workflow.tex 1.85 KB
Newer Older
1
2
3
4
% !TeX root = BasilLab.tex
\begin{savequote}
In the computer model, all the microfilaments were given certain quantitative properties with names that mean something to physicists: a `viscous damping coefficient' and an `elastic spring constant'. Never mind exactly what these mean: they are the kind of things physicists like to measure in a spring. \qauthor{Richard Dawkins \cite{Dawkins2009}}
\end{savequote}
Mark van Turnhout's avatar
Mark van Turnhout committed
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
\chapter{Workflow}

Before you can use BasilLab, you wil need to take two steps. First, add the directory that contains the (Matlab) scripts, possibly <basillab> to your Matlab search path, e.g. go (in Matlab) to that directory and issue \texttt{addpath(pwd);} on the command line. 

Second, tell your local copy of BasilLab where the raw MRI-data is to be found, and where to store and for look processed MRI-data. You should use the functions \texttt{bas\_setMRIroot} and \texttt{bas\_setDataRoot} to do that (once). 

The directory with the raw MRI-data (\texttt{bas\_setMRIroot}) remains untouched. The MRI-data is read and copied to the directory \texttt{<basilid>} which is created in the directory \texttt{<basilhome>} (\texttt{bas\_setDataRoot}). The link between the raw MRI-data folder inside  \texttt{<MRI-root>} and  \texttt{<basilid>} is \textsl{hard-coded} in \texttt{bas\_getMeta.m}. 

Next the workflow can be roughly divided into four steps:
\begin{enumerate}
\item Pre-processing of (raw) MRI-data. Including reading and copying (raw) MRI-data, segmentation of MR images,and processing (segmented) MRI-data. Requires Matlab (and human intervention).
\item Building the FE model. Requires Matlab and Abaqus.
\item Running the FE model, Requires Abaqus.
\item Post-processing of FE results. Requires Abaqus.
\end{enumerate}



\section{Pre-processing of MRI-data}

\section{Building the FE model}

\section{Running the FE model}

\section{Post-processing of FE results}