wiki plugins

.gitignore

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 _config-claire.yml
 Gemfile.lock
 code/plugins/github/
+.*/.DS_Store
+.DS_Store

plugins/NFT/Chapter_01_Getting_Started_with_NFT.md

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+---
+layout: default
+title: Chapter_01_Getting_Started_with_NFT
+long_title: Chapter_01_Getting_Started_with_NFT
+parent: NFT
+grand_parent: Plugins
+---
+Introduction
+------------
+
+The Neuroelectromagnetic Forward Head Modeling Toolbox is an open-source
+software toolbox running under MATLAB (The Mathworks, Inc.) for
+generating realistic head models from available data (MRI and/or
+electrode locations) and for solving the forward problem of
+electro-magnetic source imaging. The toolbox includes tools for
+segmenting scalp, skull, cerebrospinal fluid (CSF) and brain tissues
+from T1-weighted magnetic resonance (MR) images. After extracting the
+segmented tissue volumes, mesh generation can be performed. When MR
+images are not available, it is possible to warp a template head model
+to measured electrode locations to obtain a better-fitting head model.
+The toolbox also includes electrode scalp mesh co-registration and
+generation of a uniform source space inside the brain volume for to be
+used in coarse source localization. The Boundary Element Method (BEM) is
+used for the numerical solution of the forward problem. Toolbox
+functions can be called from either a graphic user interface or from the
+command line. Function help messages and a tutorial are included. The
+toolbox is freely available under the GNU Public License for
+noncommercial use and open source development.
+
+The toolbox uses the following third party tools and libraries for
+segmentation, mesh generation and forward problem solution. The source
+codes for these tools are available.
+
+1\. ASC - for triangulation of 3D volumes.
+
+2\. Qslim - for mesh coarsening.
+
+3\. Matitk - Matlab interface to the ITK image processing toolkit.
+
+4\. Metu-bem - Boundary Element Method solver.
+
+The NFT toolbox provides a user interface (UI) for segmentation, mesh
+generation and for creating the numerical head model. It also has a well
+defined MATLAB command-line interface.
+
+This manual explains how to use the NFT toolbox. The head modeling UI,
+the command line API and the structures are described. An overview of
+the implementation is provided.
+
+The next section describes the installation of the toolbox. The Getting
+Started section provides an overview of the interface. Head modeling
+from 3D MR images is described next, followed by head modeling from
+template warping. This is followed by a section on forward modeling and
+examples. The [final
+section](Chapter_05_NFT_Commands_and_Functions "wikilink") is a
+summary of all toolbox functions and commands.
+
+Installation and Configuration
+------------------------------
+
+This section describes installation and configuration of the NFT
+Toolbox. The following steps are necessary for a proper installation of
+the toolbox:
+
+1\. Extract or copy the toolbox directory to a suitable place on your
+computer file system.
+
+2\. The extracted directory will contain m-files, and C++ executables.
+
+3\. Add the toolbox directory to the MATLAB path. You can use the File →
+SetPath menu item or the addpath() function. Under linux/unix, you may
+add the directory to the MATLABPATH.
+
+The toolbox can also make use of the Matlab Parallel Processing toolbox
+(if installed) to distribute the computation of the transfer and
+lead-field matrices to multiple processors. To do this, before running
+NFT, the user must simply enter
+
+\>\> matlabpool(n) % where n is the number of compute nodes available
+
+In parallel mode, wait bars do not appear while computing the transfer
+and lead-field matrices.
+
+Getting Started
+---------------
+
+The toolbox starts by typing
+Neuroelectromagnetic_Forward_Modeling_Toolbox or NFT on command window.
+Main window appears as shown in Figure 1. This window is divided into
+three panels. The first panel is used to select the working folder, and
+to name the subject and the session. The NFM toolbox requires a subject
+folder to be specified at startup. All subject specific output is saved
+into this folder. The filenames are derived from the subject and session
+names entered into this panel. The second panel is the Head modeling
+panel. The head model can either be created from MR images, or a
+template head model can be warped to digitized sensors. The head
+modeling panel provides the following operations when creating a head
+model from MR images:
+
+![NFT_ui](NFT_ui.png)
+
+**Image Segmentation**
+
+
+
+Interface for tissue classification from 3D MR Images.
+
+**Mesh Generation**
+
+
+
+Uses the segmentation results to generate realistic BEM meshes.
+
+**Source Space Generation**
+
+
+
+Generates a regular grid sources within the brain mesh.
+
+**Electrode Co-Registration**
+
+
+
+Registers digitized electrode locations to the scalp mesh.
+
+When generating a template-based head model from digitized electrode
+positions, the only option is Template Warping. The final panel in the
+main menu is for Forward Model Generation. This opens up the Forward
+Model Generation interface which is used to compute the BEM coefficient
+matrix, create the transfer matrices for each sensor, and generate lead
+field matrices for a source distribution.