# Latest

**URL:** https://discourse.slicer.org/latest.md?page=55

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

**Page:** 56

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## [Help with IJK to LPS Conversion Mismatch When Rendering CT Volume Outside Slicer](https://discourse.slicer.org/t/help-with-ijk-to-lps-conversion-mismatch-when-rendering-ct-volume-outside-slicer/43099)

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**Author:** [@Khaleel\_Ur\_Rehman](https://discourse.slicer.org/u/Khaleel_Ur_Rehman)\
**Replies:** 2\
**Last updated:** [May 26, 2025, 7:54pm UTC](https://discourse.slicer.org/t/help-with-ijk-to-lps-conversion-mismatch-when-rendering-ct-volume-outside-slicer/43099 "2025-05-26T19:54:16Z")

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Hello Slicer Community, I’m currently working on a custom algorithm that requires rendering a CT volume in 3D using VTK (outside of Slicer). As part of this, I need to convert the CT image from IJK space to LPS (or RAS)…

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## [Project Week 43 Preparation Meeting (May 27)](https://discourse.slicer.org/t/project-week-43-preparation-meeting-may-27/43042)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 2\
**Last updated:** [May 26, 2025, 4:48pm UTC](https://discourse.slicer.org/t/project-week-43-preparation-meeting-may-27/43042 "2025-05-26T16:48:50Z")

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Dear Project Week community, The next project week preparation meeting will be next Tuesday, May 27th, at 10:00 AM ET. If you are interested in discussing a possible project, please reply to this post with your topic. …

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## [TorchIO Segmentation](https://discourse.slicer.org/t/torchio-segmentation/43105)

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**Author:** [@j\_bu](https://discourse.slicer.org/u/j_bu)\
**Replies:** 0\
**Last updated:** [May 26, 2025, 3:20pm UTC](https://discourse.slicer.org/t/torchio-segmentation/43105 "2025-05-26T15:20:31Z")

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Hi all, I want to use the extension TorchIO to change my CT Scan. Is there any way to change my segmentation along with it so that the organs are still segmentated? As I tried it the segmentation stayed the same and jus…

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## [Easy Hip Planner - how to -easy- turn code to extension?](https://discourse.slicer.org/t/easy-hip-planner-how-to-easy-turn-code-to-extension/43083)

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**Author:** [@Przemek\_Czuma](https://discourse.slicer.org/u/Przemek_Czuma)\
**Replies:** 2\
**Last updated:** [May 26, 2025, 11:41am UTC](https://discourse.slicer.org/t/easy-hip-planner-how-to-easy-turn-code-to-extension/43083 "2025-05-26T11:41:03Z")

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Here’s the situation: I built an application (a Python script) for simple total hip arthroplasty planning. I can’t code at all – I used a few LLMs to get it done. I was testing how far I could go with programming without…

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## [Is possible to create segments by color pallete?](https://discourse.slicer.org/t/is-possible-to-create-segments-by-color-pallete/43094)

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**Author:** [@GioM](https://discourse.slicer.org/u/GioM)\
**Replies:** 1\
**Last updated:** [May 25, 2025, 7:44pm UTC](https://discourse.slicer.org/t/is-possible-to-create-segments-by-color-pallete/43094 "2025-05-25T19:44:42Z")

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Hi all, is it possible to select all the voxels of an image by specifying a color? I have some CT maps of the brain that highlight the areas with different colors, the simplest one has only one color per map. This is a…

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## [CT perfusion coregistration to atlas](https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561)

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**Author:** [@GioM](https://discourse.slicer.org/u/GioM)\
**Replies:** 2\
**Last updated:** [May 25, 2025, 8:40am UTC](https://discourse.slicer.org/t/ct-perfusion-coregistration-to-atlas/42561 "2025-05-25T08:40:34Z")

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Hi all, starting from the CT perfusion DICOM files I obtained the nifti penumbra VOI. Now I want to check which anatomical areas are affected based on the AAL atlas. I am stuck in the coregistration phase. How can I ad…

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## [Which one is the best method for cbct voxel based registration , voxel based from cmf module sometimes doesnt work even doing same thing again and again](https://discourse.slicer.org/t/which-one-is-the-best-method-for-cbct-voxel-based-registration-voxel-based-from-cmf-module-sometimes-doesnt-work-even-doing-same-thing-again-and-again/43082)

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**Author:** [@Pedro\_Flores](https://discourse.slicer.org/u/Pedro_Flores)\
**Replies:** 0\
**Last updated:** [May 25, 2025, 4:31am UTC](https://discourse.slicer.org/t/which-one-is-the-best-method-for-cbct-voxel-based-registration-voxel-based-from-cmf-module-sometimes-doesnt-work-even-doing-same-thing-again-and-again/43082 "2025-05-25T04:31:53Z")

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I have issues with voxel based from CMf module suddenly it just wont work , wich one is the best method for cbct scaners voxel based comparison ?

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## [Thresholding creates squares](https://discourse.slicer.org/t/thresholding-creates-squares/43076)

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**Author:** [@vivaciousviscera](https://discourse.slicer.org/u/vivaciousviscera)\
**Replies:** 1\
**Last updated:** [May 24, 2025, 2:26pm UTC](https://discourse.slicer.org/t/thresholding-creates-squares/43076 "2025-05-24T14:26:56Z")

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When I press “Apply” after setting the threshold values for my segment, it creates squares instead of smooth painted areas over my structures. Any idea on what’s going on here and how to fix this?

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## [Dental Arch Research](https://discourse.slicer.org/t/dental-arch-research/43060)

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**Author:** [@cekrebs](https://discourse.slicer.org/u/cekrebs)\
**Replies:** 2\
**Last updated:** [May 23, 2025, 9:05pm UTC](https://discourse.slicer.org/t/dental-arch-research/43060 "2025-05-23T21:05:37Z")

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Hi everyone! I am currently trying to compare two scans of lower teeth (one scan of a plastic typodont, one scan of a 3D printed version of the typodont). The STL files of the models after being scanned are almost identi…

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## [Automated Dental Tools ALI fail](https://discourse.slicer.org/t/automated-dental-tools-ali-fail/43059)

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**Author:** [@eric6](https://discourse.slicer.org/u/eric6)\
**Replies:** 1\
**Last updated:** [May 23, 2025, 4:02pm UTC](https://discourse.slicer.org/t/automated-dental-tools-ali-fail/43059 "2025-05-23T16:02:31Z")

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Been trying to run ALI on 5.2.2 but this “ModuleNotFoundError: No module named ‘pydicom.pixels’” keeps popping up. Also tried 5.4.0, 5.6.1, and 5.8.1 and different kinds of error messages appeared. Any fixes to this?

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## [Segmenting CT scans taken by circular acquisition](https://discourse.slicer.org/t/segmenting-ct-scans-taken-by-circular-acquisition/43062)

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**Author:** [@sldamico131](https://discourse.slicer.org/u/sldamico131)\
**Replies:** 1\
**Last updated:** [May 23, 2025, 3:04pm UTC](https://discourse.slicer.org/t/segmenting-ct-scans-taken-by-circular-acquisition/43062 "2025-05-23T15:04:47Z")

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Operating system: mac OS Sequoia Slicer version: 5.8.1 I am trying to segment the ossicles in a seal skull. The CT scans were taken I believe using circular acquisition. When I load them into slicer, there are no slice…

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## [Slicermorph GPA outputData.csv query](https://discourse.slicer.org/t/slicermorph-gpa-outputdata-csv-query/43056)

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**Author:** [@elg67](https://discourse.slicer.org/u/elg67)\
**Replies:** 1\
**Last updated:** [May 23, 2025, 2:59pm UTC](https://discourse.slicer.org/t/slicermorph-gpa-outputdata-csv-query/43056 "2025-05-23T14:59:48Z")

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Hiya! Potentially a silly question but have the landmark data within the outputData.csv file from the GPA Slicermorph module already undergone superimposition? Just wondering if I need to use the gpagen() function before…

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## [Registration is now open for Project Week 43](https://discourse.slicer.org/t/registration-is-now-open-for-project-week-43/43064)

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**Author:** [@drouin-simon](https://discourse.slicer.org/u/drouin-simon)\
**Replies:** 0\
**Last updated:** [May 23, 2025, 1:55pm UTC](https://discourse.slicer.org/t/registration-is-now-open-for-project-week-43/43064 "2025-05-23T13:55:41Z")

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Dear Project Week community, We are happy to announce that registration is now open for the 43rd edition of the NAMIC Project Week that will take place at École de Technologie Supérieure in Montreal, Canada, June 23-27 …

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## [how to change the section angle and save it in the files that, when I use other App to open it, the setting is still what I wanted](https://discourse.slicer.org/t/how-to-change-the-section-angle-and-save-it-in-the-files-that-when-i-use-other-app-to-open-it-the-setting-is-still-what-i-wanted/43061)

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**Author:** [@xiaoqian](https://discourse.slicer.org/u/xiaoqian)\
**Replies:** 0\
**Last updated:** [May 23, 2025, 11:10am UTC](https://discourse.slicer.org/t/how-to-change-the-section-angle-and-save-it-in-the-files-that-when-i-use-other-app-to-open-it-the-setting-is-still-what-i-wanted/43061 "2025-05-23T11:10:35Z")

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PC(Mac OS ,3D slicer 5.8.1) My problem is that I do not want to change the actual spatial information or rotate the image itself; instead, I simply want to redefine the default slice orientations so that the data is di…

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## [Morphocloud instance leads to empty black screen](https://discourse.slicer.org/t/morphocloud-instance-leads-to-empty-black-screen/43049)

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**Author:** [@cliftong](https://discourse.slicer.org/u/cliftong)\
**Replies:** 1\
**Last updated:** [May 22, 2025, 11:55pm UTC](https://discourse.slicer.org/t/morphocloud-instance-leads-to-empty-black-screen/43049 "2025-05-22T23:55:18Z")

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I unshelved a new instance (instance-278, g.xl), but it never fully loads, leaving an empty black screen. I can open up the side toolbar, but nothing else. I can’t even right-click to bring up the desktop menu. I tried t…

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## [Turn off Slice edge in 3d view](https://discourse.slicer.org/t/turn-off-slice-edge-in-3d-view/43047)

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**Author:** [@bgoodell](https://discourse.slicer.org/u/bgoodell)\
**Replies:** 1\
**Last updated:** [May 22, 2025, 10:44pm UTC](https://discourse.slicer.org/t/turn-off-slice-edge-in-3d-view/43047 "2025-05-22T22:44:37Z")

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Problem report for Slicer 5.8.1 win-amd64: In settings-\>view I have unchecked the “Show slice edge in 3d” checkbox but after restarting the red, green and yellow rectangular outlines are still shown in the 3d view. it …

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## [Error writing MRML and MRB files on mapped drive](https://discourse.slicer.org/t/error-writing-mrml-and-mrb-files-on-mapped-drive/43029)

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**Author:** [@ezgimercan](https://discourse.slicer.org/u/ezgimercan)\
**Replies:** 1\
**Last updated:** [May 22, 2025, 3:54pm UTC](https://discourse.slicer.org/t/error-writing-mrml-and-mrb-files-on-mapped-drive/43029 "2025-05-22T15:54:08Z")

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I am using latest stable, 5.8.1 on Ubuntu 22.04. I have some research drives mounted with autofs (nfs). Slicer complains that the locations is not writable when I try to save MRB or MRML files. I can save/write/export ev…

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## [Are there any non medical development and application cases here?](https://discourse.slicer.org/t/are-there-any-non-medical-development-and-application-cases-here/31650)

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**Author:** [@iwangwangwang](https://discourse.slicer.org/u/iwangwangwang)\
**Replies:** 3\
**Last updated:** [September 12, 2023, 5:47pm UTC](https://discourse.slicer.org/t/are-there-any-non-medical-development-and-application-cases-here/31650 "2023-09-12T17:47:44Z")

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Are there any non medical development and application cases here? Please give me some guidance

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## [How to Hide Specific Toolbars in Custom AppSlicer Build (Markups, Sequence Browser, etc.)](https://discourse.slicer.org/t/how-to-hide-specific-toolbars-in-custom-appslicer-build-markups-sequence-browser-etc/43033)

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**Author:** [@software](https://discourse.slicer.org/u/software)\
**Replies:** 0\
**Last updated:** [May 22, 2025, 8:18am UTC](https://discourse.slicer.org/t/how-to-hide-specific-toolbars-in-custom-appslicer-build-markups-sequence-browser-etc/43033 "2025-05-22T08:18:18Z")

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Hi everyone, I’ve created a custom NewAppSlicer build using Kitware’s 3D Slicer source. Everything is working great, but I’m running into a UI customization issue. From the View \> Toolbars menu, I want to permanently h…

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## [Graphics processor in MorphoCloud not working?](https://discourse.slicer.org/t/graphics-processor-in-morphocloud-not-working/43027)

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**Author:** [@Dave\_Matthews](https://discourse.slicer.org/u/Dave_Matthews)\
**Replies:** 2\
**Last updated:** [May 21, 2025, 8:22pm UTC](https://discourse.slicer.org/t/graphics-processor-in-morphocloud-not-working/43027 "2025-05-21T20:22:15Z")

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I recently initiated a MorphoCloud instance (Instance-277, g3.xl) and it was working great this morning. However, this afternoon I unshelved it and tried to load in the same dataset I was working with earlier. This time…

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## [SlicerUltrasound extension - when might it be updated through the manager?](https://discourse.slicer.org/t/slicerultrasound-extension-when-might-it-be-updated-through-the-manager/43025)

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**Author:** [@Tina\_Kapur](https://discourse.slicer.org/u/Tina_Kapur)\
**Replies:** 1\
**Last updated:** [May 21, 2025, 7:37pm UTC](https://discourse.slicer.org/t/slicerultrasound-extension-when-might-it-be-updated-through-the-manager/43025 "2025-05-21T19:37:54Z")

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Hello, we’ve fixed a few bugs in the SlicerUltrasound extension and would like current users to download it using the extension manager. Where can I look up the status of where it is stuck? Sorry that I don’t know alread…

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## [How to Create and Export En Face Images in 3D Slicer?](https://discourse.slicer.org/t/how-to-create-and-export-en-face-images-in-3d-slicer/43021)

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**Author:** [@Ahmed\_Raza](https://discourse.slicer.org/u/Ahmed_Raza)\
**Replies:** 1\
**Last updated:** [May 21, 2025, 7:01pm UTC](https://discourse.slicer.org/t/how-to-create-and-export-en-face-images-in-3d-slicer/43021 "2025-05-21T19:01:38Z")

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Hi everyone, I’m working with volumetric OCT data in 3D Slicer and would like to generate en face images. Could someone please guide me on: How to create en face views from a 3D volume? How to extract or export these…

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## [Loading and displaying DICOM Structured Reports](https://discourse.slicer.org/t/loading-and-displaying-dicom-structured-reports/42754)

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**Author:** [@DeepaKrishnaswamy](https://discourse.slicer.org/u/DeepaKrishnaswamy)\
**Replies:** 9\
**Last updated:** [May 21, 2025, 6:50pm UTC](https://discourse.slicer.org/t/loading-and-displaying-dicom-structured-reports/42754 "2025-05-21T18:50:19Z")

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Hi, I have been working on some changes to the QuantitativeReporting plugin for loading DICOM Structured Reports. Currently, the extension supports the loading of measurements. Now, we can load and display bounding boxe…

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## [Using Slicer for Diffusion MRI in cancer research? We want to hear from you!](https://discourse.slicer.org/t/using-slicer-for-diffusion-mri-in-cancer-research-we-want-to-hear-from-you/42986)

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**Author:** [@ljod](https://discourse.slicer.org/u/ljod)\
**Replies:** 1\
**Last updated:** [May 21, 2025, 3:03pm UTC](https://discourse.slicer.org/t/using-slicer-for-diffusion-mri-in-cancer-research-we-want-to-hear-from-you/42986 "2025-05-21T15:03:22Z")

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Are you using Slicer for diffusion MRI in cancer research? We’d love to hear how you’re using it and get your quick feedback! Please respond by Monday May 19 (or Tuesday at the latest) to help our funding efforts to impr…

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## [Incorrect method signature for addAttribute of qMRMLNodeComboBox?](https://discourse.slicer.org/t/incorrect-method-signature-for-addattribute-of-qmrmlnodecombobox/43015)

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**Author:** [@jamesobutler](https://discourse.slicer.org/u/jamesobutler)\
**Replies:** 2\
**Last updated:** [May 21, 2025, 10:48am UTC](https://discourse.slicer.org/t/incorrect-method-signature-for-addattribute-of-qmrmlnodecombobox/43015 "2025-05-21T10:48:07Z")

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Using Slicer Preview 5.9.0-2025-05-16 When calling a qMRMLNodeComboBox addAttribute with 2 input arguments I observe no error however the help method indicates there should be 3 input arguments: node\_combobox = slicer.…

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## [Make it possible to pan in Flood Fill](https://discourse.slicer.org/t/make-it-possible-to-pan-in-flood-fill/43017)

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**Author:** [@Fishguy](https://discourse.slicer.org/u/Fishguy)\
**Replies:** 0\
**Last updated:** [May 21, 2025, 4:58am UTC](https://discourse.slicer.org/t/make-it-possible-to-pan-in-flood-fill/43017 "2025-05-21T04:58:19Z")

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I still use flood fill as a segmentation tool. it seems that the ability to pan by holding down the shift key is not enabled. Clicking on a slice with the shift down elicits the flood fill rather than allowing me to shi…

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## [SlicerSALT 5.0: Summary, Highlights and Changelog](https://discourse.slicer.org/t/slicersalt-5-0-summary-highlights-and-changelog/39546)

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**Author:** [@bpaniagua](https://discourse.slicer.org/u/bpaniagua)\
**Replies:** 10\
**Last updated:** [May 21, 2025, 2:13am UTC](https://discourse.slicer.org/t/slicersalt-5-0-summary-highlights-and-changelog/39546 "2025-05-21T02:13:41Z")

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The SlicerSALT team is proud to announce that version 5.0 is now available for download. This release introduces new features as well as bug fixes for better performance and stability. This release of SlicerSALT includes…

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## ['Global' FW/FA Inquiry - whitematteranalysis](https://discourse.slicer.org/t/global-fw-fa-inquiry-whitematteranalysis/40989)

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**Author:** [@kvandeloo](https://discourse.slicer.org/u/kvandeloo)\
**Replies:** 1\
**Last updated:** [May 20, 2025, 3:56pm UTC](https://discourse.slicer.org/t/global-fw-fa-inquiry-whitematteranalysis/40989 "2025-05-20T15:56:02Z")

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I’m using whitematteranalysis for whole-brain tractography analysis (Tutorial - whitematteranalysis 0.4.0 documentation). Using this tutorial, I’m able to derive FA and FW from anatomical tracts and/or 800 fibre clusters…

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## [Please help me to interpret the following running bone texture module](https://discourse.slicer.org/t/please-help-me-to-interpret-the-following-running-bone-texture-module/43008)

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**Author:** [@BsNghia](https://discourse.slicer.org/u/BsNghia)\
**Replies:** 0\
**Last updated:** [May 20, 2025, 6:36am UTC](https://discourse.slicer.org/t/please-help-me-to-interpret-the-following-running-bone-texture-module/43008 "2025-05-20T06:36:47Z")

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Hi, everone, I dont know the parameters unit, so it is so hard to figure out. Thank you!

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## [ZEISS .zinspect microCT conversion](https://discourse.slicer.org/t/zeiss-zinspect-microct-conversion/43000)

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**Author:** [@arumiat](https://discourse.slicer.org/u/arumiat)\
**Replies:** 3\
**Last updated:** [May 20, 2025, 5:46am UTC](https://discourse.slicer.org/t/zeiss-zinspect-microct-conversion/43000 "2025-05-20T05:46:51Z")

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Dear Slicer Community, Does anyone know of any workflows, tools or extensions that would allow the conversion of a ZEISS .zinspect microCT study to be converted to a format readable by Slicer3D or other imaging software…

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