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<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, 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
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> <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 runs with a set of mandatory arguments, and
also optional arguments which depend on what one wants to ask the data for. <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'>Above is a command for probtrackx with all the
possible arguments called. 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> -s <<a href="#basename">basename</a>>
-m <<a href="#mask">mask</a>> -x <<a href="#seed">seed</a>></b></span><span
lang=EN-US style='font-size:11.0pt'> --mode=<<a href="#mode">chosenMode</a>>
--<a href="#opd">opd </a><span style="mso-spacerun: yes"> </span>--<a
href="#pd">pd=<n></a> --<a href="#os2t">os2t</a> --targetmasks=<<a
href="#targetmasks">filename</a>> --<a href="#omatrix2">omatrix2</a> --lrmask=<<a
href="#lrmask">filename</a>> -o <<a href="#outputfile">outputfile</a>>
--mask2=<<a href="#mask2">filename</a>> --waypoints=<<a
href="#waypoints">filename</a>> --seedref=<<a href="#seedref">filename</a>>
--xfm=<<a href="#xfm">transformation</a>> --dir=<<a href="#dir">directory</a>>
--<a href="#forcedir">forcedir</a> --rubbish=<<a href="#rubbish">filename</a>>
<span style="mso-spacerun: yes"> </span><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> --<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'>You can also reach specific sections depending on what
questions you want to ask. Click on a link to have a typical command line for
each of these question. Of course, you can combine the options for different
commands if more than one question needs to be answered.<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:l2 level1 lfo4;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:l2 level1 lfo4;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:l2 level1 lfo4;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:l2 level1 lfo4;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question4">I want to segment an ROI on
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'>After using probtrackx, some useful tools are
available to further anatyse the results:<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:l3 level1 lfo5;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:l3 level1 lfo5;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'>This is the basename for the orientation distribution
given by probtrackx, which in general are of the form (in 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 directory where these file 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'>This is a 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. 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'>This is the 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 mode, <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 seemask mode or twomask_sym 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'>In both cases (text file or image file), you can use
either the diffusion space, or another space (e.g. structural, standard spaces),
provided the –<b>seedref</b></span><span lang=EN-US style='font-size:11.0pt'> and
–<b>xfm</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 on 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:2'> </span><span
style='mso-tab-count:1'> </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.<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: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=<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:11.0pt'><n> is either 1 (default value) or 2.<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'>n=1<span style='mso-tab-count:1'> </span>:
the pathway distribution is the total number of pathways that crossed each
voxel 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:11.0pt'>n=2<span style='mso-tab-count:1'> </span>:
the pathway distribution is the mean length of the pathways that cross each
voxel (to correct for the effect of the distance to the seed mask).<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'>--</span><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><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
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><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 a 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>/target_1<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>/target_2<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>/target_n<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><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.<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, <span
style="mso-spacerun: yes"> </span>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><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 had 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'>avwmaths 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><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><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><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><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 space.<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 (ROIs
drawn on the structural image, or in the standard space, coming from FMRI group
activation or some template), you must provide probtrackx with a reference image
and a 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'><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><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 mak.<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><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 text file containing the
transformation matrix (as computed by flirt) 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><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 fiew 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><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><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><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'>Use this option if you want to overwrite the ouput
directory if there is 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><span style="mso-spacerun: yes"> </span>--rubbish=<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 somehow opposite
to waypoints. Note that if a pathway goes into this region, only the part that
is inside the region will be removed, the rest of the pathway is kept as a part
of the distribution.<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><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><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><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><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'>Step between two successive steps 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><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><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><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><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><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 fix, 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:l2 level1 lfo4;
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 just one wants to draw all the
pathways (in terms of probability distribution) that run from 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'>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:l2 level1 lfo4;
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:12.0pt'>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 results. 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:l2 level1 lfo4;
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:12.0pt'>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:l2 level1 lfo4;
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:12.0pt'>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:l2 level1 lfo4;
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:12.0pt'>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><span lang=EN-US><span style="mso-spacerun: yes"> </span><o:p></o:p></span></p>
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