Commit 5bdd747a authored by Mark van Turnhout's avatar Mark van Turnhout
Browse files

refer to Willeke and some typos

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\Huge{\textbf{BasilLab User Manual }}\\
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\hfill\href{https://xkcd.com/1247/}{\normalsize https://xkcd.com/1247/}\\
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......@@ -15,7 +15,7 @@ Until recently, (animal specific) FE analysis of the experiments was restricted
BasilLab consists of a number of (pre-processing) Matlab-scripts that extract information from the MR images of the experiments and subsequently write a python script that can be fed to Abaqus: the FE software that runs the analysis. Parts of the pre-processing, in particular the segmentation of the MR images, rely on the \gibbon{} toolbox\footnote{``The Geometry and Image-Based Bioengineering add-On''. Source available from \href{https://github.com/Kevin-Mattheus-Moerman/GIBBON}{https://github.com/Kevin-Mattheus-Moerman/GIBBON}} developed by Kevin Moerman \cite[\href{http://kevinmoerman.org/portfolio/gibbon/}{http://kevinmoerman.org/ portfolio/gibbon/}]{Moerman2013}.
Next to the pre-processing Matlab scripts, a number of python scripts is provided to extract model results from the Abaqus output file. These results can be easily fed back to Matlab for post-processing puposes\footnote{Other than these python scripts to write the Abaqus results to a Matlab- and human-readable text file, no post-processing is provided in BasilLab.}.
Next to the pre-processing Matlab scripts, a number of python scripts is provided to extract model results from the Abaqus output file. These results can be easily fed back to Matlab for post-processing purposes\footnote{Other than these python scripts to write the Abaqus results to a Matlab- and human-readable text file, no post-processing is provided in BasilLab.}.
\begin{table}[h!]
\center
\caption{Software used for development and testing of BasilLab.}\label{tab:software}
......@@ -47,3 +47,7 @@ BasilLab is released under a \href{https://creativecommons.org/licenses/by-nc/2.
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}. BasilLab is maintained in a Git repository that is hosted at \href{https://bitbucket.org/matecellab/mylab}{BitBucket}. If you wish to have access to that Git repository, again: contact the \href{mailto:m.c.v.turnhout@tue.nl}{author}.
\section{Honour due and `backward compatibility'}
BasilLab evolved out of a set of scripts written by Willeke Traa that were meant to do this kind of `MRI-data-to-FE-model' for FE modelling in FEBio. The general work flow was set-up by Willeke and changed little to nothing in BasilLab. When this document refers to `backward compatibility' it means backward compatibility with Willeke's proto-BasilLab (e.g.\ in BasilLab some names may have been changed, to protect the innocent).
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