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e871c035 · Saad Jbabdi · dfe816e9 · e871c035 · e871c035 · e871c035
Commit e871c035 authored 17 years ago by Saad Jbabdi
--- a/doc/fdt_bedpostx.html
+++ b/doc/fdt_bedpostx.html
 <HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
+<IMG ALIGN=RIGHT hspace=20 vspace=20 SRC="fdt_images/fdt_bedpost.gif"
+ALT="Bedpost GUI view">
 <p><h3>Bedpost</h3>
 <p>Bedpost stands for Bayesian Estimation of Diffusion Parameters Obtained using Sampling
 Techniques. Bedpost runs Markov Chain Monte Carlo sampling to build up distributions on diffusion parameters at each voxel. It creates all the
 files necessary for running probabilistic tractography. For an overview of
-the modelling carried out within Bedpost see the <a
-href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">appendix.</a>
+the modelling carried out within Bedpost see the <ahref="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">appendix.</a>
+
+<p>Bedpost now allows to model crossing fibres within each voxel on the brain. Crucially, Bedpost only models crossing fibres in voxels where the data support crossing fibres. For details on the model used in this case, see Behrens et al, NeuroImage 2007, 34:144-55.

 <p>Bedpost takes about 24 hours to run but can easily be <a href="fdt_bedpost_parallel.html">parallelised</a> if multiple
 processors are available.
@@ -19,7 +22,7 @@ That directory must contain the following files:
 include diffusion-weighted volumes and volume(s) with no diffusion weighting.</li>
 <li><b>nodif</b>: 3D volume with no diffusion weighting</li>
 <li><b>nodif_brain_mask</b>: 3D binary brain mask volume derived
-from running <a href="../bet/index.html" target="_top">bet</a> on nodif</li>
+from running <a href="http:www.fmrib.ox.ac.uk/fsl/bet/index.html" target="_top">bet</a> on nodif</li>
 <li><b>bvecs</b>:  A text file containing a list
 of gradient directions applied during diffusion weighted volumes.  The
 order of entries in this file must match the order of volumes in <b>data</b>.
@@ -28,37 +31,35 @@ The format is<pre>
 x_1 x_2 x_3 ... x_n
 y_1 y_2 y_3 ... y_n
 z_1 z_2 z_3 ... z_n<br></pre> 
-Vectors should be normalised. For volumes in which there was no
-diffusion weighting, the entry should still be present, although the
+For volumes in which there was no diffusion weighting, the entry should still be present, although the
 direction of the vector does not matter!  </li>
-<li><b>bvals</b> A text file containing a list of bvalues applied during
-each volume acquisition. The order of entries in this file must match the
-order of volumes in the input data and entries in the gradient directions text
-file.
+<li><b>bvals</b> A text file containing a list of bvalues applied during each volume acquisition. The order of entries in this file must match the
+order of volumes in the input data and entries in the gradient directions text file.
 <br>
 The format is <br><pre>
 b_1 b_2 b_3 ... b_n<br></pre>
 The order of <b>bvals</b> must match the order of <b>data.</b></li>
 </ul>
+
 <p><h4>Outputs of Bedpost</h4>
 Bedpost creates a new directory at the same level as the input directory
 called &lt;indir&gt;.bedpost which contains all the files you need for probabilistic
-tractography.  Highlights are:
+tractography.  Highlights are (&#60;i&#62; indicates the i-th fibre. It ranges from 1 to the maximum number of fibres set in the advanced options.):

 <ul>
-<li><b>merged_thsamples</b> - 4D volume -  Samples from the distribution on theta </li>
-<li><b>merged_phsamples</b> - Samples from the distribution on phi
+<li><b>merged_th&#60;i&#62;samples</b> - 4D volume -  Samples from the distribution on theta </li>
+<li><b>merged_ph&#60;i&#62;samples</b> - Samples from the distribution on phi
 </li><ul><li>theta and phi together represent the principal diffusion
 direction in <a href="fdt_images/fdt_spherical_polars.gif">spherical polar co-ordinates</a></li></ul>
-<li><b>merged_fsamples</b> - 4D volume - Samples from the distribution
+<li><b>merged_f&#60;i&#62;samples</b> - 4D volume - Samples from the distribution
 on anisotropic volume fraction (see <a
 href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">technical
 report</a>).</li>
-<li><b>mean_thsamples</b> - 3D Volume - Mean of distribution on theta  </li>
-<li><b>mean_phsamples</b> - 3D Volume - Mean of distribution on phi  </li>
-<li><b>mean_fsamples</b> -  3D Volume - Mean of distribution on <i>f</i>
+<li><b>mean_th&#60;i&#62;samples</b> - 3D Volume - Mean of distribution on theta  </li>
+<li><b>mean_ph&#60;i&#62;samples</b> - 3D Volume - Mean of distribution on phi  </li>
+<li><b>mean_f&#60;i&#62;samples</b> -  3D Volume - Mean of distribution on <i>f</i>
 anisotropy  </li>
-<li><b>dyadic_vectors</b> - Mean of PDD distribution in vector form.
+<li><b>dyads&#60;i&#62;</b> - Mean of PDD distribution in vector form.
 Note that this file can be loaded into fslview for easy <a href="fdt_display.html">viewing of diffusion directions</a></li>
 <li><b>nodif</b> - Single volume with no diffusion weighting -
 copied from input directory </li>
@@ -69,5 +70,13 @@ copied from input directory
 </li>
 </ul>

+<p><h4>Advanced options</h4>
+You may change some options before running Bedpost, depending on the questions you want to ask or the quality of your diffusion data. The default values of these parameters are the ones used in the corresponding paper (Behrens et al, NeuroImage 2007).
+<ul>
+<li><b>Fibres</b>: Number of fibres modelled per voxel. 
+<li><b>Weight</b>: Multiplicative factor for the prior on the additional modelled fibres. A smaller factor means more weighting for the additional fibres.
+<li><b>Burnin</b>: Number of iterations before starting the sampling. These might be increased if the data are noisy, and the MCMC needs more iterations to converge.
+</ul>
+
 <p><h4>command line utility</h4>
-<verb>bedpost &#60;indir&#62; </verb>
\ No newline at end of file
+<verb>bedpost &#60;indir&#62; [-f &#60;nfibres&#62; -w &#60;weight&#62; -b &#60;niter&#62;]</verb>
--- a/doc/fdt_display.html
+++ b/doc/fdt_display.html
 <HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-<IMG ALIGN=RIGHT hspace=20 vspace=20 SRC="fdt_images/fslview_dti.gif"
-ALT="Example GUI view">
+<IMG ALIGN=MIDDLE hspace=10 vspace=20 SRC="fdt_images/fdt_vectorsx.jpg"
+ALT="Visualising vector data">
 <h3>Displaying DWI images in fslview</h3>
-Outputs of <b>Bedpost</b> or <b>DtiFit</b> can be conveniently displayed
-in fslview.  If you open an image of diffusion vectors (e.g., dtifit_V1
-output of DtiFit or merged_dyadic_vectors output of Bedpost) then it is
-possible to display these vectors using <b>RGB</b> coding (where the colours
-red,green and blue represent diffusion in the x,y,z axes respectively) or
+Outputs of <b>Bedpost</b> or <b>DtiFit</b> can be conveniently displayed in fslview.  
+If you open an image of diffusion vectors (e.g., dtifit_V1 output of DtiFit or dyads&#60;i&#62; output of Bedpost) then it is
+possible to display these vectors using <b>RGB</b> coding (where the colours red,green and blue represent diffusion in the x,y,z axes respectively) or
 using <b>lines</b> where a line at each voxel represent the principle
-diffusion direction at that voxel.  For more details see the relevant fslview
+diffusion direction at that voxel.<br>
+It is also possible to display multiple lines per voxel. Each line will be displayed in a different colour.<br>
+If you only want to visualise fibres within voxels where multiple fibres are supported (e.g. above a certain threshold for the corresponding mean_fsamples), then you first have to create a vector file where the voxels below a certain f-threshold are zeroed. You may use the two following commands for that:<br><br>
+<verb>fslmaths mean_fisamples -thr 0.05 -bin tmpmask</verb><br>
+<verb>fslmaths dyadsi -mas tmpmask dyadsi_masked</verb>
+
+
+<p>
+For more details see the relevant fslview
 <a href="http://www.fmrib.ox.ac.uk/fsl/fslview/dti.html"
 target="_top">tutorial</a>.

--- a/doc/fdt_images/fdt_bedpost.gif
+++ b/doc/fdt_images/fdt_bedpost.gif
--- a/doc/fdt_images/fdt_bedpost.tiff
+++ b/doc/fdt_images/fdt_bedpost.tiff
--- a/doc/fdt_images/fdt_gui.gif
+++ b/doc/fdt_images/fdt_gui.gif
--- a/doc/fdt_images/fdt_gui.tiff
+++ b/doc/fdt_images/fdt_gui.tiff
--- a/doc/fdt_images/fdt_vectors.jpg
+++ b/doc/fdt_images/fdt_vectors.jpg
--- a/doc/fdt_images/fdt_vectorsx.jpg
+++ b/doc/fdt_images/fdt_vectorsx.jpg
--- a/doc/fdt_images/fdt_xfibres_axial.png
+++ b/doc/fdt_images/fdt_xfibres_axial.png
--- a/doc/fdt_images/fdt_xfibres_coronal.png
+++ b/doc/fdt_images/fdt_xfibres_coronal.png
--- a/doc/fdt_intro.html
+++ b/doc/fdt_intro.html
 <HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-<IMG ALIGN=RIGHT hspace=20 vspace=20 SRC="fdt_images/gui_intro.gif"
+<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
@@ -23,13 +23,14 @@ The main FDT programmes, which are accesible from the GUI are:

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

 <p>Additional FDT programmes, that can be run only from the command line, are:
 <ul><li><a href="fdt_thresh.html">proj_thresh</a> - for thresholding some outputs
 of probtrack</li>
 <li><A href="fdt_biggest.html">find_the_biggest</a> - for performing hard
-segmentation on the outputs of connectivity-based thresholding in probtrack</li></ul>
+segmentation on the outputs of connectivity-based thresholding in probtrack</li>
+<li><A href="fdt_vecreg.html">vecreg</a> - for registering vector data</li></ul>

 <p>The probabilistic tractography tools within FDT are very flexible and allow
 the user to generate connectivity distributions from single or multiple

--- a/doc/fdt_vecreg.html
+++ b/doc/fdt_vecreg.html
@@ -25,12 +25,10 @@ from bedpost: dyads1, dyads2, etc. <br>
 vecreg -i input_vector -o output_vector -r reference_image -t flirt_transform.mat<br>
 <b>using a warpfield</b><br>
 vecreg -i input_vector -o output_vector -r reference_image -w warp_field<br>
-<br>
-<b>more options</b><br>

-<pre>
-Usage: 
-vector_flirt -i &lt;input4Dvector&gt; -o &lt;output4D&gt; -t &lt;transformation&gt;
+<br><b>more options</b>
+<pre> 
+vecreg -i &lt;input4Dvector&gt; -o &lt;output4D&gt; -t &lt;transformation&gt;

 Compulsory arguments (You MUST set one or more of):
        -i,--input      filename of input vector