diff --git a/doc/fdt_bedpostx.html b/doc/fdt_bedpostx.html
index 32ada2bb097be3d9042e16774b4d54d23c0adbe8..a4225b68e61891697bcd9c0724316d604c4c1b13 100644
--- a/doc/fdt_bedpostx.html
+++ b/doc/fdt_bedpostx.html
@@ -6,40 +6,31 @@ content="text/html;charset=utf-8">
href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<BODY><OBJECT data="fdt_top.html"></OBJECT>
-<IMG ALIGN=RIGHT hspace=20 vspace=20 SRC="fdt_images/fdt_bedpost.gif" ALT="Bedpost GUI view">
-<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 <ahref="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">appendix.</a>
+<IMG ALIGN=RIGHT hspace=20 vspace=20 SRC="fdt_images/fdt_bedpostx.gif" ALT="Bedpost GUI view">
+<h3>BEDPOSTX</h3>
+<p>BEDPOSTX stands for Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques. The X stands for modelling Crossing Fibres. <b>bedpostx</b> 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 <b>bedpostx</b> 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><b>bedpostx</b> now allows to model crossing fibres within each voxel on the brain. Crucially, <b>bedpostx</b> allows to automatically determine the number of crossing fibres per voxel. 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.
+<p><b>bedpostx</b> takes about 24 hours to run but can easily be <a href="fdt_bedpostx_parallel.html">parallelised</a> if multiple processors are available.
+
+<p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the <b>FDT</b> button. Use the top left drop down menu to select <b>BEDPOSTX</b>.
-<p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the
-<b>FDT</b> button. Use the top left drop down menu to select <b>Bedpost</b>.
<p>
-<b>Input directory:</b> Use the browse button to select an input directory.
-That directory must contain the following files:
+<b>Input directory:</b> Use the browse button to select an input directory. That directory must contain the following files:
<ul>
-<li><b>data</b>: A 4D series of data volumes. This will
-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="../bet2/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>.
+<li><b>data</b>: A 4D series of data volumes. This will 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="../bet2/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>.
<br>
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>
-For volumes in which there was no diffusion weighting, the entry should still be present, although the
+Vectors are normalised to unit length within the <b>bedpostx</b> code. 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
+<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>
@@ -47,9 +38,9 @@ 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 <indir>.bedpost which contains all the files you need for probabilistic
+<p><h4>Outputs of BEDPOSTX</h4>
+<b>bedpostx</b> creates a new directory at the same level as the input directory
+called <indir>.bedpostX which contains all the files you need for probabilistic
tractography. Highlights are (<i> indicates the i-th fibre. It ranges from 1 to the maximum number of fibres set in the advanced options.):
<ul>
@@ -65,6 +56,7 @@ report</a>).</li>
<li><b>mean_ph<i>samples</b> - 3D Volume - Mean of distribution on phi </li>
<li><b>mean_f<i>samples</b> - 3D Volume - Mean of distribution on <i>f</i>
anisotropy </li>
+<ul><li>Note that in each voxel, fibres are ordered according to a decreasing mean f-value</li></ul>
<li><b>dyads<i></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 -
@@ -76,13 +68,13 @@ 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).
+<p><h4>Advanced Options</h4>
+You may change some options before running <b>bedpostx</b>, 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, 34:144-55).
<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 <indir> [-f <nfibres> -w <weight> -b <niter>]</verb>
+<p><h4>Command line utility</h4>
+<verb>bedpostx <indir> [-f <nfibres>] [-w <weight>] [-b <niter>]</verb>
diff --git a/doc/fdt_biggest.html b/doc/fdt_biggest.html
index 3d0a553ddfef512170ea6d5d713b5bb86666c6f5..f11b7a762cef1bc52993b103f5217af3b92bbc5a 100644
--- a/doc/fdt_biggest.html
+++ b/doc/fdt_biggest.html
@@ -8,9 +8,10 @@ href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<h3>find_the_biggest</h3>
<b>find_the_biggest</b> is a command line utility that performs hard
-segmentation of a seed region on the basis of outputs from the <b>Connectivity-based seed classification</b> mode
-within <a
-href="fdt_probtrackx.html"><b>probtrack</b></a>. <p>The output of <b>Connectivity-based seed classification</b> is a single volume for
+segmentation of a seed region on the basis of outputs of <a
+href="fdt_probtrackx.html"><b>probtrackx</b></a> when <b>classification targets</b> are being used.
+
+<p>The output of <b>Connectivity-based seed classification</b> is a single volume for
each target mask, named <b>seeds_to_{target}</b> where {target} is replaced
by the file name of the relevant target mask. In these output images, the
value of each voxel within the seed mask is the number of samples seeded
@@ -23,6 +24,6 @@ classification</b> (i.e., files named seeds_to_target1 etc etc).
<p><IMG ALIGN=RIGHT height=300 SRC="fdt_images/fdt_seeds2targets_thal.gif"
ALT="connectivity-based classification of thalamus">
-<p>The example on the right uses ProbTrack and find_the_biggest to perform hard segmentation
+<p>The example on the right uses <a href="fdt_probtrackx.html"><b>probtrackx</b></a> and find_the_biggest to perform hard segmentation
of the thalamus on the basis of its connections to cortex.
diff --git a/doc/fdt_display.html b/doc/fdt_display.html
index 0a1b16ba0b69da8595e92abc04c3ebc5588d8750..848f3c2b55d6d92db1a2ec26f4043f3f2b6e43ca 100644
--- a/doc/fdt_display.html
+++ b/doc/fdt_display.html
@@ -6,17 +6,18 @@ content="text/html;charset=utf-8">
href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<BODY><OBJECT data="fdt_top.html"></OBJECT>
-<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 dyads<i> output of Bedpost) then it is
+Outputs of <a href="fdt_bedpostx.html"><b>bedpostx</b></a> or <a href="fdt_dtifit.html"><b>dtifit</b></a> can be conveniently displayed in fslview.
+If you open an image of diffusion vectors (e.g., dtifit_V1 output of <b>dtifit</b> or dyads<i> output of <b>bedpostx</b>) 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.<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>
+using <b>lines</b> where a line at each voxel represents the principle
+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. In the example above, the red lines represent the main fibre orientation, and the green lines represent the secondary fibre orientations (thresholded at an f-value of 0.05), as calculated by bedpostx.<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_f<i>samples), 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_f<i>samples -thr 0.05 -bin tmpmask</verb><br>
+<verb>fslmaths dyads<i> -mas tmpmask dyads<i>_masked</verb>
<p>
diff --git a/doc/fdt_dtifit.html b/doc/fdt_dtifit.html
index 1509fd53d52f6e85ff94979874a4c19588d9f33f..c8a1faf13cf320a990b642a18cd552fe56a25135 100644
--- a/doc/fdt_dtifit.html
+++ b/doc/fdt_dtifit.html
@@ -6,16 +6,16 @@ content="text/html;charset=utf-8">
href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<BODY><OBJECT data="fdt_top.html"></OBJECT>
-<h3>DTIFit</h3>
+<h3>DTIFIT</h3>
-<b>DTIFit</b> fits a diffusion tensor model at each voxel. You would
-typically run DTIFit on data that has been pre-processed and
-eddy current corrected. Note that DTIFit is not necessary in order to
+<b>DTIFIT</b> fits a diffusion tensor model at each voxel. You would
+typically run <b>dtifit</b> on data that has been pre-processed and
+eddy current corrected. Note that <b>dtifit</b> is not necessary in order to
use the probabilistic tractography (which depends on the output of
-BEDPOST not DTIFit).
+BEDPOSTX not DTIFIT).
<p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the
-<b>FDT</b> button. Use the top left drop down menu to select <b>DTIFit</b>.
+<b>FDT</b> button. Use the top left drop down menu to select <b>DTIFIT</b>.
<p><b>Input:</b> You can specify an input directory containing all the required files
with standardized filenames,
@@ -32,7 +32,7 @@ volume in diffusion space containing ones inside the brain and zeroes outside
the brain.</li>
<li><b>Output basename:</b> User specifies a basename that will be used to name the
-outputs of DTIFit. If the directory input option is used then the basename
+outputs of <b>dtifit</b>. If the directory input option is used then the basename
will be dti</li>
<li><b>Gradient directions</b> (bvecs): A text file containing a list
@@ -40,11 +40,13 @@ of gradient directions applied during diffusion weighted volumes. The
order of entries in this file must match the order of volumes in the
input data series.
<br>
-The format is <br><pre>
+The format is <br>
+<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 to unit length. For volumes in which there was no
+z_1 z_2 z_3 ... z_n<br>
+</pre>
+Vectors are normalised to unit length within the <b>dtifit</b> code. 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>
@@ -59,7 +61,7 @@ b_1 b_2 b_3 ... b_n<br></pre>
</li>
</ul>
-<h4>Outputs of DTIFit</h3.
+<h4>Outputs of <b>dtifit</b></h3.
<ul>
<li><b><basename>_V1</b> - 1st eigenvector</li>
<li><b><basename>_V2</b> - 2nd eigenvector</li>
@@ -130,4 +132,4 @@ Optional arguments (You may optionally specify one or more of):
-X,--xmax max x
-</pre>
\ No newline at end of file
+</pre>
diff --git a/doc/fdt_pipeline.html b/doc/fdt_pipeline.html
index 3f1f63bb5a0b695da416ba38956f7dfc4b7e47e0..868cf74c39ee4144386066b1030d7986ec463fa4 100644
--- a/doc/fdt_pipeline.html
+++ b/doc/fdt_pipeline.html
@@ -17,12 +17,12 @@ would consist of:
<li>Any study or scanner-specific pre-processing (e.g., averaging of multiple
acquisitions, removal of images affected by large artifacts). This would be
done manually by the user.</li>
-<li><a href="fdt_eddy.html">Eddy current correction</a> using FDT (around 3 minutes per volume).</li>
-<li><a href="fdt_dtifit.html">DTIFit</a> - Fitting of diffusion tensors on corrected data using dtifit within FDT to check data quality (1 minute)
-<li><a href="fdt_bedpost.html">Bedpost</a> - Fitting of the probabilistic diffusion model on corrected data
+<li><a href="fdt_eddy.html">eddy current correction</a> using FDT (around 3 minutes per volume).</li>
+<li><a href="fdt_dtifit.html">dtifit</a> - Fitting of diffusion tensors on corrected data using dtifit within FDT to check data quality (1 minute)
+<li><a href="fdt_bedpostx.html">bedpostx</a> - Fitting of the probabilistic diffusion model on corrected data
(20 hours, or less if parallelised)</li>
-<li><a href="fdt_reg.html">Registration</a> - (3-6 minutes) </li>
-<li><a href="fdt_probtrack.html">ProbTrack</a> - Probabilistic tractography run on the outputs of bedpost (endless.. - depends very much on what the
+<li><a href="fdt_reg.html">registration</a> - (3-6 minutes) </li>
+<li><a href="fdt_probtrackx.html">probtrackx</a> - Probabilistic tractography run on the outputs of bedpost (endless.. - depends very much on what the
user wishes to do. Generating a connectivity distribution from a single voxel
of interest takes about 10 seconds)</li>
<li>Further post-processing of ProbTrack outputs can be carried out if
diff --git a/doc/fdt_probtrackx.html b/doc/fdt_probtrackx.html
index db6e45289ed9b810c8e4fe7ab4f5d3906a767417..40315feeaa21649c00759fa3afa4c27dde81db91 100644
--- a/doc/fdt_probtrackx.html
+++ b/doc/fdt_probtrackx.html
@@ -12,36 +12,34 @@ href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
see <a
href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">here</a>, and for details about crossing fibre modelling in FDT, see Behrens et al, NeuroImage 2007, 34(1):144-55.<br><br>
- Briefly, FDT repetitively samples from the distributions on
- voxel-wise principal diffusion directions, each time computing a
- streamline through these local samples to generate a
- <em>probabilistic streamline</em> or a <em>sample</em> from the
- distribution on the location of the true streamline. By taking many
- such samples FDT is able to build up the posterior distribution on the
-streamline location or the <em>connectivity distribution</em>. The local diffusion directions are calculated using bedpost, and allow modelling multiple fibre orientations per voxel.
-
-<p>After Bedpost has been applied it is possible to run tractography analyses
-using Probtrackx. When only one fibre per voxel is modelled in bedpost, then probtrackx runs in the same way as probtrack.<br><br>
-
-Probtrackx has two main modules:
+ Briefly, FDT repetitively samples from the distributions on voxel-wise principal diffusion directions, each time computing a streamline through these local samples to generate a <em>probabilistic streamline</em> or a <em>sample</em> from the distribution on the location of the true streamline. By taking many such samples FDT is able to build up the posterior distribution on the streamline location or the <em>connectivity distribution</em>. The local diffusion directions are calculated using <b>bedpostx</b>, and allow modelling multiple fibre orientations per voxel.
+
+<p>After <b>bedpostx</b> has been applied it is possible to run tractography analyses using <b>probtrackx</b>.
+
+<p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the <b>FDT</b> button. Use the top left drop down menu to select <b>PROBTRACKX</b>.
+
+<p>
+PROBTRACKX has two main modules:
<ul>
<li><a href="#seeds">Seed Space</a></li>
<li><a href="#targets">Optional Targets</a></li>
</ul>
-Also, probtrackx requires the specification of a bedpost directory. This directory must contain the following images:<br><br>
+Also, <b>probtrackx</b> requires the specification of a bedpostX directory. This directory must contain the following images:<br><br>
<li><b>merged_ph<i>samples</b></li>
<li><b>merged_th<i>samples</b></li>
<li><b>nodif_brain_mask</b></li>
-<p>As explained below, results from probtrackx can be binned in any available space -e.g.,
+<br> <i>Note that users of previous versions of FDT can still use <b>probtrackx</b> on the old bedpost directories.</i><br>
+
+<p>As explained below, results from <b>probtrackx</b> can be binned in any available space -e.g.,
diffusion space, structural space or standard space. Note, however,
that tractography itself ALWAYS takes place in diffusion space - it is
-simply the <em>results</em> of probtrackx that are stored in the
-required space. If probtrackx results are to be stored in a space
+simply the <em>results</em> of <b>probtrackx</b> that are stored in the
+required space. If <b>probtrackx</b> results are to be stored in a space
other than diffusion space then you will need transformations from
-this space back into the space of the diffusion data. The <a href="fdt_reg.html">FDT registration tab</a> creates the following transformations in the <code>xfms</code> subdirectory of the bedpost directory.
+this space back into the space of the diffusion data. The <a href="fdt_reg.html">FDT registration tab</a> creates the following transformations in the <code>xfms</code> subdirectory of the bedpostX directory.
<p>for running analyses in structural space:
<li><b>xfms/str2diff.mat</b></li>
@@ -53,13 +51,13 @@ this space back into the space of the diffusion data. The <a href="fdt_reg.html"
<hr>
<h3>Overview</h3>
-ProbTrackX involves generating connectivity distributions from user-specified seed voxel(s). The output will be a single image in the space of the specified seed like <a href="fdt_images/fdt_simple_tract3.gif">this</a>. All brain voxels will have a value (though many of these will be zero) representing the connectivity value between that voxel and the seed voxel (i.e., the number of samples that pass through that voxel). Note that when connectivity distributions are generated from multiple seed voxels within a region of interest then the time required for the analysis to run will be approximately the number of seed voxels multiplied by the time taken to generate a distribution from a single voxel. ProbtrackX also allows to specify targets for the tractography. These can either be inclusion/exclusion masks, or targets for seed classification based on connectivity.
+PROBTRACKX involves generating connectivity distributions from user-specified seed voxel(s). The output will be a single image in the space of the specified seed like <a href="fdt_images/fdt_simple_tract3.gif">this</a>. All brain voxels will have a value (though many of these will be zero) representing the connectivity value between that voxel and the seed voxel (i.e., the number of samples that pass through that voxel). Note that when connectivity distributions are generated from multiple seed voxels within a region of interest then the time required for the analysis to run will be approximately the number of seed voxels multiplied by the time taken to generate a distribution from a single voxel. <b>probtrackx</b> also allows to specify targets for the tractography. These can either be inclusion/exclusion masks, or targets for seed classification based on connectivity.
<a name="seeds"></a>
<h3>Seed specification - prologue</h3>
-A common feature for all seed specification modes is the ability to provide the seed in another space than the diffusion space. If <b>seed space is not diffusion</b>, then check the corresponding button. Set the transformation matrix from seed space to diffusion space (e.g., subject1.bedpost/xfms/str2diff.mat if seed space is structural space or subject1.bedpost/xfms/standard2diff.mat if seed space is standard space). Note that, in all cases, the smaller the voxel size in your seed space image, the lower will be the resulting connectivity values to these voxels (This is intuitive - the smaller a voxel is, the less chance that the true streamline will pass through it!). This highlights the problem with binning a continuous distribution into meaningless discrete bins. In order for the probability values to be truly meaningful, the dicrete bins chosen should be anatomically meaningful, as is the case when using <a href="#targets">classification targets</a>.
+A common feature for all seed specification modes is the ability to provide the seed in another space than the diffusion space. If <b>seed space is not diffusion</b>, then check the corresponding button. Set the transformation matrix from seed space to diffusion space (e.g., subject1.bedpostX/xfms/str2diff.mat if seed space is structural space or subject1.bedpostX/xfms/standard2diff.mat if seed space is standard space). Note that, in all cases, the smaller the voxel size in your seed space image, the lower will be the resulting connectivity values to these voxels (This is intuitive - the smaller a voxel is, the less chance that the true streamline will pass through it!). This highlights the problem with binning a continuous distribution into meaningless discrete bins. In order for the probability values to be truly meaningful, the dicrete bins chosen should be anatomically meaningful, as is the case when using <a href="#targets">classification targets</a>.
<p><h4>Single voxel</h4>
@@ -68,7 +66,7 @@ A common feature for all seed specification modes is the ability to provide the
Generates a connectivity distribution from a single, user-specified voxel.
<p>GUI Options: <br>
-<b>Seed reference image</b> Use the browse button to locate a reference image (e.g., subject1.bedpost/struct.hdr if seed space is structral space or subject1.bedpost/standard.hdr if seed space is standard space).<br>
+<b>Seed reference image</b> Use the browse button to locate a reference image (e.g., subject1.bedpostX/struct.hdr if seed space is structral space or subject1.bedpostX/standard.hdr if seed space is standard space).<br>
<b>Seeds:</b> Enter the x,y,z co-ordinates of a single seed voxel. Use the buttons to the right to specify whether the co-ordinates are given in voxels or millimetres. Note if the "seed space is not diffusion" is set, and the seed space reference image is the MNI152 average brain, then mm coordinates will have their origin at the AC.
<p>The output will be a single image <b>in the space of the specified seed</b>. All brain voxels will have a value (though many of these will be zero) representing the connectivity value between that voxel and the seed voxel (i.e., the number of samples that pass through that voxel). The example on the right shows the connectivity distribution from a single seed in the internal capsule overlaid on an FA image. Note that when the seed space is a single voxel, the classification targets in the <a href="#targets">Optional Targets</a> tab is turned off.
@@ -77,10 +75,10 @@ Generates a connectivity distribution from a single, user-specified voxel.
Generates a connectivity distribution from a user-specified region of interest.
<p>GUI Options: <br>
-<b>Seed image:</b> Use the browse button to locate the seed image - this should be a binary mask. Probabilistic tractography will be run from every voxel with a value greater than 0 in this mask.
+<b>Seed image:</b> Use the browse button to locate the seed image. Probabilistic tractography will be run from every voxel with a value different than 0 in this mask.
<p>The output directory will contain: <br>
-<b>probtrack.log</b> - a text record of the command that was run.<br>
+<b>probtrackx.log</b> - a text record of the command that was run.<br>
<b>fdt.log</b> - a log of the setup of the FDT GUI when the analysis was run. To recover this GUI setup, type <code>Fdt fdt.log</code><br>
<b>fdt_paths</b> - a 3D image file containing the output connectivity distribution to the seed mask.<br>
<b>waytotal</b> - a text file containing a single number corresponding to the total number of generated tracts that have not been rejected due to exclusion masks.<br><br>
@@ -93,35 +91,29 @@ The output connectivity distribution file will be a single image in the space of
Generates a connectivity distribution between a mask image and all the other mask images in a list of images, retaining only those tracts that pass through <b>at least</b> one of the other images. Output is the sum of the connectivity distributions from each of the seed masks.
<p>GUI Options: <br>
-<b>Masks list</b>: Use the add button to locate each seed mask. Seed masks must all be binary masks in the same space. When all masks are loaded you can press the save list button to save the list of masks as a text file. If you already have a text file list of required seed masks (including their path) then you can load it with the load list button.
+<b>Masks list</b>: Use the add button to locate each seed mask. Seed masks should all be in the same space (e.g., diffusion, structural or standard space). When all masks are loaded you can press the save list button to save the list of masks as a text file. If you already have a text file list of required seed masks (including their path) then you can load it with the load list button.
<p>The output directory will contain:
<br>
-<b>probtrack.log</b> - a text record of the command that was run.<br>
-<b>fdt.log</b> - a log of the setup of the FDT GUI when the analysis
-was run. To recover this GUI setup, type <code>Fdt fdt.log</code><br>
+<b>probtrackx.log</b> - a text record of the command that was run.<br>
+<b>fdt.log</b> - a log of the setup of the FDT GUI when the analysis was run. To recover this GUI setup, type <code>Fdt fdt.log</code><br>
<b>fdt_paths</b> - a 3D image file containing the output connectivity distribution.<br>
-<br>The output file will be a single image in the space of the
-specified masks. All brain voxels will have a value (though many of
-these may be zero) representing the number of samples that pass
-through that voxel from either of the seed masks and which also pass
-through one of the other seedmasks. Connectivity distributions from multiple
-seed voxels are summed to produce this output. Therefore the
-connectivity values will depend on the number of voxels in the seed
-masks.
+<br>The output file will be a single image in the space of the specified masks. All brain voxels will have a value (though many of these may be zero) representing the number of samples that pass through that voxel from either of the seed masks and which also pass through one of the other seedmasks. Connectivity distributions from multiple seed voxels are summed to produce this output. Therefore the connectivity values will depend on the number of voxels in the seed masks.
<hr>
<a name="targets"></a>
<h3>Including targets for tractography - rationale</h3>
-Probtrackx allows to include target masks for any tractography experiment. Every target mask <b>must be in the same space as the seed masks</b>. Targets can be waypoint masks, for selecting only tracts passing through particular points in the brain; exclusion masks, for excluding tracts passing through parts of the brain; termination masks, for forcing tracts to stop whenever they reach a certain area; or classification target masks for connectivity-based seed classification. All these targets are optional.
+<b>probtrackx</b> allows to include target masks for any tractography experiment. <br><br>
+<b>Very Important:</b> Every target mask <b>must be in the same space as the seed masks</b> (or the <b>reference image</b> in the case of a single voxel mode). <br><br>
+Targets can be waypoint masks, for selecting only tracts passing through particular points in the brain; exclusion masks, for excluding tracts passing through parts of the brain; termination masks, for forcing tracts to stop whenever they reach a certain area; or classification target masks for connectivity-based seed classification. All these targets are optional.
<p><h4>Waypoint masks</h4>
<IMG ALIGN=RIGHT height=200 SRC="fdt_images/fdt_twomasks_tracts.gif" ALT="constraining tracts">
Use inclusion masks in the tractography. Tracts that do not pass through ALL these masks will be discarded from the calculation of the connectivity distribution.<br>
The example on the right shows the outputs from two different analyses which use the same seed mask (orange) but different waypoint masks (red).
<br><br>
-Use the add and remove buttons to make a list of waypoint masks. These must be in the same space as the seed image.
+Use the add and remove buttons to make a list of waypoint masks.
<p><h4>Exclusion mask</h4>
If an <b>exclusion mask</b> is to be used then check the box and use the browse button to locate the mask file. Pathways will be discarded if they enter the exclusion mask. For example, an exclusion mask of the midline will remove pathways that cross into the other hemisphere.
@@ -131,23 +123,23 @@ If a <b>termination mask</b> is to be used then check the box and use the browse
<p><h4>Classification targets</h4>
<IMG ALIGN=RIGHT height=150 SRC="fdt_images/fdt_seeds2targets_quant_eg.gif" ALT="connectivity-based classification of thalamus">
-When using classification targets, probtrackx will quantify connectivity values between a seed mask and any number of user-specified target masks. This option is only active when the seed mask is a single mask. In the example on the right, seed voxels in the thalamus are classified according to the probability of connection to different cortical target masks.
+When using classification targets, <b>probtrackx</b> will quantify connectivity values between a seed mask and any number of user-specified target masks. This option is only active when the seed mask is a single mask. In the example on the right, seed voxels in the thalamus are classified according to the probability of connection to different cortical target masks.
<br><br>
-Use the add button to locate each target mask. Targets must be binary masks in the same space as the seed mask. When all targets are loaded you can press the save list button to save the list of targets as a text file. If you already have a text file list of required targets (including their path) then you can load it with the load list button.<br>
+Use the add button to locate each target mask. Targets must be in the same space as the seed mask. When all targets are loaded you can press the save list button to save the list of targets as a text file. If you already have a text file list of required targets (including their path) then you can load it with the load list button.<br>
The output directory will contain a single volume for each target mask, named <b>seeds_to_{target}</b> where {target} is replaced by the file name of the relevant target mask. In these output images, the value of each voxel within the seed mask is the number of samples seeded from that voxel reaching the relevant target mask. The value of all voxels outside the seed mask will be zero.
<p>
<IMG ALIGN=RIGHT height=150 SRC="fdt_images/fdt_seeds2targets_thal.gif" ALT="connectivity-based classification of thalamus">
There are command line utilities that can be run on these outputs:
-<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_bigggest</a> - for performing hard segmentation on the outputs of connectivity-based thersholding in ProbTrack, see example on the right</li></ul>
+<ul><li><a href="fdt_thresh.html">proj_thresh</a> - for thresholding some outputs of <b>probtrackx</b></li>
+<li><A href="fdt_biggest.html">find_the_bigggest</a> - for performing hard segmentation on the outputs of connectivity-based thersholding in <b>probtrackx</b>, see example on the right</li></ul>
<hr>
<a name="options"></a>
<h3>Options Tab </h3>
-Before running probtrackx, the user is able to change the setting of certain parameters by clicking the <b>options</b> tab.
+Before running <b>probtrackx</b>, the user is able to change the setting of certain parameters by clicking the <b>options</b> tab.
<p><b>Number of samples</b> (default 5000): This determines the number of individual pathways (or samples) that are drawn through the probability distributions on principle fibre direction (see <a href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/"> appendix </a>for more details on the modelling and tractography methods). By default this is set to 5000 as we are confident that convergence is reached with this number of samples. However, reducing this number will speed up processing and can be useful for preliminary or exploratory analyses.
@@ -168,5 +160,5 @@ streamlines. More accurate but slower.
(e.g., infants or animals).
<p><b>Use anisotropy to constrain tracking</b>:
-Use this option if you want the fractional anisotropic volumes (stored in merged_fsamples) to influence the tractography. The tracts stop if the anisotropy is lower than a random variable between 0 (low anisotropy) and 1 (high anisotropy).
+Use this option if you want the fractional anisotropic volumes (stored in merged_f<i>samples) to influence the tractography. The tracts stop if the anisotropy is lower than a random variable between 0 (low anisotropy) and 1 (high anisotropy).
<p><b>Use distance correction</b>: This option corrects for the fact that connectivity distribution drops with distance from the seed mask. If this option is checked, the connectivity distribution is the mean length of the pathways that cross each voxel.
diff --git a/doc/fdt_reg.html b/doc/fdt_reg.html
index a0affd0ccf5f9b06ef1b88cd8481eb6585978059..3d47f88cc21545e0f8ae02aaeef49c9af623b057 100644
--- a/doc/fdt_reg.html
+++ b/doc/fdt_reg.html
@@ -10,21 +10,12 @@ href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<p>If tractography results are to be stored in any space other than diffusion
space then registration must be run.
-<p>Registration within Fdt uses <a href="http://www.fmrib.ox.ac.uk/fsl/flirt/index.html" target="_top">flirt</a>. Registration can only be
-applied after Bedpost has been run. Typically, registration will be run
-between three spaces:
-<ul><li>Diffusion space (using the nodif_brain image in the Bedpost directory)</li>
-<li>Structural space (using the struct image in the Bedpost
-directory, e.g., the space of a high resolution T1-weighted image of
-the same subject)</li>
-<li>Standard space (by default, the MNI152 brain stored within $FSLDIR/data/standard)</li></ul>
+<p>Registration within Fdt uses <a href="http://www.fmrib.ox.ac.uk/fsl/flirt/index.html" target="_top">flirt</a>. Registration can only be applied after <b>bedpostx</b> has been run. Typically, registration will be run between three spaces:
+<ul><li>Diffusion space (using the nodif_brain image in the bedpostX directory)</li>
+<li>Structural space (using the struct image in the bedpostX directory, e.g., the space of a high resolution T1-weighted image of the same subject)</li>
+<li>Standard space (by default, the MNI152 brain stored within $FSLDIR/etc/standard)</li></ul>
-<p>Note that struct must have had <a href="http://www.fmrib.ox.ac.uk/fsl/bet/index.html" target="_top">bet</a> applied. The nodif_brain image should be
-the brain extracted version of the nodif image that is automatically stored in
-the Bedpost directory. The user will
-have to manually apply bet to this image after running bedpost and before
-running registration. (it is important that the user check the quality of bet
-results on these images and adjust the settings in bet where appropriate).
+<p>Note that struct must have had <a href="http://www.fmrib.ox.ac.uk/fsl/bet/index.html" target="_top">bet</a> applied. The nodif_brain image should be the brain extracted version of the nodif image that is automatically stored in the bedpostX directory. The user will have to manually apply bet to this image after running <b>bedpostx</b> and before running registration. (it is important that the user check the quality of bet results on these images and adjust the settings in bet where appropriate).
<p>Transformation matrices, and their inverses, will be derived from diffusion to structural space and
from structural to standard space. Relevant matrices will be concatenated to
@@ -43,4 +34,4 @@ derived using 6 degrees of fredom, the mutual information cost
function and normal search; transformations matrices between structural and standard space
are derived using 12 degrees of freedom, the correlation ratio cost
function and normal search. These parameters may be adjusted if required
-using the drop down menus in the reigistration panel.
+using the drop down menus in the registration panel.
diff --git a/doc/fdt_thresh.html b/doc/fdt_thresh.html
index 8fbf57aaa0ec77c682e98b479c0a06335920de79..ee1a56ac57093a01f8d11d7cd469eeafb1a24206 100644
--- a/doc/fdt_thresh.html
+++ b/doc/fdt_thresh.html
@@ -9,8 +9,8 @@ href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<h3>proj_thresh</h3>
<b>proj_thresh</b> is a command line utility that provides an alternative way of
expressing connection probability in connectivity-based segmentation. It is
-run on the output of the <b>connectivity-based seed
-classification</b> mode within <a href="fdt_probtrackx.html"> <b>ProbTrack</b></a>.
+run on the output of <a href="fdt_probtrackx.html"> <b>probtrackx</b></a> when <b>classification targets</b> are used.
+
<p>The output of <b>Connectivity-based seed classification</b> is a single volume for
each target mask, named <b>seeds_to_{target}</b> where {target} is replaced
by the file name of the relevant target mask. In these output images, the
diff --git a/doc/fdt_top.html b/doc/fdt_top.html
index b60139adb7a2c7ecb3f686b36c068cecbb17ac56..0f7dfed0f606790a2254a3dc1684689eb2b1cfe8 100644
--- a/doc/fdt_top.html
+++ b/doc/fdt_top.html
@@ -21,6 +21,7 @@
<a href="fdt_probtrackx.html" target="_top">probtrackx</a> -
<a href="fdt_thresh.html" target="_top">proj_thresh</a> -
<a href="fdt_biggest.html" target="_top">find_the_biggest</a> -
+<a href="fdt_vecreg.html" target="_top">vecreg</a> -
<a href="fdt_display.html" target="_top">using fslview</a> -
<a href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/" target="_top">FDT theory</a>
diff --git a/doc/fdt_vecreg.html b/doc/fdt_vecreg.html
index 25e3db61a9e2ae15f74dcbf491b6ac28f343ac68..414d01e9ad1d5b6cc3b5a54c767067097e786ed9 100644
--- a/doc/fdt_vecreg.html
+++ b/doc/fdt_vecreg.html
@@ -6,23 +6,23 @@ content="text/html;charset=utf-8">
href="../fsl.css"><TITLE>FSL</TITLE></HEAD>
<BODY><OBJECT data="fdt_top.html"></OBJECT>
-<h3>Registration of vector images using vecreg</h3>
+<h3>vecreg - Registration of vector images</h3>
<p>
<IMG ALIGN=RIGHT height=200 SRC="fdt_images/fdt_vecreg.gif"
ALT="vecreg applied to V1">
-After running dtifit or bedpost, it is often useful to register vector data to another space. For example, one might want to represent V1 for different subjects in standard space. <b>vecreg</b> is a command line tool that allows to perform such registration.<br>
-Vector images cannot be registered by simply applying a transformation (as calculated by, say, flirt) to every voxel's coordinates. The corresponding vectors have to be reoriented accordingly (see D. Alexander 2001, IEEE-TMI 20:1131-1139). vecreg perform this operation for you.
-The image shows the effect of applying vecreg (right) to the V1 image on the left, compared to simply apply voxelwise transformation (e.g. using applyxfm4D) to the vectors (centre).
+After running dtifit or bedpostx, it is often useful to register vector data to another space. For example, one might want to represent V1 for different subjects in standard space. <b>vecreg</b> is a command line tool that allows to perform such registration.<br><br>
+Vector images cannot be registered by simply applying a transformation (as calculated by, say, <a href="http://www.fmrib.ox.ac.uk/fsl/flirt/index.html">FLIRT</a>) to every voxel's coordinates. The corresponding vectors have to be reoriented accordingly (see D. Alexander 2001, IEEE-TMI 20:1131-39). <b>vecreg</b> performs this operation for you.
+The image on the right shows the effect of applying vecreg (right) to the V1 image on the left, compared to simply applying voxelwise transformation (e.g. using applyxfm4D) to the vectors (centre).
<br><br>
-<b> Important: </b> vecreg does not calculate a transformation, but simply applies a given transformation to the input vector field. vecreg can apply a linear transformation calculated with FLIRT, or a non-linear transformation calculated using either IRTK or FNIRT, using a warpfield calculated by dof2warp.
+<b> Important: </b> vecreg does not calculate a transformation, but simply applies a given transformation to the input vector field. vecreg can apply a linear transformation calculated with FLIRT, or a non-linear transformation calculated by IRTK, using a warpfield calculated using dof2warp.
<p>
types of vectors that may be used for vecreg<br>
-from dtifit: V1,V2,V3<br>
-from bedpost: dyads1, dyads2, etc. <br>
+from <a href="fdt_dtifit.html"><b>dtifit</b></a>: V1,V2,V3<br>
+from <a href="fdt_bedpostx.html"><b>bedpostx</b><a>: dyads1, dyads2, etc. <br>
<p>
diff --git a/doc/index.html b/doc/index.html
index 9658479ccc48cb90dc1b8b155b2b7ea8749fd204..dbd0ad1e49205ff77dc460157cc9185c8d3d5d21 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -20,8 +20,8 @@ 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_bedpost.html">bedpost</a> - for local modelling of diffusion parameters.</li>
-<li><a href="fdt_probtrackx.html">probtrack</a> - for tractography and connectivity-based segmentation</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
diff --git a/fdt.tcl b/fdt.tcl
index 60a511fb5c37656292f9e094a03d7474b83d1c98..d8b51804c0f2fae2ca51c7d84536ce51b39f0841 100644
--- a/fdt.tcl
+++ b/fdt.tcl
@@ -52,7 +52,7 @@ proc fdt:dialog { w tclstartupfile } {
#-------- Stage and Mode Options --------
frame $w.tool
- optionMenu2 $w.tool.menu probtrack(tool) -command "fdt:select_tool $w" eddy_current "Eddy current correction" bedpost "BEDPOSTX Estimation of diffusion parameters" registration "Registration" probtrack "ProbTrackX Probabilistic tracking" xutilssx "----------------------------------------------------" dtifit "DTIFit Reconstruct diffusion tensors"
+ optionMenu2 $w.tool.menu probtrack(tool) -command "fdt:select_tool $w" eddy_current "Eddy current correction" bedpost "BEDPOSTX Estimation of diffusion parameters" registration "Registration" probtrack "PROBTRACKX Probabilistic tracking" xutilssx "----------------------------------------------------" dtifit "DTIFIT Reconstruct diffusion tensors"
$w.tool.menu.menu entryconfigure 4 -state disabled -background black
pack $w.tool.menu -side left -pady 3 -padx 6 -anchor nw