#DEETO

seeg electroDE rEconstruction TOol:

This tool reconstructs the position of SEEG electrode contacts from a post-implant Cone-beam CT scan.

USAGE: 

   deeto  [-1] [-t <string>] [-o <string>] [-f <string>] [-c <string>] [--]
          [--version] [-h]


Where: 

   -1,  --vtk-single-fout
     Single output file for implant

   -t <string>,  --o_type <string>
      Output Type

   -o <string>,  --out <string>
     fname OUT

   -f <string>,  --fid <string>
     Fiducials File IN

   -c <string>,  --ct <string>
     CT File IN

   --,  --ignore_rest
     Ignores the rest of the labeled arguments following this flag.

   --version
     Displays version information and exits.

   -h,  --help
     Displays usage information and exits.

##Software requirments For builiding the tool you have to install some dependecies.

Library	Version	URL
Cmake	2.8	download
ITK	4.3.1	download
tclap	1.2.1	download.
VTK (optional)	5.6	download

The version should be intended as a suggestion (ie we developped and tested with these) but any minor revision of the above mentioned library should work as well.

For Debian- and RedHat-based distribution use apt-get or yum to install the required libraries. If you want to proceed with the manual installation follow the steps below.

##MANUL INSTALLATION

###Download and install tclap

Download the latest version 1.2.1 from tclap download page. Extract the archive and enter in the unpacked directory. The directory contains the autoconf and automake configuration files required for compilining and installing the library. It is sufficient to run within the unpacked directory:

$ ./configure
$ make && sudo make install

For problems with installation of this third-party library please refer to the sourceforge project page.

###Download and Install CMake

Moreover, you need to download and install CMAKE in your computer. Cmake is a cross-platform compiler and can be downloaded from CMake website

Soon after the download has ended, extract the downloaded file and from the terminal

$ ./configure
$ make
$ sudo make install

###Download and Install ITK

Download the latest ITK files from ITK website Extract all ITK files and enter in the unpacked directory. For an easier cleanup process create a build directory where the code will be compiled that can be removed later on when the entire process has finished

$ mkdir ./build && cd ./build

####Default configuration $ cmake ../ ( assuming standard installation path and configurations) ####Advanced configuration $ ccmake ../ to call the ncursed configuration gui.

	Press c to configure the ITK setup. After configuration process press c again.

	Press g to generate and exit from configuration window.

Once the process has ended, and the Makefile has been created in your directory

$ make 
$ sudo make install

You can now clean the build directory, assuming that you are still within it, as normal user type

$ rm -Rf *

###Download and Install VTK (optional)

Download VTK from VTK webpage Then extract vtk files. Goto vtk folder using Terminal and type

$ ccmake .

After processing it will prompt a configuration option, press ‘c‘ to configure.

Edit its settings as required and press c, if generate option (g) is not present press c again.

Press g to generate.

$ make
$ sudo make install

###Build and Run

Build the project with cmake as we have done before with both ITK and VTK

$ cmake CMakeLists.txt

$ make

Run the generated executable file in directory bin