Commit 4fed87ba authored by Turnhout, M.C. van's avatar Turnhout, M.C. van
Browse files

update URL (again...) and ref to Willeke

parent a6b79eef
BasilLab
========
https://bitbucket.org/matecellab/basillab
http://mategit.wtb.wfw.tue.nl/STEM/basillab
FYI (for your inspiration): a toolbox to get from raw MRI data to a
3D Abaqus FE model with as little user interaction as possible.
Originally written for specific in vivo experiments by Willeke Traa.
See also: Traa et al. MRI based 3D finite element modelling to investigate deep tissue injury, CMBBE, 2018.
https://dx.doi.org/10.1080/10255842.2018.1517868
using & downloading
===================
You do not need (to run or use) Git to able to use basillab. You can
download your favourite version from https://bitbucket.org/matecellab/basillab
download your favourite version from http://mategit.wtb.wfw.tue.nl/STEM/basillab
Once downloaded, the code is yours to (ab)use to your liking (as
long as you do not violate the GPL license).
......
......@@ -302,14 +302,16 @@
Url = {http://repository.tue.nl/posters/801419.pdf}
}
@Article{Traa2018,
@Article{Traa2019,
author = {Traa, Willeke A. and \noopsort{Turnhout}van Turnhout, Mark C. and Moerman, Kevin M. and Nelissen, Jules L. and Nederveen, Aart J. and Strijkers, Gustav J. and Bader, Dan L. and Oomens, Cees W.J.},
title = {{MRI} based {3D} finite element modelling to investigate suspected deep tissue injury in a rat model},
journal = {Computer Methods in Biomechanics \& Biomedical Engineering},
title = {{MRI} based 3{D} finite element modelling to investigate deep tissue injury},
journal = {Computer Methods in Biomechanics and Biomedical Engineering},
year = {2018},
note = {Submitted},
abstract = {Pressure ulcers occur due to sustained mechanical loading. Deep tissue injury is a severe type of pressure ulcer, which is believed to originate in subcutaneous tissues adjacent to bony prominences. In previous experimental-numerical studies the relationship between internal tissue state and damage development was investigated using a 2D analysis. However, recent studies suggest that a local analysis is not sufficient. In the present study we developed a method to create animal-specific 3D finite element models of an indentation test on the tibialis anterior muscle of rats based on MRI data. A detailed description on how the animal specific models are created is given. Furthermore, two indenter geometries are compared and the influence of errors in determining the indenter orientation on the resulting internal strain distribution in a defined volume of tissue was investigated. We conclude that with a spherically-shaped indenter errors in estimating the indenter orientation do not unduly influence the results of the simulation.},
doi = {10.1080/10255842.2018.1517868},
keywords = {pressure ulcer, deep tissue injury, finite element modelling (FE), magnetic resonance imaging (MRI), indentation test},
owner = {tue},
timestamp = {2018.04.11},
timestamp = {2018.11.06},
}
@Comment{jabref-meta: databaseType:bibtex;}
......@@ -5,9 +5,9 @@ The use of an ovine model circumvents the ethical and financial problems associa
\chapter{Introduction}
Pressure ulcers are localised injuries to the skin and/or underlying tissue due to mechanical loading. Deep Tissue Injury is a severe type of pressure ulcer originating subcutaneously. To better understand the aetiology of Deep Tissue Injury, \href{https://www.tue.nl/stem}{our group} studies physiological changes due to mechanical loading in a rat model \cite{Bosboom2003,Loerakker2010,Loerakker2011,Loerakker2011a,Oomens2010,Nierop2010,Ceelen2008, Stekelenburg2006, Stekelenburg2006a, Stekelenburg2007}. In this rat model, the animal's tibialis anterior muscle is deformed with an indenter inside a magnetic resonance (MR) imaging scanner. MR imaging allows for assessment of physiological changes, e.g. (re)perfusion and tissue damage, due to the deformation of the muscle. Animal specific finite element (FE) models are used to assess the relationship between the mechanical internal tissue state and tissue damage in the rat model.
Until recently, (animal specific) FE analysis of the experiments was restricted to cross sectional (2D) FE models. In the current project \textsl{Non-invasive monitoring of deep tissue injury} \cite{Traa2015} the aim is to extend a previously developed cross sectional (2D) FE models \cite{Loerakker2010} to a FE model of the complete leg (i.e.\ 3D) \cite{Traa2014}. The first objective of these animal specific full leg 3D models is to assess the shortcomings of cross sectional 2D modelling (or: to assess what extra information can be obtained by switching to full leg 3D modelling).\\
Until recently, (animal specific) FE analysis of the experiments was restricted to cross sectional (2D) FE models. In the current project \textsl{Non-invasive monitoring of deep tissue injury} \cite{Traa2015} the aim is to extend a previously developed cross sectional (2D) FE models \cite{Loerakker2010} to a FE model of the complete leg (i.e.\ 3D) \cite{Traa2014,Traa2019}. The first objective of these animal specific full leg 3D models is to assess the shortcomings of cross sectional 2D modelling (or: to assess what extra information can be obtained by switching to full leg 3D modelling).\\
\noindent BasilLab is a collection of scripts to facilitate the animal specific full leg 3D modelling of these experiments.
\noindent BasilLab is a collection of scripts to facilitate the animal specific full leg 3D modelling of these experiments. BasilLab was (hacked and) used for the publications by Willeke Traa \textsl{et al.} \cite{Traa2019}.
% \nocite{Loerakker2013,Loerakker2012,Loerakker2011,Loerakker2011a,Loerakker2010,Oomens2010,Nagel2009,Nierop2010,Ceelen2008,Ceelen2008a,Stekelenburg2006,Stekelenburg2006a,Stekelenburg2007}
......@@ -46,7 +46,7 @@ BasilLab is released under a \href{https://www.gnu.org/licenses/gpl-3.0.en.html}
Note that there is ABSOLUTELY NO WARRANTY; not even for FITNESS FOR A PARTICULAR PURPOSE, and certainly not for MERCHANTABILITY.\warning\\
\noindent BasilLab is available from the \href{mailto:m.c.v.turnhout@tue.nl}{author}. It is maintained in a Git repository that is hosted at \href{https://bitbucket.org/matecellab/basillab}{BitBucket}, where you can find the \href{https://bitbucket.org/matecellab/basillab/downloads}{latest version}. The \href{mailto:m.c.v.turnhout@tue.nl}{author} welcomes your contributions.
\noindent BasilLab is available from the \href{mailto:m.c.v.turnhout@tue.nl}{author}. It is maintained in a Git repository that is hosted at \href{http://mategit.wtb.wfw.tue.nl/STEM/basillab}{http://\-mategit.wtb.wfw.tue.nl/STEM/basillab}, where you can find the \href{http://mategit.wfw.wtb.tue.nl/STEM/basillab/tree/master}{latest version}. The \href{mailto:m.c.v.turnhout@tue.nl}{author} welcomes your contributions.
\section{Honour due and `backward compatibility'}
......@@ -54,7 +54,6 @@ BasilLab evolved out of a set of scripts written by Willeke Traa that were meant
\noindent When you use (parts of) BasilLab, or adapt BasilLab to your own needs, we kindly ask you to cite:\\
~\\
\cite{Traa2018} Willeke A.\ Traa, Mark C.\ van Turnhout, Kevin M.\ Moerman, Jules L.\ Nelissen, Aart J.\ Nederveen,
Gustav J.\ Strijkers, Dan L.\ Bader and Cees W.J.\ Oomens. MRI based 3D finite element modelling
to investigate suspected deep tissue injury in a rat model. \textsl{Computer Methods in Biomechanics \&
Biomedical Engineering}, 2018. Submitted.
\cite{Traa2019} Willeke A.\ Traa, Mark C.\ van Turnhout, Kevin M.\ Moerman, Jules L.\ Nelissen, Aart J.\ Nederveen,
Gustav J.\ Strijkers, Dan L.\ Bader and Cees W.J.\ Oomens. \href{https://dx.doi.org/10.1080/10255842.2018.1517868}{MRI based 3D finite element modelling to investigate deep tissue injury.} \textsl{Computer Methods in Biomechanics \&
Biomedical Engineering}, 2018.
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