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Accuracy of manual and automatic placement of an anatomical coordinate system for the full or partial radius in 3D space.

ABSTRACT: Accurate placement of a coordinate system on the radius is important to quantitatively report 3D surgical planning parameters or joint kinematics using 4D imaging techniques. In clinical practice, the scanned length of the radial shaft varies among scanning protocols and scientific studies. The error in positioning a radial coordinate system using a partially scanned radius is unknown. This study investigates whether the imaged length of the radius significantly affects the positioning of the coordinate system. For different lengths of the radius, the error of positioning a coordinate system was determined when placed automatically or manually. A total of 85 healthy radii were systematically shortened until 10% of the distal radius remained. Coordinate systems were placed automatically and manually at each shortening step. A linear mixed model was used to associate the positioning error with the length of the radial shaft. The accuracy and precision of radial coordinate system placement were compared between automatic and manual placement. For automatic placement of the radial coordinate system, an increasing positioning error was associated with an increased shortening of the radius (P?=?

SUBMITTER: de Roo MGA

PROVIDER: S-EPMC7229017 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Accuracy of manual and automatic placement of an anatomical coordinate system for the full or partial radius in 3D space.

de Roo Marieke G A MGA Dobbe Johannes G G JGG Peymani Abbas A van der Made Anne D AD Strackee Simon D SD Streekstra Geert J GJ

Scientific reports 20200515 1

Accurate placement of a coordinate system on the radius is important to quantitatively report 3D surgical planning parameters or joint kinematics using 4D imaging techniques. In clinical practice, the scanned length of the radial shaft varies among scanning protocols and scientific studies. The error in positioning a radial coordinate system using a partially scanned radius is unknown. This study investigates whether the imaged length of the radius significantly affects the positioning of the co ...[more]

PMID: 32415290

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Project description:BackgroundVarious forms of the so-called loop closure problem are crucial to protein structure prediction methods. Given an N- and a C-terminal end, the problem consists of finding a suitable segment of a certain length that bridges the ends seamlessly. In homology modelling, the problem arises in predicting loop regions. In de novo protein structure prediction, the problem is encountered when implementing local moves for Markov Chain Monte Carlo simulations. Most loop closure algorithms keep the bond angles fixed or semi-fixed, and only vary the dihedral angles. This is appropriate for a full-atom protein backbone, since the bond angles can be considered as fixed, while the (phi, psi) dihedral angles are variable. However, many de novo structure prediction methods use protein models that only consist of Calpha atoms, or otherwise do not make use of all backbone atoms. These methods require a method that alters both bond and dihedral angles, since the pseudo bond angle between three consecutive Calpha atoms also varies considerably.ResultsHere we present a method that solves the loop closure problem for Calpha only protein models. We developed a variant of Cyclic Coordinate Descent (CCD), an inverse kinematics method from the field of robotics, which was recently applied to the loop closure problem. Since the method alters both bond and dihedral angles, which is equivalent to applying a full rotation matrix, we call our method Full CCD (FCDD). FCCD replaces CCD's vector-based optimization of a rotation around an axis with a singular value decomposition-based optimization of a general rotation matrix. The method is easy to implement and numerically stable.ConclusionWe tested the method's performance on sets of random protein Calpha segments between 5 and 30 amino acids long, and a number of loops of length 4, 8 and 12. FCCD is fast, has a high success rate and readily generates conformations close to those of real loops. The presence of constraints on the angles only has a small effect on the performance. A reference implementation of FCCD in Python is available as supplementary information.

Dataset Information

Accuracy of manual and automatic placement of an anatomical coordinate system for the full or partial radius in 3D space.

Publications

Accuracy of manual and automatic placement of an anatomical coordinate system for the full or partial radius in 3D space.

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