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<![endif]--><title>FDT - FMRIB's Diffusion Toolbox - User Guide</title><!--[if gte mso 9]><xml>
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<o:Created>2006-09-08T10:26:00Z</o:Created>
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</o:shapelayout></xml><![endif]--></head><bodybgcolor=whitebackground="fdt_images/fsl-bg.jpg"lang=EN-GBlink=bluevlink=bluestyle='tab-interval:36.0pt'><divclass=Section1><h3><spanlang=EN-USstyle='font-size:14.0pt'>PROBTRACKX - probabilistic
tracking with crossing fibres<o:p></o:p></span></h3><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><br></span><spanlang=EN-USstyle='font-size:11.0pt'>For details about
probabilistic tractography as implemented by FDT, see <ahref="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 <ahref="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><spanlang=EN-USstyle='font-size:11.0pt'>After BedpostX has been applied it
is possible to run tractography analyses using probtrackx.</span><spanlang=EN-US><o:p></o:p></span></p><divclass=MsoNormalalign=centerstyle='margin:0cm;margin-bottom:.0001pt;
text-align:center'><spanlang=EN-US><hrsize=2width="100%"align=center></span></div><h3><spanlang=EN-USstyle='font-size:14.0pt'>Using probtrackx in command line<o:p></o:p></span></h3><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>probtrackx<b> -s <<ahref="#basename">basename</a>>
-m <<ahref="#mask">mask</a>> -x <<ahref="#seed">seed</a>></b></span><spanlang=EN-USstyle='font-size:11.0pt'> --mode=<<ahref="#mode">chosenMode</a>>
--<ahref="#opd">opd </a><spanstyle="mso-spacerun: yes"> </span>--<ahref="#pd">pd=<n></a> --<ahref="#os2t">os2t</a> --targetmasks=<<ahref="#targetmasks">filename</a>> --<ahref="#omatrix2">omatrix2</a> --lrmask=<<ahref="#lrmask">filename</a>> -o <<ahref="#outputfile">outputfile</a>>
--mask2=<<ahref="#mask2">filename</a>> --waypoints=<<ahref="#waypoints">filename</a>> --seedref=<<ahref="#seedref">filename</a>>
--xfm=<<ahref="#xfm">transformation</a>> --dir=<<ahref="#dir">directory</a>>
--<ahref="#forcedir">forcedir</a> --rubbish=<<ahref="#rubbish">filename</a>><spanstyle="mso-spacerun: yes"> </span><ahref="#nsamples">--nsamples=<n></a><ahref="#cthr">--cthr=<n></a><ahref="#steplength">--steplength=<n></a>
--<ahref="#loopcheck">loopcheck</a> --<ahref="#usef">usef</a> --<ahref="#randfib">randfib</a> --<ahref="#modeeuler">modeuler</a> --<ahref="#rseed">rseed</a> --<ahref="#verbose">verbose</a> --<ahref="#help">help</a><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><ulstyle='margin-top:0cm'type=disc><liclass=MsoNormalstyle='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l2 level1 lfo4;tab-stops:list 36.0pt'><spanlang=EN-USstyle='font-size:12.0pt'><ahref="#question1">I want to see all the tracts
that go from my ROI<spanstyle="mso-spacerun: yes"> </span>to the
rest of the brain</a><o:p></o:p></span></li><liclass=MsoNormalstyle='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l2 level1 lfo4;tab-stops:list 36.0pt'><spanlang=EN-USstyle='font-size:12.0pt'><ahref="#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><liclass=MsoNormalstyle='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l2 level1 lfo4;tab-stops:list 36.0pt'><spanlang=EN-USstyle='font-size:12.0pt'><ahref="#question3">I want to segment an ROI
depending on its connections with another set of ROIs</a><o:p></o:p></span></li><liclass=MsoNormalstyle='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l2 level1 lfo4;tab-stops:list 36.0pt'><spanlang=EN-USstyle='font-size:12.0pt'><ahref="#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><pclass=MsoNormalstyle='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:
11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:
11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>After using probtrackx, some useful tools are
available to further anatyse the results:<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><ulstyle='margin-top:0cm'type=disc><liclass=MsoNormalstyle='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l3 level1 lfo5;tab-stops:list 36.0pt'><spanlang=EN-USstyle='font-size:11.0pt'><ahref="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><liclass=MsoNormalstyle='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l3 level1 lfo5;tab-stops:list 36.0pt'><spanlang=EN-USstyle='font-size:11.0pt'>ccops (for matrix spectral clustering after using
the omatrix2 options)<o:p></o:p></span></li></ul><pclass=MsoNormalstyle='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><divclass=MsoNormalalign=centerstyle='margin:0cm;margin-bottom:.0001pt;
text-align:center'><spanlang=EN-US><hrsize=2width="100%"align=center></span></div><h3><spanlang=EN-USstyle='font-size:14.0pt'>Mandatory arguments<o:p></o:p></span></h3><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>There are <b>three</b></span><spanlang=EN-USstyle='font-size:11.0pt'> compulsory arguments in probtrackx. Basically, the
algorithm needs to know the local <b>orientation distributions</b></span><spanlang=EN-USstyle='font-size:11.0pt'> (output of bedpostX), <b>the brain mask</b></span><spanlang=EN-USstyle='font-size:11.0pt'> (in order not to draw pathways outside it)
and a <b>seed region</b></span><spanlang=EN-USstyle='font-size:11.0pt'> for
the probabilistic tractography. <o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=basename></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span>-s <basename ><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>merged_th1samples<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>merged_th2samples<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>merged_ph1samples<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>merged_ph2samples<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>merged_f1samples<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>merged_f2samples<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><spanlang=EN-USstyle='font-size:11.0pt'><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt;tab-stops:187.0pt'><aname=mask></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span>-m <mask><spanstyle='mso-tab-count:1'> </span><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>This is a binary brain mask that can be computed with <ahref="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><spanlang=EN-USstyle='font-size:11.0pt'><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt;tab-stops:313.0pt'><aname=roi></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><aname=seed></a>-x <seed><spanstyle='mso-tab-count:1'> </span><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>x_1<spanstyle='mso-tab-count:1'> </span>y_1<spanstyle='mso-tab-count:1'> </span>z_1<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>x_2<spanstyle='mso-tab-count:1'> </span>y_2<spanstyle='mso-tab-count:1'> </span>z_2<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>…<spanstyle='mso-tab-count:1'> </span>…<spanstyle='mso-tab-count:1'> </span>…<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>x_n<spanstyle='mso-tab-count:1'> </span>y_n<spanstyle='mso-tab-count:1'> </span>z_n<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><spanlang=EN-USstyle='font-size:11.0pt'> and
–<b>xfm</b></span><spanlang=EN-USstyle='font-size:11.0pt'> options.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><divclass=MsoNormalalign=centerstyle='margin:0cm;margin-bottom:.0001pt;
text-align:center'><spanlang=EN-US><hrsize=2width="100%"align=center></span></div><h3><spanlang=EN-USstyle='font-size:14.0pt'>Optional arguments<o:p></o:p></span></h3><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:13.0pt'>*** Choose your mode ***<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=mode></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span>--mode=<chosenMode><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>You can run probtrackx on two different modes:<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>simple<spanstyle='mso-tab-count:2'> </span><spanstyle='mso-tab-count:1'> </span>:
In case the seed is a textfile with voxel coordinates.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>seedmask (default)<spanstyle='mso-tab-count:1'> </span>:
In case the seed is a 3D image file.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:13.0pt'>*** Choose your outputs ***<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=opd></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span>--opd<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>This option allows to output the pathway distribution
in <outputfile>. <o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=pd></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span>--pd=<n><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><n> is either 1 (default value) or 2.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>n=1<spanstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>n=2<spanstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=os2t></a><spanlang=EN-USstyle='font-size:12.0pt'>--</span><spanlang=EN-USstyle='font-size:
12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun:
yes"> </span>--os2t<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'>The output are of the form:<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>seed_to_target1<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>seed_to_target2<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>…<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:11.0pt'><b>seed_to_targetn<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>Running <ahref="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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=targetmasks></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--targetmasks=<filename><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><b><full_path_dir>/target_1<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><b><full_path_dir>/target_2<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><b>…<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><b><full_path_dir>/target_n<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><b><![if!supportEmptyParas]> <![endif]><o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=omatrix2></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>---omatrix2<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>This option allows to ouput a filename, called<b>
fdt_matrix2</b></span><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>For computational and storage reasons, <spanstyle="mso-spacerun: yes"> </span>we recommend to use a low resolution
brain mask, (e.g. 5x5x5 mm^3). <o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=lrmask></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--lrmask=<filename><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><filename> is a low resolution brain mask used
along with the –omatrix2 option.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>flirt –i seed_brain_mask –ref seed_brain_mask –applyisoxfm
5 –o lowresmask<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>avwmaths lowresmask –thr 0.5 –bin lowresmask<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=outputfile></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>-o <outputfile><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>This is the pathway probability distribution. By
default, this file is called fdt_paths.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>The pathway distribution is in the same space as the
seed mask.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=mask2></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--mask2=<filename><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><b>mask2 must be in the same space as the seed mask.<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=waypoints></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun:
yes"> </span>--waypoints=<filename><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><full_path_dir>/waypoints_1<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><full_path_dir>/waypoints_2<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>…<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><full_path_dir>/waypoints_n<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:13.0pt'>*** For registration ***<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=seedref></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--seedref=<filename><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><aname=xfm></a><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun:
yes"> </span>---xfm=<transformation><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>For example :<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>str2diff.mat if the seed space is the structural
image.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>std2diff.mat if the seed space is the standard space.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:13.0pt'>*** Miscellaneous arguments ***<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=verbose></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--verbose=<n><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=help></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--help<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>This prints out the help message providing a short
description of the different options.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=dir></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--dir=<directory><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=forcedir></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--forcedir<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><aname=rubbish></a><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--rubbish=<filename><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:13.0pt'>*** Expert mode parameters ***</span><spanlang=EN-USstyle='font-size:12.0pt'><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=nsamples></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--nsamples <n><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=cthr></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--cthr <n><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=nsteps></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--nsteps=<n><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=steplength></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--steplength=<n><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>Step between two successive steps during the
tractography. The default value is 0.5 voxels (of the seed space). <spanstyle="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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=loopcheck></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--loopcheck<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=usef></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--usef<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=randfib></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--randfib<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><aname=modeeuler></a><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--modeuler<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt;font-family:Symbol'>·</span><aname=rseed></a><spanlang=EN-USstyle='font-size:12.0pt'><spanstyle="mso-spacerun: yes"> </span><spanstyle="mso-spacerun: yes"> </span>--rseed<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><divclass=MsoNormalalign=centerstyle='margin:0cm;margin-bottom:.0001pt;
text-align:center'><spanlang=EN-US><hrsize=2width="100%"align=center></span></div><h3><spanlang=EN-USstyle='font-size:14.0pt'>Command line examples<o:p></o:p></span></h3><pclass=MsoNormalstyle='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'><aname=question1></a><![if!supportLists]><spanlang=EN-USstyle='font-size:13.0pt;font-family:Symbol'>·<spanstyle='font:7.0pt "Times New Roman"'> </span></span><![endif]><spanlang=EN-USstyle='font-size:13.0pt'><b>I want to
see all the tracts that go from my seed <spanstyle="mso-spacerun:
yes"> </span>to the rest of the brain<o:p></o:p></b></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>probtrackx <ahref="#basename">–s <subject>.bedpostX/merged</a><ahref="#mask">–m <subject>.bedpostX/nodif_brain_mask</a><ahref="#seed">–x
seed_mask</a> --<ahref="#opd">opd</a><ahref="#pd">--pd=1</a><ahref="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>Below is the result with a seed in the internal
capsule.<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='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'><aname=question2></a><![if!supportLists]><spanlang=EN-USstyle='font-size:13.0pt;font-family:Symbol'>·<spanstyle='font:7.0pt "Times New Roman"'> </span></span><![endif]><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>probtrackx <ahref="#basename">–s <subject>.bedpostX/merged</a><ahref="#mask">–m <subject>.bedpostX/nodif_brain_mask</a><ahref="#seed">–x
seed_mask</a><ahref="#waypoints">--waypoints=<listOfWaypoints></a> --<ahref="#opd">opd</a><ahref="#pd">--pd=1</a><ahref="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='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'><aname=question3></a><![if!supportLists]><spanlang=EN-USstyle='font-size:13.0pt;font-family:Symbol'>·<spanstyle='font:7.0pt "Times New Roman"'> </span></span><![endif]><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>probtrackx <ahref="#basename">–s <subject>.bedpostX/merged</a><ahref="#mask">–m <subject>.bedpostX/nodif_brain_mask</a><ahref="#seed">–x
seed_mask</a><ahref="#seedref">--seedref=struct</a><ahref="#xfm">--xfm=<subject>.bedpostX/xfms/str2diff.mat</a>]<ahref="#opd">--opd</a><ahref="#pd">--pd=1</a><ahref="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='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'><aname=question4></a><![if!supportLists]><spanlang=EN-USstyle='font-size:13.0pt;font-family:Symbol'>·<spanstyle='font:7.0pt "Times New Roman"'> </span></span><![endif]><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:13.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:13.0pt'>A typical command for doing that is:<o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:13.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>probtrackx <ahref="#basename">–s <subject>.bedpostX/merged</a><ahref="#mask">–m <subject>.bedpostX/nodif_brain_mask</a><ahref="#seed">–x
seed_mask</a><spanstyle="mso-spacerun: yes"> </span><ahref="#os2t">--os2t</a><ahref="#targetmasks">--targetmasks=<listOfTargets></a><ahref="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='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]><spanlang=EN-USstyle='font-size:
13.0pt;font-family:Symbol'>·<spanstyle='font:7.0pt "Times New Roman"'> </span></span><![endif]><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='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><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-USstyle='font-size:12.0pt'>probtrackx <ahref="#basename">–s <subject>.bedpostX/merged</a><ahref="#mask">–m <subject>.bedpostX/nodif_brain_mask</a><ahref="#mask">–s
seed_mask</a><spanstyle="mso-spacerun: yes"> </span><ahref="#omatrix2">--omatrix2</a><ahref="#dir">--dir=<subject>.probtrackx</a><ahref="#lrmask">--lrmask=lowres_mask</a><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><pclass=MsoNormalstyle='margin:0cm;margin-bottom:.0001pt'><spanlang=EN-US><![if!supportEmptyParas]> <![endif]><o:p></o:p></span></p><p><spanlang=EN-US><spanstyle="mso-spacerun: yes"> </span><o:p></o:p></span></p></div></body></html>
