diff --git a/doc/fdt_bedpostx.html b/doc/fdt_bedpostx.html
index 40ca1c59a0cb412c5b478d799eff02eb31baf2a4..32ada2bb097be3d9042e16774b4d54d23c0adbe8 100644
--- a/doc/fdt_bedpostx.html
+++ b/doc/fdt_bedpostx.html
@@ -1,7 +1,13 @@
-<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>
+<!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><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
diff --git a/doc/fdt_bedpostx_parallel.html b/doc/fdt_bedpostx_parallel.html
index 9d3f8304d3f97917c9dd1943b9213161bfc55437..c8225d29573e90861c9c6829d195331aec30c44a 100644
--- a/doc/fdt_bedpostx_parallel.html
+++ b/doc/fdt_bedpostx_parallel.html
@@ -1,5 +1,12 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-<p><h3>Parallelising bedpost</h3> Bedpost runs Markov Chain Monte
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
+<h3>Parallelising bedpost</h3> Bedpost runs Markov Chain Monte
Carlo sampling to build up distributions on diffusion parameters at
each voxel. This is a very slow process, so bedpost is very processor
hungry (a typical bedpost run might take around 20hrs for 60
diff --git a/doc/fdt_before.html b/doc/fdt_before.html
deleted file mode 100644
index c1fa6eba08669b64d0439ba288e5e5df7bad8f77..0000000000000000000000000000000000000000
--- a/doc/fdt_before.html
+++ /dev/null
@@ -1,13 +0,0 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-
-
-<h3>Before running</h3>
-
-<p>Fdt requires 4D analyze data. This will consist of a series of diffusion
-weighted volumes and some volumes with no diffusion weighting applied. If you
-are running Bedpost or dtifit you
-will need text files describing the b-values applied during acquisition of
-each volume ('bvals'), and the direction in which diffusion weighting was
-applied ('bvecs').
-
-
diff --git a/doc/fdt_biggest.html b/doc/fdt_biggest.html
index f6675e5111384469d4d97243e1389c5dc64ea8a1..3d0a553ddfef512170ea6d5d713b5bb86666c6f5 100644
--- a/doc/fdt_biggest.html
+++ b/doc/fdt_biggest.html
@@ -1,5 +1,11 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY
-BACKGROUND="fdt_images/fsl-bg.jpg">
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
<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
diff --git a/doc/fdt_bottom.html b/doc/fdt_bottom.html
deleted file mode 100644
index 2c1e8c05a1b7204638d27cdfce14bf1734f55cb3..0000000000000000000000000000000000000000
--- a/doc/fdt_bottom.html
+++ /dev/null
@@ -1,3 +0,0 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-<hr><font size="1">Copyright © 2007, University of Oxford. Written
-by <a href="http://www.fmrib.ox.ac.uk/~heidi/index.html" target="_top">H. Johansen-Berg</a>, <a href="http://www.fmrib.ox.ac.uk/~behrens/index.html" target="_top"> T. Behrens</a> and <a href="http://www.fmrib.ox.ac.uk/~saad/index.html" target="_top"> S. Jbabdi</a>.</font>
diff --git a/doc/fdt_display.html b/doc/fdt_display.html
index fa266fe808dd99d9c2bd6a18ccdc92041bde562a..0a1b16ba0b69da8595e92abc04c3ebc5588d8750 100644
--- a/doc/fdt_display.html
+++ b/doc/fdt_display.html
@@ -1,6 +1,12 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-<IMG ALIGN=MIDDLE hspace=10 vspace=20 SRC="fdt_images/fdt_vectorsx.jpg"
-ALT="Visualising vector data">
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
+<IMG ALIGN=RIGHT hspace=20 vspace=20 SRC="fdt_images/fslview_dti.gif" ALT="Example GUI view">
<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
diff --git a/doc/fdt_documentation.html b/doc/fdt_documentation.html
deleted file mode 100644
index 3a944051979a0aadad19b6510bb16ee75e86786b..0000000000000000000000000000000000000000
--- a/doc/fdt_documentation.html
+++ /dev/null
@@ -1,323 +0,0 @@
-<h3>Introduction</h3>
-<p>For other information on FDT and updated journal references, see the <a href="http://www.fmrib.ox.ac.uk/analysis/research/fdt/">FDT web
-page</a>. If you use FDT in your research, please quote the journal
-references listed there.
-
-<p>FDT (FMRIB 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">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 are:
-
-<p>eddycorrect - for correction of eddy current distortion
-<br>Bedpost - for local modelling of diffusion parameters.
-<br>ProbTrack - for tractography and connectivity-based segmentation
-<br>DtiFit - for local of fitting of diffusion tensors
-
-<br>The FDT GUI also includes a registration option that registers images using <a
-href="http://www.fmrib.ox.ac.uk/fsl/flirt/index.html"> FLIRT </a>
-
-<p>A typical processing pipeline (and approximate time required for each
-stage, based on an Intel 2.4GHz processor, and a 60 direction whole brain
-dataset of dimensions 256x208x72)
-would consist of:
-<br>1. 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.
-<br>2. Eddy current correction using FDT (??minutes).
-<br>3. Fitting of diffusion tensors on corrected data using dtifit within FDT to check data quality (10 minutes)
-<br>4. Fitting of the probabilistic diffusion model on corrected data using Bedpost within FDT
-(24 hours, or less if parallelised)
-<br>5. 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)
-
-The probabilistic tractography tools within FDT are very flexible and allow
-the user to generate connectivity distributions from single or multiple
-voxels; to limit these distribution based on anatomical criteria and to
-perform segmentation based on the probability of connection to user-defined
-target regions.
-
-
-<p>Before running:
-
-<p>Fdt requires 4D analyze data. This will consist of a series of diffusion
-weighted volumes and some volumes with no diffusion weighting applied. You
-will need text files describing the b-values applied during acquisition of
-each volume ('bvals'), and the direction in which diffusion weighting was
-applied ('bvecs')
-
-
-<p><hr><h3>Eddy Current Correction</h3>
-
-<p><hr><h3>Bedpost</h3>
-<p>Bedpost stands for Bayesian Estimation of Diffusion Parameters obtained using sampling
-techniques
-
-
-
-<p><hr><h3>Registration </h3>
-<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">>flirt</a>. Registration can only be
-applied after Bedpost has been run. Typically, registration will be run
-between three spaces:
-<br>Diffusion space (using the nodif_brain.{hdr,img} file stored in the Bedpost directory)
-<br>Structural space (using the struct.{hdr,img} file stored in the Bedpost
-directory, e.g., the space of a high resolution T1-weighted image of
-the same subject)
-<br>Standard space (by default, the MNI152 brain stored within the fsldirectory).
-
-<p>Note that struct must have had bet 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 qualtiy of bet
-results on these images and adjust the settings in bet where appropriate)
-
-<p>Transformation matrices, and their inverses, will be dervied from diffusion to structural space and
-from structural to standard space. Relevant matrices will be concatenated to
-produce transformation matrices between diffusion and standard space. The resulting matrices are stored within
-the 'xfms' subdirectory of the bedpost directory and named as follows:
-
-<p>diff2str.mat - from diffusion to structural space
-<br>str2diff.mat - from structural to diffusion space
-<br>diff2standard.mat - from diffusion to standard space
-<br>standard2diff.mat - from standard to diffusion space
-<br>str2standard.mat - from structural to standard space
-<br>standard2str.mat - from standard to structural space
-
-<p>By default, transformation matrices between diffusion and structural space are
-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.
-
-<p><b>******** PROBTRACK - probabilistic tracking *********</b>
-
-<p>After Bedpost has been applied it is possible to run tractography analyses
-using ProbTrack.
-Probtrack can be run in multiple different modes. Every mode requires the user to
-specify a bedpost directory. For all modes, the bedpost directory must contain the following files:
-
-<br>merged_phsamples.{img,hdr}
-<br>merged_thsamples.{img,hdr}
-<br>nodif_brain_mask.{img,hdr}
-
-<p>Results from probtract can be stored 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
-results of probtrack that are transformed into the required space before saving. If probtrack results are to be stored in a space other than diffusion space
-then the following files must be in the xfms subdirectory of the bedpost directory:
-
-<p>for running analyses in structural space:
-<br>struct.{img,hdr}
-<br>xfms/str2diff.mat
-<br>xfms/diff2str.mat
-
-<p>for running analyses in standard space:
-<br>standard.{img,hdr}
-<br>xfms/standard2diff.mat
-<br>xfms/diff2standard.mat
-
-<p>OPTIONS TAB
-<br>For all modes in probtrack, the user is able to change the setting of certain
-parameters by clicking the options tab.
-
-<p>Number of samples (default 5000): This determines the number of individual
-pathways (or samples) that are drawn through the probability distrubutions on
-principle fibre direction (see <a href="appendix"> 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 particles. However, reducing
-this number will speed up processing and can be useful for preliminary or
-exploratory analyses.
-
-<p>Curvature Threshold (default 0.2): We limit how sharply pathways can turn
-in order to
-exclude implausible pathways. This number is the cosine of the minimum allowable
-angle between two steps. By default this is set to 0.2 (corresponding to a
-minimum angle of approximately 80 degrees). Adjusting this number can enable
-pathways with sharper angles to be detected.
-
-<p>Verbose: If this option is selected then FDT prints additional logging
-information to screen while it is running.
-
-<p>Loopcheck: By default, we terminate pathways that loop back on themselves
--i.e paths that travel to a point where they have already been.
-
-<p>Advanced options:
-<br>Clicking the triangle reveals some further options:
-
-<p>Use anisotropy constraints: By default, pathways are traced regardless of
-anisotropy values. However, it is possible to constrain tracking according to
-aniostropy values. ?? dunno what this does exactly
-
-<p>Use modified Euler streamlining: hmmmm
-
-<p>Maximum number of steps (default 1000): By default, particles are terminated
-when they have travelled 1000 steps. Using a step length of 0.5mm this
-corresponds to a distance of 50cm. These values can be adjusted if required.
-
-<p>Step length (default 0.5mm): This determines the length of each step. This
-setting may be adjusted from default e.g., depending on the voxel size being
-used, or if tracking is being performed on different sized brains
-(e.g,. infants of non-human animals).
-
-<p><b>PATH DISTRIBUTION ESTIMATION</b>
-<br>The first four modes of ProbTrack involve 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="pic"> 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 particles that pass through that voxel). Note that when
-connectivity distributions are generated from multiple seed voxel 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 distrubiton from a single voxel.
-
-<p>SETTING UP THE GUI FOR PATH DISTRIBUTION ESTIMATION - SETTINGS COMMON TO ALL
-MODES:
-
-<p>Seeds space: specification of seeds is different for each mode - see below.
-
-<p>If seed space is not diffusion, then check the button and use the browse
-buttons 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) and 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).
-
-<p>If an exclusion mask is to be used then check the box and use the browse button
-to locate the mask file. This must be a binarised analyze file in seed
-space. Pathways will be terminated if they enter the exclusion mask. For
-example, an exclusion mask of the midline will terminate pathways that cross
-into the other hemisphere. (Note that paths are always terminated when they reach the
-brain surface as defined by nodif_brain_mask)
-
-<p>Output:
-<br>Use the browse button to specify an output name. This will be a filename or a
-directory name depending on the mode.
-
-<p>AVAILABLE MODES AND MODE-SPECIFIC SETTINGS:
-
-<p>SINGLE SEED VOXEL: Generates a connectivity distribution from a single,
-user-specified voxel
-<br>GUI SETTTINGS
-<br>Seeds space:
-<br>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.
-
-<br>OUTPUT
-The output will be a single image in the space of the specified seed. 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 particles that pass through that voxel).
-
-<p>SEED MASK MODE: Generates a connectivity distribution from a user-specified
-region of interest.
-
-<br>Settting up the GUI
-<br>Seed image: Use the browse button to locate the seed image - this should be a binary mask.
-<br>OUTPUT
-<br>The output directory will contain:
-<br>logfile - a text record of the command that was run
-<br>The output file - will be a single image in the space of the specified seed
-mask. All
-brain voxels will have a value (though many of these may be zero)
-representing the number of particles that pass through that voxel from the
-seed mask. 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 mask.
-
-<p>SEED MASK AND TARGET MASK - generates a connectivity distribution from voxels
-in the seed mask and retains only those paths that pass through the target
-mask.
-
-<br>Setting up the GUI
-<br>Seed image and Target image: Use the browse buttons to locate binary masks of
-the seed and target. These must be in the same space.
-<br>OUTPUT:
-<br>The output directory will contain:
-<br>logfile - a text record of the command that was run
-<br>The output file - will be a single image in the space of the specified seed mask. All
-brain voxels will have a value (though many of these may be zero)
-representing the number of particles that pass through that voxel from the
-seed mask. 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 mask.
-
-<p>TWO MASKS - SYMMETRIC - generates a connectivity distribution from all
-voxels in mask image 1 and retains only those pathways that pass through mask
-image 2. Also
-generates a connectivity distribution from all voxels in mask image 2 and retains
-pathways that pass through mask image 1. Ouput is the sum of these connectivity
-distributions.
-<br>Setting up the GUI
-<br>Mask image 1 and Mask image 2: Use the browse buttons to locate your binary
-mask of area one and area two. These must be in the same space.
-
-<br>OUTPUT:
-<br>The output directory will contain:
-<br>logfile - a text record of the command that was run
-<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 particles that pass through that voxel from either
-of the
-seed masks. 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.
-
-<p><b>CONNECTIVITY BASED SEED CLASSIFICATION</b>
-<br>This mode quantifies connectivity values
-between a seed mask and any number of user-specified target masks.
-<br>Setting up the GUI
-<br>Seed image: use the browse button to locate your binary mask of seed voxels.
-<br>Target list: 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>OUTPUT:
-<br>The output directory will contatin:
-<br>logfile - a text record of the command that was run
-<br>A single volume for each target mask, named seeds_to_<target>.(img,hdr) 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 particles seeded from that voxel reaching the
-target mask. The value of all voxels outside the seed mask will be zero.
-
-
-<p><b>********* DTIFit ***************</b>
-<br>FDT can be used to fit a diffusion tensor model at each voxel.
-<br>Setting up the GUI
-<br>Input: You can specify an input directory containing all the required files
-with standardized filenames,
-or alternatively you can specific input files manually. If an input directory is specified then all files must be named as shown in
-parentheses below. If input files are specified manually they can have any
-filename. Required files are:
-
-<br>Diffusion weighted data (data.{img,hdr}): A 4-dimensional series of analyze images. This will
-include diffusion-weighted volumes and volume(s) with no diffusion weighting.
-
-<br>BET binary brain mask (nodif_brain_mask.{hdr,img}): A single binarised
-volume in diffusion space containing ones inside the brain and zeroes outside
-the brain.
-
-<br>Output basename: User specifies a basename that will be used to name the
-outputs of DTIFit. If the directory input option is used then the basename
-will be dtifit (??IS THIS RIGHT)
-
-<br>Gradient directions (bvecs): 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 the input data series.(??in x,y,z, or phase,
-read, slice? Do you only include rows for diffusion weighted vols? one entry
-per row?)
-
-<br>bvalues (bvals): 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.
\ No newline at end of file
diff --git a/doc/fdt_dtifit.html b/doc/fdt_dtifit.html
index b080db1c34c096ba779e12d4a9604a397ec543cf..1509fd53d52f6e85ff94979874a4c19588d9f33f 100644
--- a/doc/fdt_dtifit.html
+++ b/doc/fdt_dtifit.html
@@ -1,4 +1,11 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
<h3>DTIFit</h3>
<b>DTIFit</b> fits a diffusion tensor model at each voxel. You would
diff --git a/doc/fdt_eddy.html b/doc/fdt_eddy.html
index 03a54e0ed23a88e425115f790808ceb9dd2cd859..f152e87ae4127e2f4a67511a2b4ceb22fb3e5308 100644
--- a/doc/fdt_eddy.html
+++ b/doc/fdt_eddy.html
@@ -1,5 +1,12 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-<p><h3>Eddy Current Correction</h3>
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
+<h3>Eddy Current Correction</h3>
Eddy currents in the gradient coils induce (approximate) stretches and shears
in the diffusion weighted images. These distortions are different for
different gradient directions. Eddy Current Correction corrects for these
diff --git a/doc/fdt_intro.html b/doc/fdt_intro.html
deleted file mode 100644
index c3c61eacbcfb63b6c13cc8cba22c90056f34710d..0000000000000000000000000000000000000000
--- a/doc/fdt_intro.html
+++ /dev/null
@@ -1,46 +0,0 @@
-<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_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_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_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 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>
-<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
-voxels; 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>.
-
diff --git a/doc/fdt_modelling.html b/doc/fdt_modelling.html
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index 0645712245e963c5f4503e932f421add336bed06..0000000000000000000000000000000000000000
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+++ /dev/null
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-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-<p><h3>An overview of local diffusion modelling carried out in Bedpost</h3>
-Its all bollox really - Tim just plucks it out of his arse
\ No newline at end of file
diff --git a/doc/fdt_pipeline.html b/doc/fdt_pipeline.html
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--- a/doc/fdt_pipeline.html
+++ b/doc/fdt_pipeline.html
@@ -1,4 +1,10 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
+<!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><OBJECT data="fdt_top.html"></OBJECT>
<h3>Processing pipeline</h3>
<p>To call the FDT GUI, either run <b>Fdt</b>, or run <b>fsl</b> and press the <b>FDT</b> button.
diff --git a/doc/fdt_probtrack.html b/doc/fdt_probtrack.html
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-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY
-BACKGROUND="fdt_images/fsl-bg.jpg">
-<p><h3>PROBTRACK - probabilistic tracking</h3><br>
-
- For details about probabilistic tractography as implemented by FDT,
- see <a
- href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">here</a>.
- Briefly, FDT repetitively samples from the distributions on
- voxel-wise principal diffusion directions, each time comupting 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>.
-
-<p>After Bedpost has been applied it is possible to run tractography analyses
-using ProbTrack.
-
-Probtrack can be run in several different modes:
-<ul><li><a href="#path">Path distribution estimation</a></li>
-<ul><li><a href="#single">Single seed voxel</a></li>
-<li><a href="#seedmask">Seed mask</a></li>
-<li><a href="#seedwaypoint">Seed mask and waypoint masks</a></li>
-<li><a href="#twomask">Two masks - symmetric </a></li></ul>
-<li><a href="#seedclass">Connectivity-based seed classification</a></li>
-</ul>
-
-Each mode is explained in detail below.
-Every mode requires the user to
-specify a bedpost directory. For all modes, the bedpost directory must contain the following 4D images:
-
-<li><b>merged_phsamples</b></li>
-<li><b>merged_thsamples</b></li>
-<li><b>nodif_brain_mask</b></li>
-
-<p>Results from probtrack 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 probtrack that are stored in the
-required space. If probtrack 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 thediffusion data. The <a
-ref="fdt_registration.html">FDT registration tab</a> creates the
-following transformations in the <code>xfms</code> subdirectory of the
-bedpost directory.
-
-
-<p>for running analyses in structural space:
-<li><b>xfms/str2diff.mat</b></li>
-<li><b>xfms/diff2str.mat</b></li>
-
-<p>for running analyses in standard space:
-<li><b>xfms/standard2diff.mat</b></li>
-<li><b>xfms/diff2standard.mat</b></li>
-
-<hr>
-<a name="path"></a>
-<h3>Path Distribution Estimation - basics</h3>
-The first four modes of ProbTrack involve 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.
-
-<p><h4>Setting up the GUI for Path Distribution Estimation - settings common
-to all modes:</h4>
-
-<p><b>Seeds space:</b> specification of seeds is different for each mode - see below.
-
-<p>If <b>seed space is not diffusion</b>, then check this button. If
-you are in <b>Single seed voxel</b> mode use the browse buttons 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). Next 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 in <a href="#seedclass">Connectivity-based
-seed classification</a>.
-
-<p>If an <b>exclusion mask</b> is to be used then check the box and
-use the browse button to locate the mask file. This must be a
-binarised analyze file in seed space. Pathways will be terminated if
-they enter the exclusion mask. For example, an exclusion mask of the
-midline will terminate pathways that cross into the other
-hemisphere. (Note that paths are always terminated when they reach the
-brain surface as defined by nodif_brain_mask)
-
-<br>Use the browse button to specify an <b>output</b> name. This will
-be a filename or a directory name depending on the mode.
-
-<hr>
-
-<h3>Path Distribution Estimation - available modes and mode-specific settings:</h3>
-<ul><li><a href="#single">Single seed voxel</a></li>
-<li><a href="#seedmask">Seed mask</a></li>
-<li><a href="#seedwaypoint">Seed mask and waypoint masks</a></li>
-<li><a href="#twomask">Two masks - symmetric </a></li></ul>
-
-<a name="single"></a>
-
-<h3>Single Seed Voxel:</h3>
-<IMG ALIGN=RIGHT height=100 SRC="fdt_images/fdt_simple_tract3.gif"
-ALT="simple tract">
-Generates a connectivity distribution from a single,
-user-specified voxel
-<p>Gui Options: <br><b>Seeds space:</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 in the space of the specified seed. 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.
-
-<a name="seedmask"></a>
-<h3>Seed Mask Mode:</h3>
-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.
-<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>The output file - will be a
-single image in the space of the specified seed mask. 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 the seed mask.
-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 mask.
-
-<a name="seedwaypoint"></a> <h3>Seed Mask and Waypoint Masks</h3> <IMG
-ALIGN=RIGHT height=200 SRC="fdt_images/fdt_twomasks_tracts.gif"
-ALT="constraining tracts"> Generates a connectivity distribution from
-voxels in the seed mask and retains only those paths that pass through
-all of the waypoint masks. The example on the right shows the outputs
-from two different analyses which use the same seed mask (orange) but
-different waypoint masks (red).
-
-<p>GUI Options:
-<br><b>Seed Image:</b> Use the browse button to locate the binary seed mask.
-
-<br><b>Waypoint Masks:</b> Use the add and remove buttons to make a
-list of waypoint masks. These must be in the same space as the seed image.
-
-<BR>
-<br>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>The output file - will be a single image in the space of the
-specified seed mask. All brain voxels will have a value (though many
-of these may be zero) representing the number of samples that pass
-through that voxel starting the seed mask and which have also passed through all of
-the waypoint masks. 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 mask.
-
-<a name="twomask"></a>
-<h3>Two Masks - symmetric</h3>
- Generates a connectivity distribution from all
-voxels in <b>mask image 1</b> and retains only those pathways that pass
- through <b>mask image 2</b>. Also
-generates a connectivity distribution from all voxels in <b>mask image 2</b> and retains
-pathways that pass through <b>mask image 1</b>. Ouput is the sum of these connectivity
-distributions.
-<p>GUI Options:
-<br><b>Mask image 1</b> and <b>Mask image 2</b>: Use the browse buttons to locate your binary
-mask of area one and area two. These must be in the same space.
-
-<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>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 the other seedmask. 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="seedclass"></a>
-<h3>Connectivity-based seed classification</h3>
-<IMG ALIGN=RIGHT height=150 SRC="fdt_images/fdt_seeds2targets_quant_eg.gif"
-ALT="connectivity-based classification of thalamus">
-This mode quantifies connectivity values
-between a seed mask and any number of user-specified target masks. In the
-example on the right, seed voxels in the thalamus are classified according to
-the probabilty of connection to different cortical target masks.
-<p>Setting up the GUI
-<br><b>Seed image</b>: use the browse button to locate your binary mask of seed voxels.
-<br><b>Target list</b>: 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.
-<p>
-
-<br>The output directory will contatin:
-<IMG ALIGN=RIGHT height=150 SRC="fdt_images/fdt_seeds2targets_thal.gif"
-ALT="connectivity-based classification of thalamus">
-<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>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>
-There are command line utilities that can be run on the outputs of
-<b>Connectivity-based seed classification</b>:
-<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>
-<hr>
-<a name="options"></a>
-<h3>Options Tab </h3>
-For all modes in probtrack, 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.
-
-<p><b>Curvature Threshold</b> (default 0.2): We limit how sharply pathways can turn
-in order to
-exclude implausible pathways. This number is the cosine of the minimum allowable
-angle between two steps. By default this is set to 0.2 (corresponding to a
-minimum angle of approximately ±80 degrees). Adjusting this number can enable
-pathways with sharper angles to be detected.
-
-<p><b>Verbose:</b> If this option is selected then FDT prints additional logging
-information to screen while it is running.
-
-<p><b>Loopcheck:</b> By default, we terminate pathways that loop back on themselves
--i.e paths that travel to a point where they have already been.
-
-<p><h4>Advanced options:</h4>
-
-<p><b>Use modified Euler streamlining:</b> Use modified Euler
-integration as opposed to simple Euler for computing probabilistic
-streamlines. More accurate but slower.
-
-<p><b>Maximum number of steps</b> (default 2000): By default, samples are terminated
-when they have travelled 2000 steps. Using a step length of 0.5mm this
-corresponds to a distance of 1m. These values can be adjusted if required.
-
-<p><b>Step length</b> (default 0.5mm): This determines the length of each step. This
-setting may be adjusted from default e.g., depending on the voxel size being
-used, or if tracking is being performed on different sized brains
-(e.g., infants or animals).
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</head>
<body bgcolor=white background="fdt_images/fsl-bg.jpg" lang=EN-GB link=blue
vlink=blue style='tab-interval:36.0pt'>
<div class=Section1>
<h3><span lang=EN-US style='font-size:14.0pt'>PROBTRACKX - probabilistic
tracking with crossing fibres<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><br>
</span><span lang=EN-US style='font-size:11.0pt'>For details about
probabilistic tractography as implemented by FDT, look <a
href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">here</a>.
Briefly, FDT repetitively samples from the distributions on voxel-wise
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 major
difference with <a href="http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_probtrack.html">Probtrack</a>
is that the local samples have a more complex distribution. They can model
different diffusion directions, allowing to track finer pathways and resolve
crossing fibres in regions with complex fibre architecture. <o:p></o:p></span></p>
<p><span lang=EN-US style='font-size:11.0pt'>After BedpostX has been applied it
is possible to run tractography analyses using probtrackx.</span><span
lang=EN-US> Note that probtrackx can also be run after bedpost. In that case,
probtrackx simply samples from the single fibre orientation given by bedpost.<o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Using probtrackx in command line<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Probtrackx requires a set of mandatory arguments. The
optional arguments allow further specifications. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Below is a command for probtrackx with all possible arguments.
The bold faced arguments are mandatory. Click on each argument to have a
precise description. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>probtrackx<b> <span style='mso-tab-count:1'> </span>-s
<<a href="#basename">basename</a>> <span style='mso-tab-count:1'> </span>-m
<<a href="#mask">mask</a>> <span style='mso-tab-count:1'> </span>-x
<<a href="#seed">seed</a>></b></span><span lang=EN-US style='font-size:
11.0pt'> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--mode=<<a href="#mode">chosenMode</a>> <span
style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#opd">opd </a><span style="mso-spacerun:
yes"> </span><span style="mso-spacerun: yes"> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#os2t">os2t</a> <span style='mso-tab-count:
1'> </span>--targetmasks=<<a href="#targetmasks">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#omatrix2">omatrix2</a> <span
style='mso-tab-count:1'> </span>--lrmask=<<a
href="#lrmask">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>-o <<a href="#outputfile">outputfile</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--network<o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--waypoints=<<a href="#waypoints">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--seedref=<<a href="#seedref">filename</a>> <span
style='mso-tab-count:1'> </span>--xfm=<<a href="#xfm">transformation</a>>
<o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--dir=<<a href="#dir">directory</a>> <span
style='mso-tab-count:1'> </span>--<a
href="#forcedir">forcedir</a> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--stop=<<a href="#stop">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--avoid=<<a href="#rubbish">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'><a href="#nsamples">--nsamples=<n></a> <a
href="#cthr">--cthr=<n></a> <a href="#steplength">--steplength=<n></a>
--<a href="#loopcheck">loopcheck</a> --<a href="#usef">usef</a> --<a
href="#randfib">randfib</a> --<a href="#modeeuler">modeuler</a> --<a
href="#rseed">rseed</a> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#verbose">verbose</a> --<a href="#help">help</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Below you can find a few typical command lines.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<ul style='margin-top:0cm' type=disc>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question1">I want to see all the tracts
that go from my ROI<span style="mso-spacerun: yes"> </span>to the
rest of the brain</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question2">I want to use the high
resolution structural image (or the standard space image) to draw my ROIs</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question3">I want to segment an ROI
depending on its connections with another set of ROIs</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question4">I want to segment an ROI
into different parts having different connections with the rest of the
brain</a> <o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US style='font-size:
11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US style='font-size:
11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The output of probtrackx can be analysed further with:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<ul style='margin-top:0cm' type=disc>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l1 level1 lfo6;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:11.0pt'><a
href="http://www.fmrib.ox.ac.uk/fsl/fdt/find_the_biggest.html">find_the_biggest</a>
(for seed2target classification)<o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l1 level1 lfo6;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:11.0pt'>ccops (for matrix spectral clustering after using
the omatrix2 options)<o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Mandatory arguments<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>There are <b>three</b></span><span lang=EN-US
style='font-size:11.0pt'> compulsory arguments in probtrackx. Basically, the
algorithm needs to know the local <b>orientation distributions</b></span><span
lang=EN-US style='font-size:11.0pt'> (output of bedpostX), <b>the brain mask</b></span><span
lang=EN-US style='font-size:11.0pt'> (in order not to draw pathways outside it)
and a <b>seed region</b></span><span lang=EN-US style='font-size:11.0pt'> for
the probabilistic tractography. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=basename></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>-s <basename ><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><basename> is the prefix of the file containing
the orientation distribution given by bedpostX, which in general are of the
form (in the case of two fibres per voxel):<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_th1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_th2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_ph1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_ph2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_f1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_f2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>If the path to the directory where these files are
stored is <pathdir>, then the basename is <b><pathdir>/merged.</b></span><span
lang=EN-US style='font-size:11.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt;tab-stops:187.0pt'><a
name=mask></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>-m <mask><span style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Binary brain mask that can be computed with <a
href="http://www.fmrib.ox.ac.uk/fsl/bet">bet</a>. This mask MUST BE IN THE
DIFFUSION SPACE (i.e. same as the diffusion data). Usually, it is computed from
the nodif image, and is named <b>nodif_brain_mask.</b></span><span lang=EN-US
style='font-size:11.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt;tab-stops:313.0pt'><a
name=roi></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span><a name=seed></a>-x <seed> <span style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Region of the brain which serves as a seed for the
tractography. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>When using the simple <a href="#mode">mode</a>,
<seed> is a textfile with the coordinates of the seed voxels stored as
follows :<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_1<span style='mso-tab-count:1'> </span>y_1<span
style='mso-tab-count:1'> </span>z_1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_2<span style='mso-tab-count:1'> </span>y_2<span
style='mso-tab-count:1'> </span>z_2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>…<span style='mso-tab-count:1'> </span>…<span
style='mso-tab-count:1'> </span>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_n<span style='mso-tab-count:1'> </span>y_n<span
style='mso-tab-count:1'> </span>z_n<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>When using seedmask mode, <seed> is a 3D image
with non-zero values inside the seed voxels. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><seed> can also be a text file with multiple
seed volumes:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdir1/volume1.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdir2/volume2.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>…<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdirk/volumek.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The program will then compute all the pathways
connecting any pair of brain regions defined in the network. The option --network
must be turned on in this case.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>In all cases (text file or image file), you can use
either the diffusion space, or another space (e.g. structural, standard
spaces), provided the –<b><a href="#seedref">seedref</a></b></span><span
lang=EN-US style='font-size:11.0pt'> and –<b><a href="#xfm">xfm</a></b></span><span
lang=EN-US style='font-size:11.0pt'> options.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Optional arguments<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Choose your mode ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=mode></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--mode=<chosenMode><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>You can run probtrackx in two different modes:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>simple<span style='mso-tab-count:3'> </span>:
In case the seed is a textfile with voxel coordinates.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>seedmask (default)<span style='mso-tab-count:1'> </span>:
In case the seed is a 3D image file (or ascii file of multiple 3D image files)<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US>The
voxel coordinates as well as the seedmask can be in a different space than the
diffusion space (e.g. high resolution structural space or standard space),
provided the transformation that goes from this space to the diffusion space
(see the options --<a href="#seedref">seedref</a> and --<a href="#xfm">xfm</a>).</span><span
style='mso-ansi-language:EN-GB'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Choose your outputs ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=opd></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--opd<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>This option allows to output the pathway distribution
in <outputfile>. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=pd></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--pd<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Activate the distance correction option. : The output pathway
distribution is the sum of the lengths of the pathways that cross each voxel.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=os2t></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--os2t<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>This option allows to output the probability that each
individual voxel in the seed mask is connected to each of the target masks
(provided a target mask list).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The output are of the form:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_target1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_target2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_targetn<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Each of these files is a volume with non-zero values
only within the seed mask. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The value in each voxel of seed_to_target1 within the
seed mask is the number of tracts seeded from this voxel that arrived at
target1.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Running <a
href="http://www.fmrib.ox.ac.uk/fsl/fdt/find_the_biggest">find_the_biggest</a>
on these outputs gives a segmentation of the seed mask into parts connected to
the different targets.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a
name=targetmasks></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--targetmasks=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is either a 3D file with one target
mask, or a text file containing a list of target masks (with the full path) as
following:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/target1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/target2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/targetn<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><![if !supportEmptyParas]> <![endif]><o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=omatrix2></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>---omatrix2<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This option allows to ouput a filename, called<b>
fdt_matrix2</b></span><span lang=EN-US style='font-size:12.0pt'>, which is a
NxP matrix, where N is the number of voxels in the seed mask, and P is the
number of voxels in the rest of the brain mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The values stored in this matrix represent the
probability that each voxel in the seed mask is connected with each voxel of
the rest of the brain. This value depends on the choice of the option --<a
href="#pd">pd</a>.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This matrix is useful for seed classification based on
connectivity profile with the spectral reordering tool : ccops.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For computational and storage reasons, we recommend to
use a low resolution brain mask, (e.g. 5x5x5 mm^3). <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=lrmask></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--lrmask=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is a low resolution brain mask used
along with the --omatrix2 option<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>To create a low resolution mask, take a whole brain mask
(e.g. using bet), of the same image as the one on which the seeds have been
drawn, and subsample it with the command:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>flirt –i seed_brain_mask –ref seed_brain_mask
–applyisoxfm 5 –o lowresmask<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>fslmaths lowresmask –thr 0.5 –bin lowresmask<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><span style="mso-spacerun: yes"> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=outputfile></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>-o <outputfile><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This is the pathway probability distribution. By
default, this file is called fdt_paths.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The pathway distribution is in the same space as the
seed mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=mask2></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--mask2=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Add this option if you want to draw all the pathways
that go from the seed mask to a second region (drawn in mask2), and all the
pathways that go from this second region to the seed region.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>mask2 must be in the same space as the seed mask.<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=waypoints></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--waypoints=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Add this option if you want to track only the pathways
that happen to cross a (or a set of) region(s) in the brain. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is either a 3D file with a region
mask, or a text file with a list of 3D region masks along with their full path
as follows:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_1<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_2<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>…<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_n<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>The waypoint masks must all be in the same space as
the seed mask<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** For registration ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>When the seed mask is not in the diffusion space (i.e.
ROIs were drawn on the structural image, or in the standard space, coming from
FMRI group activation or some template), you must provide probtrackx with a <b>reference
image</b></span><span lang=EN-US style='font-size:12.0pt'> and a <b>transformation</b></span><span
lang=EN-US style='font-size:12.0pt'>.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=seedref></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--seedref=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is the name of an image in the same
space as the seed mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For example, struct_brain (if the seed space is the
structural space), or standard (if the seed space is the standard space).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=xfm></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>---xfm=<transformation><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><transformation> is a text file containing the
transformation matrix (as computed by <a
href="http://www.fmrib.ox.ac.uk/fsl/flirt">flirt</a>) from the seed space to
the diffusion space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For example :<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>str2diff.mat if the seed space is the structural
image.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>std2diff.mat if the seed space is the standard space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Miscellaneous arguments ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=verbose></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--verbose=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><n> varies from 0 (very few ouput comments) to 2
(a lot of comments) during the execution of probtrackx.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=help></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--help<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This prints out the help message providing a short
description of the different options.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=dir></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--dir=<directory><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Name of the directory which will contain all the
outputs (fdt_paths, fdt_matrix2, seed_to_targets etc.)<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=forcedir></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--forcedir<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Overwrites the ouput directory if there is already one
having the same name. By default, probtrackx will add “+†to an already
existing one.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=rubbish></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--avoid=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use this option if you want to exclude from the
pathway distribution all those pathways that go into a given region.
<filename> is a 3D mask of this region. This option is opposite to
waypoints. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=stop></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--stop=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use this option if you want to stop the pathways when
they enter a given region. <filename> is a 3D mask of this region. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Expert mode parameters ***</span><span lang=EN-US
style='font-size:12.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=nsamples></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--nsamples=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Number of sample pathways drawn per voxel of the seed
mask. The default value is 5000. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=cthr></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--cthr=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Threshold value for the cosine of the angle between
two successive steps during the tractography. The default value is 0.2
(corresponding to an angle of 78 degrees).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=nsteps></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--nsteps=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Maximum number of steps (default=2000). Using a step
length of 0.5mm, this corresponds to a distance of 1m.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=steplength></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--steplength=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Length of each step during the tractography. The
default value is 0.5 voxels (of the seed space).<span style="mso-spacerun:
yes"> </span>You may want to change this value depending on the voxel
size, or if the tractography is performed on different sized brain (e.g.
infants or animals).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=loopcheck></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--loopcheck<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This option removes the tracts that make a loop, which
can happen as the tractography is probabilistic. It slows down a bit the
computations.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=usef></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--usef<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>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).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=randfib></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--randfib<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Select randomly the different fibre directions when
starting the tractography at one seed voxel. By default, the tractography start
from the leading direction (the one with highest fractional volume inside the
seed voxel).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=modeeuler></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--modeuler<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use modified Euler integration instead of standard
Euler. This is more accurate, but slightly slower.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=rseed></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--rseed<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Random variable generator. By default, the value of this
variable is fixed, which means that when repeating an experiment with the same
data, one gets EXACTELY the same results. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Command line examples<o:p></o:p></span></h3>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question1></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
see all the tracts that go from my seed<span style="mso-spacerun: yes">
</span>to the rest of the brain<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>A typical command when one wants to draw all the
pathways (in terms of probability distribution) that run from the seed mask is:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a>
--<a href="#opd">opd</a> <a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Below is the result with a seed in the internal
capsule.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question2></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
see only the tracts that go from an ROI to another (set of) ROIs <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Sometimes, one is only interested in the pathways that
connect one region to one or several others. For example, one can have the
internal capsule as a seed mask, and ask for the pathways that go to M1 in the
hand area and the face area, as well as to the cerebral peduncle. Here is a
typical command using the waypoints option:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a> <a
href="#waypoints">--waypoints=<listOfWaypoints></a> --<a href="#opd">opd</a>
<a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Below is the result. Note that the resulting pathways
are a subgroup of the pathways drawn in the first example, which include only
those that reach the waypoints.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question3></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
use the high resolution structural image (or the standard space image) to draw
my ROIs<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Sometime, one needs to draw the seed mask in a high
resolution image (for example, to finely delineate some structure), or on a standard
space image (e.g. to use group activations as a common seed mask for a group of
subjects). Here is a typical command using the structural as a seed space. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Note that the resulting pathways are also in the seed
space, but all the computations are done in the diffusion space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a> <a
href="#seedref">--seedref=struct</a> <a href="#xfm">--xfm=<subject>.bedpostX/xfms/str2diff.mat</a>
<a href="#opd">--opd</a> <a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question4></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
segment an ROI depending on its connections with another set of ROIs <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>One can use probtrackx to know which part of the seed
mask is more probably connected to each target region within a list. For
example, which part of the internal capsule is connected to the hand area, and
which part is connected to the face area ? <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>A typical command for doing that is:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s <subject>.bedpostX/merged</a>
<a href="#mask">–m <subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x
seed_mask</a><span style="mso-spacerun: yes"> </span><a href="#os2t">--os2t</a>
<a href="#targetmasks">--targetmasks=<listOfTargets></a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
segment an ROI into different parts having different connections with the rest
of the brain <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>As for the SMA/preSMA study, one can ask whether the
seed region is composed of two ore more parts having different connections with
the rest of the brain, i.e. participating in different structural networks.
Probtrackx allows one to output a matrix composed of the values of the
connections between each voxel in the seed mask with the rest of the brain
(taken at a low resolution for computational reason). <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Once this matrix calculated, one can une a spectral
reordering command (ccops) to see whether there are two or more clusters within
the seed mask. Here is a typical command: <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#mask">–s seed_mask</a><span
style="mso-spacerun: yes"> </span><a href="#omatrix2">--omatrix2</a> <a
href="#dir">--dir=<subject>.probtrackx</a> <a href="#lrmask">--lrmask=lowres_mask</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p align=center style='text-align:center'><span lang=EN-US><!--[if gte vml 1]><v:shapetype
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</div>
</body>
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diff --git a/doc/fdt_probtrackx.html b/doc/fdt_probtrackx.html
index 8e2a759d3fcc421fdd55abeace1b2281d5af8366..db6e45289ed9b810c8e4fe7ab4f5d3906a767417 100644
--- a/doc/fdt_probtrackx.html
+++ b/doc/fdt_probtrackx.html
@@ -1,6 +1,12 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY
-BACKGROUND="fdt_images/fsl-bg.jpg">
-<p><h3>PROBTRACKX - probabilistic tracking</h3><br>
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
+<h3>PROBTRACKX - probabilistic tracking</h3><br>
For details about probabilistic tractography as implemented by FDT,
see <a
diff --git a/doc/fdt_reg.html b/doc/fdt_reg.html
index 62cd8aa2768d9841ab06f1dbb9674a6de88e9606..1ff9893b2545fb8774022acf8f42cbd5cf2a4e71 100644
--- a/doc/fdt_reg.html
+++ b/doc/fdt_reg.html
@@ -1,4 +1,11 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
<h3>Registration within FDT</h3>
<p>If tractography results are to be stored in any space other than diffusion
space then registration must be run.
diff --git a/doc/fdt_thresh.html b/doc/fdt_thresh.html
index f9fcc75df728b45887ad734ced12b4c7da101580..8fbf57aaa0ec77c682e98b479c0a06335920de79 100644
--- a/doc/fdt_thresh.html
+++ b/doc/fdt_thresh.html
@@ -1,5 +1,11 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY
-BACKGROUND="fdt_images/fsl-bg.jpg">
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
<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
diff --git a/doc/fdt_top.html b/doc/fdt_top.html
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@@ -1,78 +1,37 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE><BODY BACKGROUND="fdt_images/fsl-bg.jpg">
-<hr><TABLE BORDER=0 WIDTH="100%"><TR><TD ALIGN=CENTER><td align="center">
+<link REL="stylesheet" TYPE="text/css" href="../fsl.css">
-<h1>FDT - FMRIB's Diffusion Toolbox</h1>
+<TABLE BORDER=0><TR>
-User Guide - FDT version 2.0
+<TD ALIGN=CENTER WIDTH="100%">
+<TABLE BORDER=0>
+
+<tr><td align=center><font size=+3><b>FMRIB's Diffusion Toolbox - FDT v2.0</b></font></tr>
+
+<tr valign=bottom><td align=center>
+
+<a href="index.html" target="_top">intro</a> -
+<a href="fdt_pipeline.html" target="_top">processing pipeline</a> -
+<a href="fdt_eddy.html" target="_top">eddy current correction</a> -
+<a href="fdt_dtifit.html" target="_top">dtifit</a> <br>
+<a href="fdt_bedpost.html" target="_top">bedpost</a> -
+<a href="fdt_bedpost_parallel.html" target="_top">parallelising bedpost</a> -
+<a href="fdt_reg.html" target="_top">registration</a> -
+<a href="fdt_probtrackx.html" target="_top">probtrackx</a> <br>
+<a href="fdt_thresh.html" target="_top">proj_thresh</a> -
+<a href="fdt_biggest.html" target="_top">find_the_biggest</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>
+
+</tr></table>
+
+<TD ALIGN=RIGHT>
+<a href="http://www.fmrib.ox.ac.uk/fsl" target="_top">
+<IMG BORDER=0 SRC="../images/fsl-logo-big.jpg" WIDTH=165></a>
+</TD>
+
+</TR></TABLE><hr>
-<center>
-<form target="dynamic">
- <p><select name="section" size="1" language="javascript" target="dynamic" onChange="gotoPage(this.selectedIndex);">
- <option selected>----------Select Module-----------</option>
- <option>Introduction</option>
- <option>Processing pipeline</option>
- <option>Eddy current correction</option>
- <option>DTIFit</option>
- <option>Bedpost</option>
- <option>Parallelising Bedpost</option>
- <option>Registration</option>
- <option>Probtrackx</option>
- <option>Proj_thresh</option>
- <option>find_the_biggest</option>
- <option>Displaying DW images in fslview </option>
- <option>Overview of FDT theory </option>
- </select></p>
-</form>
-</center>
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- case 7:
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- case 8:
- window.top.dynamic.location="fdt_probtrackx.html";
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- window.top.dynamic.location="fdt_thresh.html";
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- case 10:
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- case 11:
- window.top.dynamic.location="fdt_display.html";
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diff --git a/doc/fdt_vecreg.html b/doc/fdt_vecreg.html
index bbc8171cfbe88d639e8f77ec4520b31d9f75aafa..25e3db61a9e2ae15f74dcbf491b6ac28f343ac68 100644
--- a/doc/fdt_vecreg.html
+++ b/doc/fdt_vecreg.html
@@ -1,5 +1,11 @@
-<HTML><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE>
-<BODY BACKGROUND="fdt_images/fsl-bg.jpg">
+<!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><OBJECT data="fdt_top.html"></OBJECT>
+
<h3>Registration of vector images using vecreg</h3>
<p>
diff --git a/doc/index.html b/doc/index.html
index d8b4fdb17d32ce02ddf3286ad7976e7e908e999b..9658479ccc48cb90dc1b8b155b2b7ea8749fd204 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -1,8 +1,49 @@
-<HTML><HEAD><TITLE>FDT - FMRIB's Diffusion Toolbox - User Guide</TITLE></HEAD>
+<!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><OBJECT data="fdt_top.html"></OBJECT>
-<frameset rows="200,*,60" frameborder="no" framespacing="0" border="0">
- <frame src="fdt_top.html" marginwidth="10" marginheight="10" frameborder="no">
- <frame name="dynamic" src="fdt_intro.html" marginwidth="10" marginheight="10" frameborder="no">
- <frame src="fdt_bottom.html" marginwidth="10" marginheight="10" frameborder="no">
-</frameset>
+<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_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_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 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>
+<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
+voxels; 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>.