# SlicerAutoscoperM

**URL:** https://discourse.slicer.org/c/community/slicerautoscoperm/30.md

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

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## [About the SlicerAutoscoperM category](https://discourse.slicer.org/t/about-the-slicerautoscoperm-category/23599)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 0

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SlicerAutoscoperM is a Slicer extension currently under development, dedicated to image-based 3D motion tracking of skeletal structures. Our goal is to provide researchers and developers with a powerful tool for precise…

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## [Applying boundary constraints to DRR volumes in SlicerAutoscoperM](https://discourse.slicer.org/t/applying-boundary-constraints-to-drr-volumes-in-slicerautoscoperm/48084)

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**Author:** [@Dorte](https://discourse.slicer.org/u/Dorte)\
**Replies:** 1\
**Last updated:** [September 14, 2026, 2:23pm UTC](https://discourse.slicer.org/t/applying-boundary-constraints-to-drr-volumes-in-slicerautoscoperm/48084 "2026-09-14T14:23:55Z")

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Hello community, I’m working with monoplanar videoradiography, and I’m trying to reduce depth ambiguity during bone tracking. I was wondering whether SlicerAutoscoperM allows applying geometric or anatomical boundary c…

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## [Recurring bug on Shoulder tracking](https://discourse.slicer.org/t/recurring-bug-on-shoulder-tracking/47656)

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**Author:** [@AlonsoFigueroa](https://discourse.slicer.org/u/AlonsoFigueroa)\
**Replies:** 12\
**Last updated:** [August 27, 2026, 4:13pm UTC](https://discourse.slicer.org/t/recurring-bug-on-shoulder-tracking/47656 "2026-08-27T16:13:35Z")

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Hello SAM team, We are encountering an issue while tracking a scapula in Autoscoper during an arm elevation task. For one participant, Autoscoper consistently crashes when saving frames within specific ranges of motion…

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## [TIFF volume orientation does not match source STL orientation](https://discourse.slicer.org/t/tiff-volume-orientation-does-not-match-source-stl-orientation/47582)

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**Author:** [@tbugajski](https://discourse.slicer.org/u/tbugajski)\
**Replies:** 9\
**Last updated:** [July 15, 2026, 4:08pm UTC](https://discourse.slicer.org/t/tiff-volume-orientation-does-not-match-source-stl-orientation/47582 "2026-07-15T16:08:41Z")

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Hi SAM team, We have been successfully using SAM to create partial volumes from CT segmentations, track these volumes, and apply the resulting transformations to AUT models in MATLAB to visualize motion. We are now try…

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## [How to convert a 4x4 matrix to inter-bone kinematic parameters](https://discourse.slicer.org/t/how-to-convert-a-4x4-matrix-to-inter-bone-kinematic-parameters/46986)

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**Author:** [@HHH](https://discourse.slicer.org/u/HHH)\
**Replies:** 3\
**Last updated:** [May 28, 2026, 1:59pm UTC](https://discourse.slicer.org/t/how-to-convert-a-4x4-matrix-to-inter-bone-kinematic-parameters/46986 "2026-05-28T13:59:11Z")

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Hello everyone, I am working on a knee joint registration project. According to the experience of predecessors, I have obtained a 4x4 matrix, but I am unable to calculate the kinematics of the knee joint. I am seeking he…

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## [Create new cfg error RadRenderer](https://discourse.slicer.org/t/create-new-cfg-error-radrenderer/46809)

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**Author:** [@Jeffrey\_K\_Spear](https://discourse.slicer.org/u/Jeffrey_K_Spear)\
**Replies:** 2\
**Last updated:** [April 22, 2026, 9:13pm UTC](https://discourse.slicer.org/t/create-new-cfg-error-radrenderer/46809 "2026-04-22T21:13:45Z")

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Hello, I am trying to create a new .cfg file. I launch Autoscoper, click ‘new file’, add the calibration files, radiographs (), and partial volumes. When I click ‘OK’ Autoscoper shuts down and the following error gets s…

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## [Inquiry about SlicerAutoscoperM-related Operations for Knee Joint Research and Video Tutorials](https://discourse.slicer.org/t/inquiry-about-slicerautoscoperm-related-operations-for-knee-joint-research-and-video-tutorials/44975)

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**Author:** [@gao](https://discourse.slicer.org/u/gao)\
**Replies:** 2\
**Last updated:** [April 21, 2026, 3:26pm UTC](https://discourse.slicer.org/t/inquiry-about-slicerautoscoperm-related-operations-for-knee-joint-research-and-video-tutorials/44975 "2026-04-21T15:26:56Z")

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As a beginner in SlicerAutoscoperM, I am currently focused on knee joint research. After successfully registering biplane data, I obtained a 4x4 homogeneous matrix. How can I derive the flexion angle, internal-external r…

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## [Generating configuration files in the Autscoper preprocessing module](https://discourse.slicer.org/t/generating-configuration-files-in-the-autscoper-preprocessing-module/36882)

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**Author:** [@Amy\_Morton](https://discourse.slicer.org/u/Amy_Morton)\
**Replies:** 3\
**Last updated:** [April 20, 2026, 5:09pm UTC](https://discourse.slicer.org/t/generating-configuration-files-in-the-autscoper-preprocessing-module/36882 "2026-04-20T17:09:07Z")

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@Jeffrey\_K\_Spear Could you add some details about your data, which you’re trying to prep for use in Autoscoper?

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## [Adaptibility AutoScoper source code](https://discourse.slicer.org/t/adaptibility-autoscoper-source-code/46579)

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**Author:** [@Sebastiaan](https://discourse.slicer.org/u/Sebastiaan)\
**Replies:** 3\
**Last updated:** [April 17, 2026, 3:36pm UTC](https://discourse.slicer.org/t/adaptibility-autoscoper-source-code/46579 "2026-04-17T15:36:16Z")

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Hi all, I am currently working on a MSc Thesis project with mono-planar fluoroscopy images. A current struggle for me is accurate registration of the 3D bone models from MRI or CT to fluoroscopy images. To further optim…

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## [Autoscoper crashes when trying to load](https://discourse.slicer.org/t/autoscoper-crashes-when-trying-to-load/45790)

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**Author:** [@Janae](https://discourse.slicer.org/u/Janae)\
**Replies:** 11\
**Last updated:** [April 6, 2026, 11:02am UTC](https://discourse.slicer.org/t/autoscoper-crashes-when-trying-to-load/45790 "2026-04-06T11:02:19Z")

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Hello, I have not been able to successfully open Autoscoper and have been receiving the error message included below. I have Slicer 5.10.0 and Autoscoper last update “Mon Nov 10 2025 (Revision: 85cd82f)”. A coworker wi…

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## [Using getImageCropped function in PyAutoscoper. Getting truncated/empty data](https://discourse.slicer.org/t/using-getimagecropped-function-in-pyautoscoper-getting-truncated-empty-data/46471)

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**Author:** [@Prabhroop\_Singh](https://discourse.slicer.org/u/Prabhroop_Singh)\
**Replies:** 3\
**Last updated:** [April 3, 2026, 7:28pm UTC](https://discourse.slicer.org/t/using-getimagecropped-function-in-pyautoscoper-getting-truncated-empty-data/46471 "2026-04-03T19:28:21Z")

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I’m trying to use getImageCropped from PyAutoscoper to extract the cropped DRR image of a volume at a given pose. My setup works fine otherwise – getPose, getNCC, optimizeFrame, and trackingDialog all work correctly. Thi…

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## [4DCT registration - Hierarchical 3D Registration not recognizing "Sequence"](https://discourse.slicer.org/t/4dct-registration-hierarchical-3d-registration-not-recognizing-sequence/46026)

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**Author:** [@taylor\_t](https://discourse.slicer.org/u/taylor_t)\
**Replies:** 0\
**Last updated:** [February 1, 2026, 6:38pm UTC](https://discourse.slicer.org/t/4dct-registration-hierarchical-3d-registration-not-recognizing-sequence/46026 "2026-02-01T18:38:30Z")

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I am trying to process 4DCT data using SlicerAutoscoper. I was able to load in the static CT images (Bone Thins Knee Bilateral), perform segmentations and export as STL files, and load in the 4D CT dynamic data (4D Knee\_…

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## [Trouble Opening the Load Data](https://discourse.slicer.org/t/trouble-opening-the-load-data/44330)

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**Author:** [@Megan\_Weaver](https://discourse.slicer.org/u/Megan_Weaver)\
**Replies:** 14\
**Last updated:** [January 28, 2026, 5:17pm UTC](https://discourse.slicer.org/t/trouble-opening-the-load-data/44330 "2026-01-28T17:17:42Z")

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Hi! I am having difficulty opening the load data every time I try to launch the data I get this error message. Any advice?

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## [Unable to load wrist, knee or ankle data for autoscoper tutorial 1](https://discourse.slicer.org/t/unable-to-load-wrist-knee-or-ankle-data-for-autoscoper-tutorial-1/44259)

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**Author:** [@delaneyem](https://discourse.slicer.org/u/delaneyem)\
**Replies:** 3\
**Last updated:** [October 2, 2025, 12:38am UTC](https://discourse.slicer.org/t/unable-to-load-wrist-knee-or-ankle-data-for-autoscoper-tutorial-1/44259 "2025-10-02T00:38:04Z")

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Hello! I am unable to load the sample data for tutorial one. I have followed all installation steps and the tutorial. The data appears to be downloaded in the same cache the autoscoper tool pull from, but when I try to u…

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## [Bones disappear at random frames (bug?)](https://discourse.slicer.org/t/bones-disappear-at-random-frames-bug/44261)

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**Author:** [@Lauren\_Swain](https://discourse.slicer.org/u/Lauren_Swain)\
**Replies:** 6\
**Last updated:** [September 8, 2025, 8:36pm UTC](https://discourse.slicer.org/t/bones-disappear-at-random-frames-bug/44261 "2025-09-08T20:36:31Z")

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Hello, I have just recently started trying to use SAM for image registration but I have run into an issue where the bone DRR will disappear (also from the world view) for random frames during my trial. When they disappe…

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## [Invalid transformation chosen error - 4DCT registration](https://discourse.slicer.org/t/invalid-transformation-chosen-error-4dct-registration/42654)

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**Author:** [@Cesar](https://discourse.slicer.org/u/Cesar)\
**Replies:** 2\
**Last updated:** [September 2, 2025, 1:59pm UTC](https://discourse.slicer.org/t/invalid-transformation-chosen-error-4dct-registration/42654 "2025-09-02T13:59:43Z")

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Any insights into why I’m getting this error (please see image below) Here’s what I’ve tried and how I managed to bypass it. FYI this dataset has some motion artifact, and part of the distal radius is not visible. I…

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## [Transform Clarifications](https://discourse.slicer.org/t/transform-clarifications/44151)

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**Author:** [@tbugajski](https://discourse.slicer.org/u/tbugajski)\
**Replies:** 4\
**Last updated:** [August 29, 2025, 3:28pm UTC](https://discourse.slicer.org/t/transform-clarifications/44151 "2025-08-29T15:28:17Z")

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Hi SAM team, I have a quick question regarding the transformation outputs when creating a partial volume. Based on the photo below, I would assume that combining {bone}.tfm and {bone}\_PVOL2AUT.tfm would give the result …

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## [Unable to see slicer autoscoper in extensions](https://discourse.slicer.org/t/unable-to-see-slicer-autoscoper-in-extensions/42421)

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**Author:** [@Melanie](https://discourse.slicer.org/u/Melanie)\
**Replies:** 6\
**Last updated:** [April 21, 2025, 4:48pm UTC](https://discourse.slicer.org/t/unable-to-see-slicer-autoscoper-in-extensions/42421 "2025-04-21T16:48:20Z")

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I am unable to see slicer autoscoper in my extensions. Slicer version Slicer-5.9.0-2025-04-01-macosx-amd64 (Preview) Mac Hardware : MacBook Pro 2020 M1 OS - macOS Sonoma 14.5 (23F79) Could you pls advise

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## [4DCT registration](https://discourse.slicer.org/t/4dct-registration/42423)

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**Author:** [@Cesar](https://discourse.slicer.org/u/Cesar)\
**Replies:** 1\
**Last updated:** [April 3, 2025, 2:10pm UTC](https://discourse.slicer.org/t/4dct-registration/42423 "2025-04-03T14:10:59Z")

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I’ve been trying to register 4DCT data, but it seems like I’m missing a step or doing something wrong. Here’s what I’ve been doing: Load the data of interest (static and dynamic). Segment the static data. Create partia…

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## [Background Processing on the Radiographs](https://discourse.slicer.org/t/background-processing-on-the-radiographs/41659)

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**Author:** [@Robert\_Chauvet](https://discourse.slicer.org/u/Robert_Chauvet)\
**Replies:** 1\
**Last updated:** [February 21, 2025, 3:21pm UTC](https://discourse.slicer.org/t/background-processing-on-the-radiographs/41659 "2025-02-21T15:21:53Z")

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Hi, Our group is having some difficulties making the 2D radiographs with enhanced edges in Autoscoper. We noticed that Autoscoper inverts the images, but we are wondering if there is any other background processing happ…

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## [Trouble loading sample data in SlicerAutoscoperM](https://discourse.slicer.org/t/trouble-loading-sample-data-in-slicerautoscoperm/41003)

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**Author:** [@Lauren\_Welte](https://discourse.slicer.org/u/Lauren_Welte)\
**Replies:** 9\
**Last updated:** [February 6, 2025, 3:32pm UTC](https://discourse.slicer.org/t/trouble-loading-sample-data-in-slicerautoscoperm/41003 "2025-02-06T15:32:57Z")

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We have downloaded 3D Slicer 5.6.2 and are using SlicerAutoscoperM version 52a6b2d (2024-12-18). We have downloaded the sample data (wrist, knee and ankle). We then launch Autoscoper (Autoscoper opens), then we clic…

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## [Autoscoper PreProcessing for Volumes and Transforms](https://discourse.slicer.org/t/autoscoper-preprocessing-for-volumes-and-transforms/36845)

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**Author:** [@Robert\_Chauvet](https://discourse.slicer.org/u/Robert_Chauvet)\
**Replies:** 10\
**Last updated:** [July 19, 2024, 8:42pm UTC](https://discourse.slicer.org/t/autoscoper-preprocessing-for-volumes-and-transforms/36845 "2024-07-19T20:42:16Z")

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Hi, I have been working with Autoscoper for my PhD project, tracking foot and ankle bones using Biplane Fluoroscopy. I have been going through the process of tracking with Autoscoper, and am having trouble with the Pre…

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## [Office hour sessions](https://discourse.slicer.org/t/office-hour-sessions/31031)

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**Author:** [@jcfr](https://discourse.slicer.org/u/jcfr)\
**Replies:** 3\
**Last updated:** [August 29, 2023, 12:00am UTC](https://discourse.slicer.org/t/office-hour-sessions/31031 "2023-08-29T00:00:14Z")

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We are excited to invite you to participate in the upcoming “Office Hour” sessions for SlicerAutoscoperM! As we strive to build a collaborative community, your input is crucial in shaping the development process. The Of…