Commit fce5af0d authored by Mark van Turnhout's avatar Mark van Turnhout
Browse files

update output MRItoMat

parent 5bdd747a
......@@ -63,6 +63,7 @@
\usepackage{transparent}
\usepackage{coffee4}
\usepackage{tabulary}
\usepackage{multirow}
% language
\usepackage[UKenglish]{babel}
\selectlanguage{UKenglish}
......@@ -86,7 +87,7 @@
\Huge{\textbf{BasilLab User Manual }}\\
\mbox{}\\
\vfill
\includegraphics[width = 0.9\linewidth]{the_mother_of_all_suspicious_files.png}\\ \smallskip
%\includegraphics[width = 0.9\linewidth]{the_mother_of_all_suspicious_files.png}\\ \smallskip
\hfill\href{https://xkcd.com/1247/}{\normalsize https://xkcd.com/1247/}\\
\vfill
\mbox{}\\
......
......@@ -61,23 +61,53 @@ To process the data for \texttt{<basilid> = 140611} and \texttt{<basilid> = 1406
\end{lstlisting}
The output of \bas{MRItoMat} consists of the files listed in table \ref{mritomatout}. These files are written to \basilhome\texttt{/<basilid>} as explained before. The bold entries are actually needed by BasilLab to prepare the model data. The other (meta) data is written for your convenience and backward compatibility.
\begin{table}[t!]
\begin{table}[p!]
\center
\caption{Output of \bas{MRItoMat}. Bold entries are required to prepare model data.}\label{mritomatout}
\caption{Output of \bas{MRItoMat}: \texttt{`\_preload'} is from the scans before indentation, \texttt{`\_loading'} is from the scans during indentation, and \texttt{`\_postload'} is from the scans after removal of the indentation; \texttt{`\_flash'} is from the flash scans. \textbf{Bold} entries are \textbf{required} to prepare model data, \textsl{slanted} entries are used for parameters that should facilitate post-processing of the FE data.}\label{mritomatout}
\begin{tabulary}{\linewidth}{l R}
\hline\noalign{\smallskip}
file & description\\
\noalign{\smallskip}\hline\noalign{\bigskip}
\texttt{<basilhome>/<basilid>/MRI\_slices.mat} & \textbf{3D matrix with MRI-slice voxel values} \\
\texttt{<basilhome>/<basilid>/IMDAT.mat} & as \texttt{MRI\_slices.mat} \\
\texttt{<basilhome>/<basilid>/MRI\_subject.mat} & `subject' from MRI meta data \\
\texttt{<basilhome>/<basilid>/MRI\_acqp.mat} & `acqp' from MRI meta data\\
\texttt{<basilhome>/<basilid>/MRI\_method.mat} & `method' from MRI meta data\\
\texttt{<basilhome>/<basilid>/MRI\_imnd.mat} & `imnd' from MRI meta data \\
\texttt{<basilhome>/<basilid>/MRI\_reco.mat} & `reco' from MRI meta data \\
\texttt{<basilhome>/<basilid>/MRI\_d3proc.mat} & `d3proc' from MRI meta data \\
\texttt{<basilhome>/<basilid>/MRI\_visupars.mat} & `visupars' from MRI meta data \\
\texttt{<basilhome>/<basilid>/MRI\_voxel.txt} & \textbf{row with the voxel sizes in $[x y z]$ in mm from MRI meta data}\\
file in \basilhome\texttt{/<basilid>/}& description\\
\noalign{\smallskip}\hline\noalign{\smallskip}
\textbf{MRI\_slices\_preload.mat} & \multirow{4}*{3D matrix $(256\times 256\times 20)$ with MRI-slice voxel values}\\
\textbf{MRI\_slices\_loading.mat} & \\
\textsl{MRI\_slices\_postload.mat} & \\
\texttt{MRI\_slices\_flash.mat} & \\ \hline\noalign{\smallskip}
\texttt{IMDAT\_preload.mat} & as \texttt{MRI\_slices\_preload.mat} \\
\texttt{IMDAT\_loading.mat} & as \texttt{MRI\_slices\_loading.mat} \\
\texttt{IMDAT\_postload.mat} & as \texttt{MRI\_slices\_postload.mat} \\
\texttt{IMDAT\_flash.mat} & as \texttt{MRI\_slices\_flash.mat} \\ \hline\noalign{\smallskip}
\texttt{MRI\_subject\_preload.mat} & \multirow{4}*{`subject' from MRI meta data}\\
\texttt{MRI\_subject\_loading.mat} & \\
\texttt{MRI\_subject\_postload.mat} &\\
\texttt{MRI\_subject\_flash.mat} &\\\hline\noalign{\smallskip}
\texttt{MRI\_acqp\_preload.mat} & \multirow{4}*{`acqp' (aquisition parameters) from MRI meta}\\
\texttt{MRI\_acqp\_loading.mat} & \\
\texttt{MRI\_acqp\_postload.mat} & \\
\texttt{MRI\_acqp\_flash.mat} & \\ \hline
\texttt{MRI\_method\_preload.mat}&\multirow{4}*{`method' from MRI meta data} \\
\texttt{MRI\_method\_loading.mat} & \\
\texttt{MRI\_method\_postload.mat} & \\
\texttt{MRI\_method\_flash.mat} & \\ \hline\noalign{\smallskip}
\texttt{MRI\_imnd\_preload.mat} & \multirow{4}*{`imnd' from MRI meta data} \\
\texttt{MRI\_imnd\_loading.mat} & \\
\texttt{MRI\_imnd\_postload.mat} & \\
\texttt{MRI\_imnd\_flash.mat} & \\ \hline\noalign{\smallskip}
\texttt{MRI\_reco\_preload.mat} & \multirow{4}*{`reco' from MRI meta data} \\
\texttt{MRI\_reco\_loading.mat} & \\
\texttt{MRI\_reco\_postload.mat} & \\
\texttt{MRI\_reco\_flash.mat} & \\ \hline\noalign{\smallskip}
\texttt{MRI\_d3proc\_preload.mat} & \multirow{4}*{`d3proc' from MRI meta data} \\
\texttt{MRI\_d3proc\_loading.mat} & \\
\texttt{MRI\_d3proc\_postload.mat} & \\
\texttt{MRI\_d3proc\_flash.mat} & \\ \hline\noalign{\smallskip}
\texttt{MRI\_visupars\_preload.mat} & \multirow{4}*{`visupars' (visualisation parameters) from MRI meta data} \\
\texttt{MRI\_visupars\_loading.mat} & \\
\texttt{MRI\_visupars\_postload.mat} & \\
\texttt{MRI\_visupars\_flash.mat} & \\\hline\noalign{\smallskip}
\textbf{MRI\_voxel\_preload.txt} & \multirow{4}*{row with the voxel sizes in $[x y z]$ in mm from MRI meta data}\\
\textbf{MRI\_voxel\_loading.txt} & \\
\textsl{MRI\_voxel\_postload.txt} & \\
\texttt{MRI\_voxel\_flash.txt} & \\
\noalign{\smallskip}\hline
\end{tabulary}
\end{table}
......@@ -85,6 +115,8 @@ file & description\\
\subsection{Segment MRI-data}
\subsection{Map bone movement}
\subsection{Map indenter movement}
......
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