\documentclass[10pt]{amsart}
\usepackage[left=.75in,right=.75in,top=.75in,bottom=.75in]{geometry}
\geometry{letterpaper}                   % ... or a4paper or a5paper or ... 
%\geometry{landscape}                % Activate for for rotated page geometry
%\usepackage[parfill]{parskip}    % Activate to begin paragraphs with an empty line rather than an indent
\usepackage{color,graphicx}
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%\DeclareGraphicsRule{.tif}{png}{.png}{`convert #1 `dirname #1`/`basename #1 .tif`.png}
\newcommand{\eqn}[1]{(\ref{#1})}
\newcommand{\numberpatients}{{33  }}
\newcommand{\numberCTImages}{{264 }}

\newcommand{\enhancingvolumechangemanual}{{-0.2\% }}
\newcommand{\enhancingvolumechangerf}{{-3\% }}
\newcommand{\enhancingvolumechangedosecorrelationmanual}{{-.24 }}
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\newcommand{\necrosisvolumechangemanual}{{-0.2\% }}
\newcommand{\necrosisvolumechangerf}{{-3\% }}
\newcommand{\necrosisvolumechangedosecorrelationmanual}{{-.57 }}
\newcommand{\necrosisvolumechangedosecorrelationrf}{{-.40 }}
\newcommand{\necrosisvolumechangettpcorrelationmanual}{{0.67 }}
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\newcommand{\DSCNecrosisPredictionError}{{.85 }}
\newcommand{\DSCEnhancingPredictionError}{{.61 }}
%\renewcommand{\labelenumi}{\arabic{enumi}. }

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%Starting with LaTeX2RTF 1.9.18, there is a handy method for
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\usepackage{boxedminipage,float}
\usepackage{wrapfig,setspace}
\usepackage[pdftex, plainpages=false, colorlinks=true, citecolor=black, filecolor=black, linkcolor=black, urlcolor=black]{hyperref}

\newcommand{\picdir}{./pdffig}
\fi

\title[Volumetric RECIST Assessment of HCC Response via RF-based Automated Segmentation]{Volumetric RECIST Assessment of Hepatocellular Carcinoma Response 
%to Sorafenib 
via Random Forest based Automated Segmentation 
%Protocol (Are feature images predictive of treatment response)
}

\author{K.~Ahmed\textsuperscript{1} \and
        D.~Fuentes\textsuperscript{1} \and
        J.S.~Lin\textsuperscript{1} \and
        R.~Ali\textsuperscript{3} \and
        A.~Kaseb\textsuperscript{3} \and
        W.~Wei\textsuperscript{4} \and
        J.D.~Hazle\textsuperscript{1} \and
        A.~Qayyum\textsuperscript{2} \and
        K.~Elsayes\textsuperscript{2} 
}

\date{ \small
The University of Texas M.D. Anderson Cancer Center,\\
Departments of \textsuperscript{1}Imaging Physics, \textsuperscript{2}Diagnostic Radiology,
\textsuperscript{3}Gastrointenstinal Oncology,
and \textsuperscript{4}Biostatistics, Houston TX 77030, USA \\
%Email: \texttt{jhazle@mdanderson.org}   \\
Received: date / Accepted: date
% Webpage: \texttt{http://wiki.ices.utexas.edu/dddas}
}



\begin{document}
 An example image set from a single study needed as input to the random
forest models is shown in Figure~\ref{Fig:OriginalImages}.

\begin{figure}[h] 
\iflatextortf 
%do nothing
\else
\begin{tabular}{ccccc} 
  \scalebox{0.40}{\includegraphics*{\picdir/mask.png}}
& \scalebox{0.40}{\includegraphics*{\picdir/precontrast.png}}
& \scalebox{0.40}{\includegraphics*{\picdir/arterial.png}   }
& \scalebox{0.40}{\includegraphics*{\picdir/venous.png}     }
& \scalebox{0.40}{\includegraphics*{\picdir/delay.png}      }
\\
mask & pre-contrast & arterial & porto-venous & delayed 
\\
Mask.nii.gz & Pre.nii.gz &  Art.nii.gz & Ven.nii.gz & Del.nii.gz  
\\ 
\end{tabular}           
\fi
\caption{Original Images. Each study consists of volumetric images from the
pre-contrast, arterial, porto-venous, delayed phase shown. 
}\label{Fig:OriginalImages}
\end{figure}  

Each image set should be in a separate directory and should follow
the below naming convention \textit{exactly}:
\begin{verbatim}
$ ls ImageDatabase/Predict0001/before/
Art.nii.gz  Del.nii.gz  Mask.nii.gz  Pre.nii.gz  Ven.nii.gz
\end{verbatim}

Example output from the random forest model is shown in Figure~\ref{Fig:ModelOutput}.
Output images are organized with respect to the model used for the
segmentation \verb#$(WORKDIR)/%/$(RFMODEL)/LABELS.GMM.nii.gz#

\begin{figure}[h] 
\iflatextortf 
%do nothing
\else
\begin{tabular}{cccccc} 
  \scalebox{0.15}{\includegraphics*{\picdir/{LABELS.GMM}.png}}
& \scalebox{0.15}{\includegraphics*{\picdir/Mask.png}}
& \scalebox{0.15}{\includegraphics*{\picdir/Pre.png}}
& \scalebox{0.15}{\includegraphics*{\picdir/Art.png}   }
& \scalebox{0.15}{\includegraphics*{\picdir/Ven.png}     }
& \scalebox{0.15}{\includegraphics*{\picdir/Del.png}      }
\\
RF & mask & pre-contrast & arterial & porto-venous & delayed 
\\
LABELS.GMM.nii.gz & Mask.nii.gz & Pre.nii.gz &  Art.nii.gz & Ven.nii.gz & Del.nii.gz  
\\ 
\end{tabular}           
\fi
\caption{Model output.
}\label{Fig:ModelOutput}
\end{figure}  

Given the segmented images, \verb#c3d# is used to extract volume
information. 
{\small
\begin{verbatim}
innovador$ make -f prediction.makefile volume
cd /workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel;
c3d LABELS.GMM.nii.gz LABELS.GMM.nii.gz -lstat > LABELS.GMM.VolStat.txt ;
sed "s/\s\+/,/g" LABELS.GMM.VolStat.txt > LABELS.GMM.VolStat.csv
innovador$ cat
/workarea/fuentes/github/LiverSegmentationExample/workdir/Predict0001/before/FeatureModel00000130/KFold.0000000000000011111111111111111110.prior.GMM.RFModel/LABELS.GMM.VolStat.csv
LabelID,Mean,StdD,Max,Min,Count,Vol(mm^3),Extent(Vox)
,0,0.00000,0.00000,0.00000,0.00000,22587824,24901854.558,512,512,93
,1,1.00000,0.00000,1.00000,1.00000,1119734,1234446.187,270,299,71
,2,2.00000,0.00000,2.00000,2.00000,609718,672181.125,243,280,69
,3,3.00000,0.00000,3.00000,3.00000,62116,68479.531,144,176,40
\end{verbatim}
}

\end{document}