\documentclass{article}
% \tolerance 2000
\usepackage{psfig,epsf,makeidx}

\begin{document}

%\frontmatter 

\pagestyle{headings}



\title{SEAL's Reference}
\author{Georges~Le~Goualher}


%McConnell Brain Imaging Centre, \\Montr\'{e}al Neurological Institute,\\
%McGill University, Montr\'{e}al, Canada \\
%georges@bic.mni.mcgill.ca








\maketitle


\begin{flushleft}
Montreal Neurological Institute\\
McConnell Brain Imaging Centre\\
3801 University Street\\
Montreal, Canada H3A 2B4\\
e-mail~: georges@bic.mni.mcgill.ca\\

\end{flushleft}

\section{Introduction}

\textbf{SEAL} stands for \textbf{S}ulcus \textbf{E}xtraction and \textbf{A}ssisted
\textbf{L}abelling and Figure \ref{overview} shows the overview of the
application. There are three main parts~:

\begin{itemize}

   \item [i)] Modelling of the cortical sulci. At this step 
     the cortical folds (the sulci) are modelled. Refer to section  \ref{SEAL script}.
         
   \item [ii)] Interactive Labelling. An anatomist can interactively label
     these sulci. This is done using a modified version
     of Display. Refer to section  \ref{Interactive Labelling}.

   \item [iii)] Automatic Labelling of the main cortical folds. Once a
     labelling of main cortical folds has been performed on several
     individuals, Statistical Probability Anatomical Maps (SP\_AMs) can be
     computed. These SPAMs represent 3D spatial-probability of finding a
     particular sulcus in the Talairach space (refer to section \ref{Sulcal
       Probability Anatomical Map}). There is one SP\_AM per sulcus. Based
     on these spatial priors an automatic labelling can be performed (refer
     to section \ref{Automatic Labelling}).

\end{itemize}       

\noindent
For data already available and work done within the ICBM project refer to
section \ref{ICBM Project}.
\noindent
For related Papers and Reports refer to section \ref{Related Reports}. 

%\begin{figure}
%\centerline{ 
%\psfig{figure=/data/icbm/sbd/seal/Image_Rapport/overview.eps}\hspace{1mm}
%}
%  \caption{Assisted Cortical Sulci  Labeling }
%  { Overview }
%\label{overview}
%\end{figure}


%\begin{figure}
%\begin{center}
%\centerline{ 
%\epsfxsize=14cm \epsfbox{/data/icbm/sbd/seal/Image_Rapport/overview.eps}\hspace{1mm}
%}
% \caption{Assisted Cortical Sulci  Labelling }
%  { Overview }
%\label{overview}
%\end{center}
%\end{figure}



\section{SEAL script}
\label{SEAL script}


SEAL is a perl script~:

\begin{verbatim}
~georges/public_bin/sulcus_graph.pl
\end{verbatim}

\begin{verbatim}
command: sulcus_graph.pl final_t1.mnc surface.obj classification.mnc output_dir
\end{verbatim}



\subsection{Input Data}


\begin{itemize}

  \item final\_t1.mnc: 
    
    3D T1 MRI volume registered and resampled in the MNI-Talairach
    coordinate system (\textit{c.f}
    http://www.bic.mni.mcgill.ca/\verb|~|louis/mri\_segmentation/, 
    \cite{Collins94a}).

  \item surface.obj:

    Ouput of cortical surface segmentation (i.e. output of 
    \verb|~|david/public\_bin/cortical\_surface.pl, 
    \cite{MacDonald94a} or grey matter surface output of
    \verb|~|georges/public\_bin/cortical\_surface\_double\_hull.pl).

  \item  classification.mnc:

           Ouput of tissue classication 
           (i.e. output of classify or classify\_clean,  \cite{Zijdenbos96a}).

  
  \item output\_dir:

    Directory where  ouput of sulcus\_graph.pl should be stored.

\end{itemize}

\noindent \textbf{NOTE}~: sulcus\_graph.pl has been applied to the ICBM
database.  Output are stored under~: \ 
/data/icbm/mri1/subjects/00XXX/seg/auto/mni\_icbm\_00XXX\_t1\_sulci For
informations on this ICBM database refer to~:\\ 
http://www.bic.mni.mcgill.ca/\verb|~|louis/icbm/icbm\_summary.html


\subsection{Output Data}

\textbf{sulcus\_graph.pl}  generates 6 \textit{object files} and one
\textit{sulgraph file} which are stored under the \textit{output\_dir} directory
\footnote{The \textit{object} data format is commonly used at the BIC and
can be read by Display (\cite{MacDonald96}). \\ The \textit{sulgraph} data
format is used only for the cortical topography encoding. This
\textit{sulgraph} data format is based on several C$^{++}$ classes. Its
associated library is ~georges/Source/LibSul/libSul.a.  I will describe
this data format later}. As an example lets consider ICBM 00100 subject. For this
subject, output files are stored under~: \\ 
/data/icbm/mri1/subjects/00100/seg/auto/mni\_icbm\_00100\_t1\_sulci \\ 
These ouput files are~:\\ 


\begin{itemize}

  \item G\_A\_L\_L.obj  (Graph\_Arcs\_Left\_Line). Contains
    a set of curves (or ``lines''). Each curve represents
     the superficial trace of a particular cortical fold
    (left hemisphere only).
    

  \item G\_A\_L\_Q.obj  (Graph\_Arcs\_Left\_Quadmesh). Contains
    a set of surfaces (or ``quadmesh''). Each surface represents
    the median surface of a cortical fold (left hemisphere only).

  \item G\_A\_R\_L.obj  (Graph\_Arcs\_Right\_Line). Equivalent of
    G\_A\_L\_L.obj  for the right hemisphere.

  \item G\_A\_R\_Q.obj  (Graph\_Arcs\_Right\_Quadmesh). Equivalent of
    G\_A\_L\_Q.obj  for the right hemisphere.

  \item G\_VERTEX\_L.obj (Graph\_Vertex\_Left). Contains all
    curve junctions. Each junction is represented
    by a 3D point (left hemisphere only).


  \item G\_VERTEX\_R.obj  (Graph\_Vertex\_Left).   Equivalent of
    G\_VERTEX\_L.obj for the right hemisphere.

  \item  GRAPH\_sulci.sulgraph. This is a \textit{sulgraph}
    data format file. This file stores all the informations already stored
    in the previous object files plus other additional data described in
    the following paragraph.

  \item LAB.mnc.gz, POT1.mnc.gz, POT2.mnc.gz and POT3.mnc.gz are minc files
    containing LABels and POTentials (from which forces are derived). These
    files are used only for post-modelling \ref{Post Segmentation}. In
    general you don't need them.
    

\end{itemize}


\paragraph{GRAPH\_sulci.sulgraph}
\label{.sulgraph}


The \textit{.sulgraph} structure is an attributed relational graph structure that
I've defined for my application \footnote{Associated code and library are
  under ~people/georges/Source/LibSul. Note that more work need to be done at
this level to construct something more generic like Volume\_io}. 
A graph contains two main features~: Arcs and Vertices \footnote{ Please
  note  that here a cortical fold is called an
\textit{arc} and a fold junction is refered to as a \textit{vertex} but
generally when speaking about a graph structure one may use the inverse~: a
fold may be  called a \textit{vertex} and a junction may be called an
\textit{arc}. This may confuse you when referring to related papers}.
 


\begin{itemize}

\item \underline {Arc}~: contains a parametrical surface representing the
  median surface of a fold. Coordinates of 3D points belonging to this
  surface are expressed in MNI-Talairach world coordinates.
  We also store~:
    \begin{itemize}
      \item length. This is the length of the sulcus superficial trace.
      \item mean depth. Mean depth of the fold.
      \item orientation. The fold's median surface
        is approximated by a plane (using a least square approximation).
        The normal vector of this plane is used to represent
        the orientation of the fold.
      \item gravity center. The location of the sulcus median
        surface's gravity center is computed. 

      \item labels. A set of labels are also assigned to an arc
        (hemisphere, lobe, name of the fold, sulcus's type i.e.: main, secondary,
        tertiary).


     \item probability vector. We also store a probability vector for each
        arc. Each component of this probability vector represents the
        probability that the associated median surface belongs to a
        given sulcus. These probabilities are computed from 
        SP\_AMs already available, i.e. computed off-line (refer to \\ 
        http://www.bic.mni.mcgill.ca/\verb|~|georges/papers/vbc\_camread/vbc\_camread.html)

    \end{itemize}
 

  \item \underline {Vertex}~: has a 3D location; the vertex contains the
    list of arcs which connect themselves at this location.

\end{itemize}



\section{Interactive Labelling}
\label{Interactive Labelling}


The goal of the Interactive Labelling is to label the sulci of interest.
Once this labelling has been performed on several individuals, it's
possible to compute sulcus SP\_AMs. The interactive labelling is performed
using an modified version of Display called Display.geo (see figure
\ref{fig_application}). The only difference between Display and Display.geo
is that Display.geo contains a specific menu for sulcal labelling
\footnote{The code for Display.geo is under ~georges/Source/Display. Have a
  look in ~georges/Source/Display/Modifs for informations on modification.
  The main file is ~georges/Source/Display/callbacks/georges.c}.

%\begin{figure}
%\begin{center}
%\centerline{ 
%\epsfxsize=16cm \epsfbox{/data/icbm/sbd/seal/Image_Rapport/application_2.eps}\hspace{1mm}
%}
%  \caption{Assisted Cortical Sulci  Labeling }
%  { This image shows the specific menu used to perform the interactive
%    labeling of cortical folds. 
%    G\_A\_L\_Q.obj object was selected and \textit{Init Guess} was applied.
%    In order to help the physician to give a name to the selected curve,
%    probabilities that this curve belongs to different sulci are
%    given with the \textit{Get Morphometrics} button. Here, results are~:
%    L\_F\_Superior\_Frontal  (proba~:~0.29)~;
%    L\_F\_Precentral     (proba~:~0.02)~;
%    This means that the most likely name (given data from
%    Sulcal Probability Maps) is ``Superior Frontal Sulcus from the left hemisphere'' 
%    (L\_F\_Superior\_Frontal).} 
%\label{fig_application}
%\end{center}
%\end{figure}



\subsection{Before Starting: disp.geo alias}

You may use directly \verb|~|georges/Source/Display/Display.geo for interactive
labelling, but I strongly suggest you create a  disp.geo alias~:

\begin{verbatim}
alias disp.geo \verb|~|georges/Source/Display/Display.geo \
~georges/Data/Model/PLANE_x.obj \
~georges/Data/Model/PLANE_y.obj \
~georges/Data/Model/PLANE_z.obj \
~georges/Data/Model/little_cortex.obj'
\end{verbatim}

\noindent
Then when you start the command  \textbf{disp.geo} you can see
that this command start Display.geo and that in this 
version there is a new button in the main menu~: \textbf{3D Sulci} (associated with the N
keyboard key).  Several geometrical objects are launched in
the 3D window~: 3 perpendicular planes and a \textit{little cortex model}.
These objects will be useful to prevent visual overlapping between
hemispheres. Of course you can hide an object by~:
\begin{itemize} 
\item selecting it with the mouse
\item selecting Objects/Invisible
\end{itemize}


\subsection{Running disp.geo}


You need~:
\begin{itemize}

\item final\_t1.mnc. The 3D T1 MRI resampled in the MNI-Talairach space.
\item surface.obj.  The cortical surface. Taking advantage of David's
  double hull surface extraction I suggest you load the White Matter/Grey
  Matter Interface where cortical sulci are more visible. Such
  a White/Grey Interface surface is 
  /data/icbm/mri9/david/White\_surfaces/Surfaces/00XXX\_81920.obj.gz.

\item G\_A\_L\_L.obj and G\_A\_R\_L.obj

\item  GRAPH\_sulci.sulgraph

\end{itemize}



Run~:
\begin{verbatim}
disp.geo final_t1.mnc surface.obj G_A_L_L.obj G_A_R_L.obj
\end{verbatim}

\subsection{3D Sulci Menu}

\%begin{figure}
%\begin{center}
%\centerline{ 
%\epsfxsize=16cm \epsfbox{/data/icbm/sbd/seal/Image_Rapport/menu.eps}\hspace{1mm}
%}
%  \caption{Assisted Cortical Sulci Labeling: Menu }
%  {  }
%
%\label{menu}
%\end{center}
%\end{figure}


\begin{itemize}

\item{Q} \textbf{Load Graph}. Load the GRAPH\_sulci.sulgraph. This is the first
  thing to do.

\item{W} \textbf{Init Guess}. This button performs an initial
  labeling of all  cortical folds based on previously computer SP\_AMs
  (refer to \\ 
  http://www.bic.mni.mcgill.ca/users/georges/papers/vbc\_submit/vbc\_submit.html
  for details). Use the keyboard arrow to select the object number 5
   (G\_A\_L\_L.obj).  Click on \textbf{Init Guess}~: on the window appears
  : \\ \textbf{`Continue ? (answer by yes or no)'} \\ enter yes \\ 
  \textbf{`Enter proba\_threshold and depth\_threshold:'} \\ enter 0.1
  0. All sulci having a probability vector such that its maximum
  component is superior to  0.1 are labelled. Note that this function works
  only if G\_A\_L\_L.obj, G\_A\_R\_L.obj, G\_A\_L\_Q.obj or  G\_A\_R\_Q.obj
  are selected.

\item{E}  \textbf{Find Side Branches}. Label a non-terminal segment as ``side
  branche'' if there is angle close to 90 degrees between this segment and
  its neighboring sulci. This button is not used in general as its output
  is not really good.

\item{R}  \textbf{Compare Two Graphs}. Allows to visualy inspect the difference
  between two graphs.

\item{Y}  \textbf{Save Graph}. Allows to save the graph once the labelling
  is done. 

\item{A} \textbf{Anat List?}. Display in the terminal window the list of
  possible labels with their IDs. For corresponding label on the right
  hemisphere add 100 to the left hemisphere's label. Example Central Sulcis
  Label is 15 for the left hemisphere and 115 for the right hemisphere.

\item{S}  \textbf{Set Name}. this button allows to enter the name of the fold
  (several folds may constitute a sulcus as defined by an anatomist). You
  don't need to enter the full name of the sulcus (wich would be too long)
  but only a number. Refer to table \ref{table_anatomical_list} for
  correspondance between number/name and colour or use the button
  \textbf{Anat List?}. Note that the probability associate with the label
  you enter is set to 1.0. (i.e. maximum confidence in the manual
  labelling). However the initial state of the probability vector is stored
  in memory and can be retreived if you set the ``unknow'' label (i.e. 0)
  to the curve.

\item{D}~: \textbf{Add}. As said before several folds may constitute a
  sulcus as defined by an anatomist. In order to accelerate such a
  labeling, use the \textbf{Add} button to set the same name (current name)
  to several lines. Pick a curve and press the \textbf{Add} button (or
  enter D on the keyboard). Note that the probability associate with the
  label you enter is set to 1.0.

\item{G} \textbf{Get Morphometrics} Informations related to the selected
  curve are displayed on the window.  For example the length and the depth
  of the selected fold are displayed.  The actual name of the curve is also
  displayed and some probability informations obtained with the SP\_AMs.
  These informations may help you to find the name of the sulcus in which
  the selected curve belongs.

\item{C} \textbf{Smalls Invisible}. All sulcus' portions having a length
  inferior to the threshold you are asked to enter becomes invisible. To
  make them visible again use button \textbf{Visible} (X).

\item{V} \textbf{Scan To Vol}. Once a curve has been selected it is
  possible to scan the associated median surface onto the MRI volume. This
  could help you to figure out the name of the selected curve based on its
  exact location in the MRI. The \textbf{Show Labels:On/off} allows to make the
  label visible or not on the MRI. The \textbf{PopMenu/Segmenting/Clear All
    Labels} allows to remove this scanning.

\item{B} \textbf{Unknown Invisible}. All black curves (i.e all curves
  labeled with the \textit{Unknown} label) become invisible.


\end{itemize}

\subsection{Available Labels}

\noindent The available labels are listed in the following table
(\ref{table_anatomical_list}).


\begin{table}[!h]
\centerline{ 
\begin{tabular}[]{|l|l|l|l|}
\hline  
number  &sulcus name         &color/scanning\_color        &scanning\_label  \\ \hline
0       &unknown\_name            &BLACK/CYAN                     &4 \\ \hline
1       &L\_F\_Ascending\_Ramus     &GREEN                          &18 \\ \hline
2       &L\_F\_Horizontal\_Ramus     &YELLOW                           &6 \\ \hline
3       &L\_F\_Incisura             &DARK\_BROWN \footnote{Camaros:black}  &14\\ \hline
4       &L\_F\_Inferior\_Frontal     &PURPLE                        &7 \\ \hline
5       &L\_F\_Middle\_Frontal       &RED                           &1 \\ \hline
6    &L\_F\_Precentral           &YELLOW                        &6 \\ \hline
7    &L\_F\_Superior\_Frontal     &ORANGE                       &99 \\ \hline
8    &L\_Fo\_Intermedius         &GREEN                         &18 \\ \hline
9    &L\_Fo\_Lateralis           &BLUE                          &3 \\ \hline
10   &L\_Fo\_Medialis            &ORANGE                       &99 \\ \hline
11   &L\_Fo\_Olfactory           &DARK\_BROWN \footnote{Camaros:black}  &14 \\ \hline
12   &L\_Fo\_Transversus         &RED                           &1 \\ \hline
13   &L\_P\_Intraparietal        &GREEN                         &18 \\ \hline
14   &L\_P\_Postcentral          &BLUE                          &3 \\ \hline
15   &L\_\_\_Central              &MAGENTA                       &8 \\ \hline
16   &L\_\_\_Sylvian              &RED                           &1 \\ \hline
17   &L\_T\_Superior\_Temporal    &GREEN                         &18 \\ \hline   
18   &L\_T\_Inferior\_Temporal    & MAGENTA                      &8  \\ \hline  
19   &L\_T\_Inferior\_Temporal\_Ascending\_Limb  & YELLOW          &6 \\ \hline   
20   &L\_O\_Lateral                           &RED              &1 \\ \hline   
50   &L\_F\_Subcentral\_anterior  &DARK\_BROWN                    &14 \\ \hline  
51   &L\_F\_Frontal\_vertical     &MAGENTA                        &8  \\ \hline 
52   &L\_F\_Precentral\_rostral   &BLUE                           &3  \\ \hline 
60   &L\_P\_Subcentral\_posterior &ORANGE                        &99 \\ \hline  
70   &L\_T\_Anterior\_Collateral    &GREEN                        &18 \\ \hline 
71   &L\_T\_Posterior\_Collateral   &MAGENTA                       &8 \\ \hline
72   &L\_T\_Posterior\_Ascending\_Superior\_Temporal    &ORANGE        &99 \\ \hline 
73   &L\_T\_Posterior\_Horizontal\_Superior\_Temporal   &YELLOW        &6 \\ \hline
99   &L\_\_\_ERROR                &CYAN/BLACK              &40 \\ \hline   
100  &L\_\_\_Side\_Branche        &WHITE                         &41 \\ \hline    
\end{tabular}
}

\parbox{12cm}{
  \renewcommand{\baselinestretch}{1.0}

\caption{\label{table_anatomical_list} Anatomical List for the Left Hemisphere }
{Anatomical List defined in SEAL for the left hemisphere. Add
100 on \textit{number} to find the equivalent table for the
right hemisphere. Example~: Central Sulcus of the right hemisphere has
the numbre 115. 
}
}
\end{table}


\section{Examples}

\noindent There are basically two situations~: i) you want to sart the
labelling of a \textit{sulgraph file}; ii) you want to continue or update
the labelling of a \textit{sulgraph file}.

\subsection{Starting a labelling}

You can do the following:

Run~:
\begin{verbatim}
disp.geo final_t1.mnc surface.obj G_A_L_L.obj G_A_R_L.obj
\end{verbatim}
\noindent
For the left hemisphere, select G\_A\_L\_L.obj in the object list
and apply~:

\noindent
\textbf{Init Guess}. \\
\texttt{`Enter proba\_threshold  and depth\_threshold:'} \\
enter 0.1 0 \\
(for right hemisphere do the same thing on object number 6, i.e G\_A\_R\_L.obj).


\noindent Now you can see that a subset of lines have been colored (other  lines are black). All colored lines are the lines that have
been labeled based on spatial priors. To figure out was is the label of a
curve select this curve with the mouse, use \textbf{Get Morphometrics} and check in
the terminal window its name (ex. name~:~L\_\_\_Central). Refer to table
\ref{table_anatomical_list} for correspondance between number/name and
colour.

\noindent
Now you can start to update the actual labeling~:
\begin{itemize}

\item pick a  curve 

\item click on \textbf{Get Morphometrics}~: some informations
related to the selected curve are displayed on the  terminal window.
These informations may help you to figure out the name of the
selected curve.

\item \textbf{Scan To Vol}~: once a curve is selected
  it is possible to scan its  associated median surface
  on  the MRI volume. This may help you to figure
  out the name of the selected curve based on its exact
  location on MRI.

\item \textbf{Set Name}~: this button allows to enter the sulcus name of
  the fold (several folds may constitute a sulcus as defined by an
  anatomist). You don't need to enter the full name of the sulcus (wich
  would be too long) but only a number. Refer to table
  \ref{table_anatomical_list} for correspondance between number/name and
  colour.

\item \textbf{Add}~: If a sulcus is composed of several lines, use the
  \textbf{Add} button to give the same name (current name) to several lines
  .

\item \textbf{Save Graph}~: this is used to save
  your labelling. You are asked to enter a \textit{sulgraph} filename
  (example: myname\_subjectID.sulgraph). Note that you can use the same name
  as the input \textit{sulgraph} file is you want to overwrite existing file.

\end{itemize}

\subsection{Updating a labelling}

\noindent In this case you have already a \textit{sulgraph} file containing
a labelling and you want to \textit{a)} see what has been already done;
\textit{b)} continue the labelling.\\ 
\noindent
Apply \textbf{Init Guess} to the appropriate object (i.e.  G\_A\_L\_L.obj, G\_A\_R\_L.obj, G\_A\_L\_Q.obj or  G\_A\_R\_Q.obj). \\
\textbf{`Enter proba\_threshold  and depth\_threshold:'} \\
enter: 0.9 0 \\

\noindent
Here the probability threshold is equal to 0.9. Therefore only
curves having a probability vector such that one component is superior to
0.9 are labelled. Considering the fact that \textbf{Set Name} and
\textbf{Add} buttons set to 1.0 the associated name's probability , these labels are those which were entered manually
(i.e. they correspond to a manual labelling). Then after application of
\textbf{Init Guess} with this 0.9 probability threshold, you can see what
has been already done. You can then follow the scheme described in the previous
paragraph  to continue and update this labelling.







\section{Computing New Sulcal Probability Anatomical Map (SP\_AMs)}
\label{Sulcal Probability Anatomical Map}

\noindent Once the labelling has been performed on several
\textit{sulgraph} files, it's possible to compute new SP\_AMs using~:

\begin{verbatim}
~georges/public_bin/mm_sulspam
\end{verbatim}

\noindent
mm\_sulspam is used like this \footnote{The code for mm\_sulspam is under:
  ~georges/Source/Minctools/Mm\_sulspam} :\\

\begin{verbatim}
mm_sulspam [<options>] <file:list_of_sulgraph> \
          <inputfile:mni_template><output_basename:SPAM>
\end{verbatim}
\noindent As an example
\footnote{~georges/Source/Minctools/Mm\_sulspam/runme.runme contains also
  other examples}:
\begin{verbatim}
mm_sulspam proto_list_51.txt \
   /data/icbm/mri1/models/average_305_mask_1.00.mnc \
   /data/icbm/sbd/seal/Spam/Spams_marita_51/L___Central.mnc \
   -clobber -sulind 15  -proba 0.9;
\end{verbatim}
\noindent
was used to generate the SP\_AM of the left central sulcus (-sulind 15)
which were manually labelled (-proba 0.9) from 51 manually labeled graphs.
``proto\_list\_51.txt'' is a text file (the actual file is stored under
\verb|~|georges/Source/Minctools/Mm\_sulspam) which contains the list of input sulgraph files:
\begin{verbatim}
proto_list_51.txt
/data/icbm/sbd/seal/00100/Sul_graph/lab_marita.sulgraph
/data/icbm/sbd/seal/00101/Sul_graph/lab_marita.sulgraph
....
/data/icbm/sbd/seal/00157/Sul_graph/lab_marita.sulgraph
/data/icbm/sbd/seal/00158/Sul_graph/lab_marita.sulgraph
\end{verbatim}

\noindent Figure \ref{fig_spams} shows an example of such a SP\_AM.


%\begin{figure}
%\centerline{ 
%\psfig{figure=/data/icbm/sbd/seal/Image_Rapport/Spamleft_3.eps,width=8cm}\hspace{1mm}
%}
%  \caption{Probability maps}
%  { Example of sulcus probability maps (SP\_AMs) computed in
%    stereotaxic space from 36 subjects. 
%    SC: central sulcus; SFs: superior frontal sulcus;
%    SFm: middle frontal sulcus; SFi: anterior part of the inferior frontal sulcus
%  }
%\label{fig_spams}
%\end{figure}



\section{The ICBM Project}
\label{ICBM Project}

\noindent The first phase of the ICBM project had consisted in studying
spatial variability of anatomical structure in the MNI-Talairach
referential frame in order to construct Statistical Probability Anatomical
Maps (SP\_AMs) of main anatomical structures \ref{ Mazziota95a,
  Evans97a}. This section present the work done within this context giving
also practical informations in order to internally retrieve data (the
utimate goal of ICBM being to share these data). A complete list of
most recent SP\_AMs is stored in~:
\verb|~|georges/Source/Minctools/Include/new\_tab\_of\_SPM.text. 


\subsection{Previously Available Data (Caramanos \cite{Caramanos97a})}
\noindent
These data were obtained before SEAL was developped. These data represent
spatial variability of sulcal superficial traces while SEAL's data (refer
to \ref{Marita}) represent spatial variability of sulcal median surfaces. I strongly
suggest to  not use these data as new data are now available
(refer to \ref{Marita}).

\noindent A trained neuroanatomist, blinded as to hemispheric location of
the sulcus by reflection of hemisphere, identified and manually labelled
the \textbf{superficial trace} of a restricted subset of 16 sulci on 51
brains~: (a) the Central Sulcus and (b) the Sylvian Fissure; (c) the
Superior, (d) the Middle, and (e) the Inferior Frontal Sulci; (f) the
Ascending and (g) the Horizontal Rami of the Sylvian Fissure, as well as
(h) the Incisura (located between these other two rami); (i) the Olfactory
Sulcus as well as (j) the Sulcus Lateralis, (k) the Sulcus Medialis, (l)
the Sulcus Intermedius, and (m) the Sulcus Transversus (all found along the
orbitofrontal surface of the brain); (n) the Precentral and (o) the
Postcentral Sulci; and finally (p) the Intraparietal Sulcus. These data
were used to construct associated sulcal SP\_AMs, representing the
likelihood of finding a particular structure at each 3-D stereotaxique
coordinates. These SPAMs are stored under~: \\ 
~sulcus/Tracing/Sulci/Sulcal\_Probability\_Maps/ \\ You can find the list
of these SP\_AMs in the file~: \\ 
\verb|~|georges/Source/Minctools/Include/tab\_of\_SPM.text.\\ The list of subjects
that were labeled can be found in table \ref{table_subject_raghu} \footnote{These
SP\_AMs were used to compute the probability vectors that are stored in the ICBM
database \textit{sulgraph} files}.





\begin{table}[!h]
\centerline{ 
\begin{tabular}[]{|l|l|l|l|l|l|l|l|l|l|l|}
\hline  
a  &00100 &00101 &00102 &00103 &00104 &00105 &00106 &00107 &00108 &00109 \\ \hline
b  &00110 &00111 &00112 &00113 &00114 &00115 &00116 &00117 &00118 &00119 \\ \hline
c  &00120 &00121 &00122 &XXX   &00124 &00125 &00126 &00127 &00128 &XXX   \\ \hline
d  &XXX   &00131 &XXX   &00133 &00134 &00135 &XXX   &00137 &00138 &00139 \\ \hline
e  &00140 &00141 &00142 &00143 &00144 &00145 &00146 &XXX   &00148 &00149 \\ \hline
f  &00150 &00151 &00152 &XXX   &XXX   &00155 &00156 &00157 &00158 &XXX   \\ \hline  
\end{tabular}
}
\parbox{12cm}{
  \renewcommand{\baselinestretch}{1.0}
  \normalsize

  \small

\caption{\label{table_subject_raghu} List of ICBM subjects labeled by
  Caramanos et \textit{all} \cite{Caramanos97a} }
{
From ~georges/Info/Marita/sulcal\_list.txt }
}
\end{table}


\subsection{Emmanuel \textsc{PROCYK}'s Labeling}
\noindent
We have also at our disposal several SP\_AMs that were computed from a set
of \textit{sulgraph} files labeled by Emmanuel \textsc{Procyk} (in collaboration
with Michael  \textsc{Petrides}).  These SP\_AMs correspond to the frontal lobe
sulci~: middle frontal s., superior frontal s., inferior frontal s. and
also the precentral s., the medial precentral s., the central s., the
subcentral anterior sulcus, the subcentral posterior sulcus.  51 brains
were studied and the associated \textit{sulgraph} were labeled. The file
/data/icbm/sbd/seal/README contains the list of subjects that were labeled
(it is the same list as the one given in table \ref{table_subject_raghu}).
Each labeling is stored in a
/data/icbm/sbd/seal/00xxx/Sul\_graph/lab\_manu\_auto.sulgraph.gz file.
Computed SP\_AMs are no more available because this labelling was updated
by Marita \textsc{SCHMITT}. 




\subsection{Marita \textsc{SCHMITT}'s Labeling}
\label{Marita}
\noindent The labels of Caramanos and Emmanuel Procyk were then transfered
to the \textit{lab\_marita.sulgraph} files and checked by Marita.\\ This
set of 51 \textit{sulgraph} files contains the most complete
\textit{sulgraph} labeling. These files are under \\ 
/data/icbm/sbd/seal/00XXX/Sul\_graph/lab\_marita.sulgraph . 
Associated SP\_AMs are stored under
/data/icbm/sbd/seal/Spam/Spams\_marita\_51. These SP\_AMs represent the
data that should be available within the ICBM project.  A complete list of
most recent SP\_AMs is stored in~: \\
\verb|~|georges/Source/Minctools/Include/new\_tab\_of\_SPM.text. \\

\noindent
These SP\_AMs represent the 3D distribution of the sulcus median surface
(not just the superficial trace distribution as done by Caramanos). 




\section{Questions}

\paragraph{Where are the SP\_AMs?}

The file \verb|~|georges/Source/Minctools/Include/new\_tab\_of\_SPM.tex contains
the filename and path of the SP\_AMs. \\

\noindent Most of the  SP\_AMs are under~:
 /data/icbm/sbd/seal/Spam/Spams\_marita\_51 \\

\noindent Some of them are also under~:\\
/data/npsych/home/sulcus/Tracing/Sulci/Sulcal\_Probability\_Maps




\paragraph{What should I do if the label I want to use is not available?}

\noindent Unfortunatly this is not straightforward as there are several
modifications to make in the code. Therefore the official ``maintainer''
will have to update the code and recompile the library LibSul, Display.geo
and then mm\_suldata.

\begin{itemize}

\item in enumeration.h (LibSul/enumeration.h) change the appropriate
  L\_\_\_NotSetYet\_XX with your new name. Do the same for the right hemisphere
  i.e. change the corresponding R\_\_\_NotSetYet\_XX with your name.

\item in extern char GLOBAL\_tab\_of\_name[NUMBER\_SPM\_VOL][SIZ\_SUL\_NAME]
  (LibSul/ARCDATA.cc) change the associated line with your name (do it
  for both hemisphere).  GLOBAL\_tab\_of\_name and enum seg\_name should 
  HAVE THE SAME SYMBOLS.

\item in label\_graph.cc (LibSul):
        change all occurence of the L/R\_\_\_NotSetYet\_XX  with
        L/R\_?\_YOURNAME.

      \item in the same file (i.e. label\_graph.cc), in Colour
        Global\_tab\_of\_color\_name(seg\_name name) choose the color you want
        to associate to your  sulcus~:\\
        \begin{verbatim}
                 case  R___NotSetYet_1  :  color = YOURCOLOR;
                   break;
        \end{verbatim}
        In the case your want to use a new colour (which was not
                 previously used, i.e. which does not appear in table 
                 \ref{table_anatomical_list}), in:
                 \begin{verbatim}
                 int compute_label_from_color(Colour col, Colour
                 *scanning_col)
                 \end{verbatim}
                 put this lines :
                 \begin{verbatim}
                 if(col == YOURCOLOR){  
                label = YOURLABEL;
                *scanning_col = YOURSCANNINGCOLOR;  
                found = YES;            //DIFFER
                }
                \end{verbatim}

\item Update ~/Source/Display/callbacks/georges.c at the section ``Display
  the anatomical list'', in order to keep the \textit{Anat List?} button up
  to date. 

\item Update \verb|~|georges/Source/Minctools/Include/ANATOMICAL\_LIST.txt file 

\item Update  this file or in its initial Latex version table
  \ref{table_anatomical_list}.

\end{itemize}

\noindent 
Note that the three last actions have no effect on the code, but you need
to make them in order to keep everything updated.

\noindent Once this is done, recompile the library LibSul, the program
mm\_suldata (make install) and Display.geo.  To recompile Display.geo, you
need to do the following (in order to have: setenv SRC\_DIRECTORY   /data/nil/david/Release)~:

\begin{verbatim}
cd ~georges/Source/Display
source ~david/Source/Makefile_multi_architecture/cshrc.csh;
source ~david/Release/cshrc.csh;
make Display.geo;
\end{verbatim}


\noindent That's it!

\paragraph{What should I do if a new SP\_AM becomes available?}

\noindent Again it's the ``maintainer'' who should do this. If a new SP\_AM
becomes available you may want to incorporate this information in the
computation of new probability vector (i.e. in the computation of new
\textit{sulgraph} file). To do that you have to update
\verb|~|georges/Source/Minctools/Include/new\_tab\_of\_SPM.text. Example~: if the
SP\_AM of L\_T\_Superior\_Temporal (17) becomes available edit line 17 of
\verb|~|georges/Source/Minctools/Include/new\_tab\_of\_SPM.text (i.e. add the
filename there). Edit also line 117 with the corresponding path for
R\_T\_Superior\_Temporal (117). Recompile and install mm\_suldata \\ (i.e. cd
\verb|~|georges/Source/Minctools/Mm\_suldata; make install) . The new version of
sulcus\_graph.pl will incorporate these new SP\_AMs in the computation of
the probability vectors.


\section{Automatic Labelling}
\label{Automatic Labelling}

\noindent As said before, automatic labelling of the main cortical sulci is
done using prior knowledge for the expected 3D spatial distribution of
these entities.  Probabilistic identification of a new graph is achieved by
integrating each sulcal spatial distribution map over a sulcus' median
surface and assigning it the sulcus name corresponding to the maximum
integrated probability value. Quantitative evaluation of the automatic labelling
accuracy with regards to the different types of errors (under-estimation of
sulcal extend, confusion between adjacent sulci) were computed. Results show
that correct identification of eight main cortical sulci studied can be
reached in 34~\% to 70~\% of the cases depending on the level of accuracy
needed. For more information on this problem, refer to
\verb|~|georges/Docs/Postdoc/Article/article.tex and
\verb|~|georges/Docs/Postdoc/Article/Script. 

\section{Post Segmentation}
\label{Post Segmentation}

\noindent Post-segmentation can be done using 
\verb|~|georges/Source/Minctools/Mm\_depth\_interac/Tcl/interact.



\section{Related Reports and Papers}
\label{Related Reports}

\begin{itemize}

\item References (some on them are available online)~:
\begin{verbatim}
http://www.bic.mni.mcgill.ca/~georges/publications/publi.html
\end{verbatim}

\item Overview (Transactions on Medical Imaging)~:
\begin{verbatim}
~georges/Docs/Postdoc/TMI/Submission/le_goualher_149_98_IEEE_TMI.ps.gz
\end{verbatim}

\item Automatic Labelling (not published)~:
\begin{verbatim}
~georges/Docs/Postdoc/Article/article.tex
\end{verbatim}

\item Shape Analysis (Principal Component Analysis) (submitted to NeuroImage)~:
\begin{verbatim}
~georges/Docs/Postdoc/Argenti/Paper1/Paper_two/Submission/goualher_neuroimage_main.ps.gz
\end{verbatim}

\item Rapport R\'egion Bretagne (in french only):
\begin{verbatim}
~georges/Data_nil/Docs/Postdoc/Repport1/rep_oct98.ps.gz
\end{verbatim}


\item Slides (showcase files)~:

\begin{verbatim}
/data/icbm/sbd/seal/Slides
\end{verbatim}

\begin{verbatim}
summary: /data/icbm/sbd/seal/Slides/MNI/summary.sho
\end{verbatim}

\item Illustrations~:
\begin{verbatim}
figures: /data/icbm/sbd/seal/Image_Rapport
\end{verbatim}

\end{itemize}




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