Skip to content
Snippets Groups Projects
Select Git revision
  • master default protected
  • streamliner
  • newnew
  • cvsHEAD
  • osx-109-branch
  • ADD_CSV_BRANCH
  • ADD_CSV_BRANCH_STABLE
  • universal
  • universal_branch
  • fsl-3_3-branch
  • sge-branch
  • fsl-3_2
  • 2202.11
  • 2202.10
  • 2202.9
  • 2202.8
  • 2202.7
  • 2202.6
  • 2202.5
  • 2202.4
  • 2202.3
  • 2202.2
  • 2202.1
  • 2202.0
  • 2111.0
  • 2103.0
  • 2101.0
  • 2012.0
  • 2011.0
  • 2010.0
  • 2007.0
  • 2001.0
32 results
Blame Permalink
index.html 3.07 KiB 
<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN" "http://www.w3.org/TR/html4/loose.dtd">
<HTML><HEAD><meta http-equiv="Content-Type" content="text/html;charset=utf-8">
<link REL="stylesheet" TYPE="text/css" href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<BODY><IFRAME width="100%" scrolling="no" frameborder="0" src="fdt_top.html">Broken</IFRAME>

<IMG ALIGN=RIGHT hspace=20 vspace=20 SRC="fdt_images/fdt_gui.gif" ALT="Example GUI view">
<h3>Introduction</h3>
For other information on FDT and updated journal references, see the <a
href="http://www.fmrib.ox.ac.uk/analysis/research/fdt/" target="_top">FDT web
page</a>.  If you use FDT in your research, please quote the journal
references listed there.

<p>FDT (FMRIB's Diffusion Toolbox) is a software tool for analysis of diffusion weighted images.  FDT is part
of <a href="http://www.fmrib.ox.ac.uk/fsl" target="_top">FSL</a> (FMRIB's Software Library)
.  FDT has an easy-to-use graphical user interface (GUI) and its component
programmes can also be run from the command line. FDT includes tools for
data preprocessing, local diffusion modelling and tractography. Each stage in FDT is run
separately.   

The main FDT programmes, which are accesible from the GUI are:

<ul><li><a href="fdt_eddy.html">eddycorrect</a> - for correction of eddy current distortion</li>
<li><a href="fdt_bedpostx.html">bedpostx</a> - for local modelling of diffusion parameters.</li>
<li><a href="fdt_probtrackx.html">probtrackx</a> - for tractography and connectivity-based segmentation</li> 
<li><a href="fdt_dtifit.html">dtifit</a> - for local fitting of diffusion tensors</li></ul>

<br>The FDT GUI also includes a <a
href="fdt_reg.html">registration</a> option that registers images
using <a href="http://www.fmrib.ox.ac.uk/fsl/flirt/index.html" target="_top">FLIRT</a>.

<p>Additional FDT <a href="fdt_utils.html">utilities</a>, that can be run only from the command line, are:
<ul><li><a href="fdt_utils.html#thresh">proj_thresh</a> - for thresholding some outputs
of probtrack</li>
<li><A href="fdt_utils.html#biggest">find_the_biggest</a> - for performing hard
segmentation on the outputs of connectivity-based thresholding in probtrack</li>
<li><A href="fdt_utils.html#vecreg">vecreg</a> - for registering vector data</li>
<li><A href="fdt_utils.html#qboot">qboot</a> - for estimating fibre
orientations and their uncertainty using ODFs and bootstrapping </li></ul>


<p>The probabilistic tractography tools within FDT are very flexible and allow
the user to generate connectivity distributions from single or multiple
voxels, or from a <a href="http://surfer.nmr.mgh.harvard.edu">FreeSurfer</a> cortical surface; 
to limit these distributions based on anatomical criteria and to
perform segmentation based on the probability of connection to user-defined
target regions.

<p>To call the FDT GUI, either run <b>Fdt</b> (<b>Fdt_gui</b> on Mac
or Windows), or run <b>fsl</b> and press the <b>FDT</b> button.

<p>For an overview of the local diffusion modelling and tractography used
within FDT see the <a href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">appendix</a>.