-database-is-initialized/32056 "2023-10-05T21:51:00Z")

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I am trying to make an extension I am developing robust when launched right after Slicer install, where DICOM database is not initialized. I would like to understand 1) how to detect this; 2) how to address this. What i…

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## [Saving/re-opening transformed data](https://discourse.slicer.org/t/saving-re-opening-transformed-data/32044)

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**Author:** [@tybone2323](https://discourse.slicer.org/u/tybone2323)\
**Replies:** 2\
**Last updated:** [October 5, 2023, 5:55pm UTC](https://discourse.slicer.org/t/saving-re-opening-transformed-data/32044 "2023-10-05T17:55:44Z")

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When I transform my data and harden the transform, the next time I load the data it is no longer oriented in the way I switched it to. Does anyone know what is happening? (I’m on Windows)

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## [Adding progress bar to centerline computation](https://discourse.slicer.org/t/adding-progress-bar-to-centerline-computation/32053)

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**Author:** [@b\_gop](https://discourse.slicer.org/u/b_gop)\
**Replies:** 0\
**Last updated:** [October 5, 2023, 2:47pm UTC](https://discourse.slicer.org/t/adding-progress-bar-to-centerline-computation/32053 "2023-10-05T14:47:01Z")

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Is there any way I can add a progress bar to the centerline computation without having to build from source and ideally just using the python console? Or some other way to visualise the progress?

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## [How to change the application name of Slicer?](https://discourse.slicer.org/t/how-to-change-the-application-name-of-slicer/13521)

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**Author:** [@Chintha\_Siva\_Prasad](https://discourse.slicer.org/u/Chintha_Siva_Prasad)\
**Replies:** 3\
**Last updated:** [October 5, 2023, 12:38pm UTC](https://discourse.slicer.org/t/how-to-change-the-application-name-of-slicer/13521 "2023-10-05T12:38:03Z")

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I changed the appllicationName, applicationDisplayName by slicer.util module. But the window title is not changing, its still Slicer(version).

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## [Setting for multi tif files](https://discourse.slicer.org/t/setting-for-multi-tif-files/32042)

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**Author:** [@jp\_jp\_jp](https://discourse.slicer.org/u/jp_jp_jp)\
**Replies:** 1\
**Last updated:** [October 4, 2023, 9:35pm UTC](https://discourse.slicer.org/t/setting-for-multi-tif-files/32042 "2023-10-04T21:35:58Z")

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Hi, I have a group of tif files that are slicers of the subject, so now what I am doing is adding the folder of the tif files, then Slicer will show me the whole object, but when the CT scanning was performed, there was …

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## [Compare chin bone orientation between the pre-operative planning and post operative result](https://discourse.slicer.org/t/compare-chin-bone-orientation-between-the-pre-operative-planning-and-post-operative-result/31753)

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**Author:** [@wael\_telha](https://discourse.slicer.org/u/wael_telha)\
**Replies:** 3\
**Last updated:** [October 4, 2023, 7:13pm UTC](https://discourse.slicer.org/t/compare-chin-bone-orientation-between-the-pre-operative-planning-and-post-operative-result/31753 "2023-10-04T19:13:24Z")

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How can i measure the yaw, pitch and roll for bone advancement of the chin to compare between the pre-operative planning and post-operative result ( material provided is in form of STL

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## [What is the best way to segment bone?](https://discourse.slicer.org/t/what-is-the-best-way-to-segment-bone/32035)

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**Author:** [@zariliusra](https://discourse.slicer.org/u/zariliusra)\
**Replies:** 0\
**Last updated:** [October 4, 2023, 5:02pm UTC](https://discourse.slicer.org/t/what-is-the-best-way-to-segment-bone/32035 "2023-10-04T17:02:16Z")

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Hi, I’m trying to segmented around 30 tibial bone CT scan. What is the best way to do it? By using threshold segmentation, seed and grow, or using TotalSegmentator?

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## [Using Flywheel Connect extension and ACPC alignment module simultaneously](https://discourse.slicer.org/t/using-flywheel-connect-extension-and-acpc-alignment-module-simultaneously/32019)

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**Author:** [@SKYslicer](https://discourse.slicer.org/u/SKYslicer)\
**Replies:** 0\
**Last updated:** [October 3, 2023, 8:24pm UTC](https://discourse.slicer.org/t/using-flywheel-connect-extension-and-acpc-alignment-module-simultaneously/32019 "2023-10-03T20:24:28Z")

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Operating system: MacOS Sonoma 14.0 Slicer version: 5.4.0 Expected behavior: Recently downloaded Flywheel-Connect Extension so that I could ACPC align brain images and bring Slicer outputs back to Flywheel. Actual b…

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## [Translating of a line](https://discourse.slicer.org/t/translating-of-a-line/32001)

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**Author:** [@Grigoriy\_Postolskiy](https://discourse.slicer.org/u/Grigoriy_Postolskiy)\
**Replies:** 4\
**Last updated:** [October 3, 2023, 12:59pm UTC](https://discourse.slicer.org/t/translating-of-a-line/32001 "2023-10-03T12:59:40Z")

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Hello! I assigned the function of moving a line to the left mouse button. But as a result, the function of moving of individual points of the line stopped working. How can I make it so that when you hover the mouse ove…

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## [Monai Label in 3d slicer -auto segmentation is not working for loaded data](https://discourse.slicer.org/t/monai-label-in-3d-slicer-auto-segmentation-is-not-working-for-loaded-data/30122)

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**Author:** [@linda\_varghese](https://discourse.slicer.org/u/linda_varghese)\
**Replies:** 15\
**Last updated:** [October 3, 2023, 7:45pm UTC](https://discourse.slicer.org/t/monai-label-in-3d-slicer-auto-segmentation-is-not-working-for-loaded-data/30122 "2023-10-03T19:45:25Z")

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Hi Team, I am facing trouble to get the model to run on auto segmentation,I tried with the sample datatsets with segmentation-spleen model and even on deepedit model,in both case autosegmentation is not showing any mode…

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