diff --git a/bedpost_datacheck b/bedpost_datacheck
index 24604233827afe4e214bf56f389de2e6749c0e47..25d654cd5f955ce2b987947a0d4ac8752b722b0f 100755
--- a/bedpost_datacheck
+++ b/bedpost_datacheck
@@ -9,7 +9,7 @@ DIR=$1;
for img in ${DIR}/data ${DIR}/nodif ${DIR}/nodif_brain_mask ;do
if [ `${FSLDIR}/bin/imtest $img` -eq 1 ] ; then
echo $img
- ${FSLDIR}/bin/avwinfo $img;
+ ${FSLDIR}/bin/fslinfo $img;
echo ""
else
echo $img does not exist;
@@ -25,14 +25,14 @@ done
if [ `${FSLDIR}/bin/imtest ${DIR}/data` -eq 1 -a `${FSLDIR}/bin/imtest ${DIR}/nodif_brain_mask` -eq 1 ];then
- dx=`${FSLDIR}/bin/avwval ${DIR}/data dim1`
- dy=`${FSLDIR}/bin/avwval ${DIR}/data dim2`
- dz=`${FSLDIR}/bin/avwval ${DIR}/data dim3`
- dt=`${FSLDIR}/bin/avwval ${DIR}/data dim4`
+ dx=`${FSLDIR}/bin/fslval ${DIR}/data dim1`
+ dy=`${FSLDIR}/bin/fslval ${DIR}/data dim2`
+ dz=`${FSLDIR}/bin/fslval ${DIR}/data dim3`
+ dt=`${FSLDIR}/bin/fslval ${DIR}/data dim4`
- nbmx=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim1`
- nbmy=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim2`
- nbmz=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim3`
+ nbmx=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim1`
+ nbmy=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim2`
+ nbmz=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim3`
if [ $dx -ne $nbmx -o $dy -ne $nbmy -o $dz -ne $nbmz ];then
diff --git a/bedpostx b/bedpostx
index b8b7306694d4d1baaeb7bdfe963bffe9004ec84b..ed404f182da3e71dfdf6653085171ca73dd63853 100755
--- a/bedpostx
+++ b/bedpostx
@@ -106,7 +106,7 @@ echo Queuing preprocessing stages
preprocid=`${FSLDIR}/bin/fsl_sub -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostX_preproc.sh ${subjdir}`
echo Queuing parallel processing stage
-nslices=`${FSLDIR}/bin/avwval ${subjdir}/data dim3`
+nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
for ((slice=0; slice < $nslices; slice++)) ; do
echo "${FSLDIR}/bin/bedpostX_single_slice.sh $subjdir $nfibres $fudge $burnin $slice" \
diff --git a/bedpostx_postproc.sh b/bedpostx_postproc.sh
index a8659b26fcbb0c016fd1863c7cf929d9d26964b7..c96ab81f697c09a3b9077a7c2ed77e6fc983a115 100755
--- a/bedpostx_postproc.sh
+++ b/bedpostx_postproc.sh
@@ -12,12 +12,12 @@ subjdir=$1
numfib=`${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples | wc -w | awk '{print $1}'`
for ((fib=1; fib<=$numfib; fib++));do
- ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
- ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
- ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
- ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
- ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
- ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
+ ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
+ ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
+ ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
+ ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
+ ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
+ ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpostX/merged_th${fib}samples ${subjdir}.bedpostX/merged_ph${fib}samples ${subjdir}.bedpostX/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}
done
diff --git a/bedpostx_preproc.sh b/bedpostx_preproc.sh
index 1bf5a061c25f84bf92db9e841eceab554c49c621..bdae3469c68f2c6083e739e8e6a7f48c66a3cfc0 100755
--- a/bedpostx_preproc.sh
+++ b/bedpostx_preproc.sh
@@ -12,11 +12,11 @@ subjdir=$1
echo Copying files to bedpost directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
-${FSLDIR}/bin/avwmaths\
+${FSLDIR}/bin/fslmaths\
${subjdir}/nodif\
-mas ${subjdir}/nodif_brain_mask\
${subjdir}.bedpostX/nodif_brain
-${FSLDIR}/bin/avwslice ${subjdir}/data
-${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
+${FSLDIR}/bin/fslslice ${subjdir}/data
+${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask
echo Done
diff --git a/correct_and_average b/correct_and_average
index 1891b78d1c98d6142414cf39f40741acc80f975f..2a9898ffb22b2279aeb099cdb6105d189b384f52 100755
--- a/correct_and_average
+++ b/correct_and_average
@@ -38,10 +38,10 @@ b0_numbers=`cat $avgfile |grep -v '^ *$' |sed -n "${numlines}p"`;
ab0=`echo $b0_numbers |awk '{print \$1}'`
eddy_correct ${1} ${$}${1}_b0_correct $ab0
-total_vols=`avwval $1 dim4`;
+total_vols=`fslval $1 dim4`;
vols_per_avg=`echo "10k $total_vols $numavgs / p"|dc -`;
-avwroi ${1} data 0 ${vols_per_avg};
-avwmaths data -mul 0 data;
+fslroi ${1} data 0 ${vols_per_avg};
+fslmaths data -mul 0 data;
avg=1;scan=1;
@@ -54,15 +54,15 @@ while [ ${avg} -le ${numavgs} ]; do
echo $avg $scan $tmp $vols_per_avg
- avwroi ${$}${1}_b0_correct ${$}avg_${avg}_scan_${scan} $tmp;
+ fslroi ${$}${1}_b0_correct ${$}avg_${avg}_scan_${scan} $tmp;
scan=`expr $scan + 1`;
done
- avwmerge -t ${$}avg_${avg}_all `imglob -oneperimage ${$}avg_${avg}_scan_*`
- avwmaths data -add ${$}avg_${avg}_all data;
+ fslmerge -t ${$}avg_${avg}_all `imglob -oneperimage ${$}avg_${avg}_scan_*`
+ fslmaths data -add ${$}avg_${avg}_all data;
avg=`expr $avg + 1`;
done
-avwmaths data -div ${numavgs} data;
+fslmaths data -div ${numavgs} data;
rm ${$}*
diff --git a/doc/fdt_probtrackx.htm b/doc/fdt_probtrackx.htm
index 34080bdb84f58a31c198099104347eff2c0f1578..555b4895a1a4e929498cda8439b55e8201b50344 100644
--- a/doc/fdt_probtrackx.htm
+++ b/doc/fdt_probtrackx.htm
@@ -1 +1 @@
-<html xmlns:v="urn:schemas-microsoft-com:vml"
xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:w="urn:schemas-microsoft-com:office:word"
xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta name=Title content="FDT - FMRIB's Diffusion Toolbox - User Guide">
<meta name=Keywords content="">
<meta http-equiv=Content-Type content="text/html; charset=utf-8">
<meta name=ProgId content=Word.Document>
<meta name=Generator content="Microsoft Word 11">
<meta name=Originator content="Microsoft Word 11">
<link rel=File-List href="fdt_probtrackx_files/filelist.xml">
<link rel=Edit-Time-Data href="fdt_probtrackx_files/editdata.mso">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]-->
<title>FDT - FMRIB's Diffusion Toolbox - User Guide</title>
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Author>Saad Jbabdi</o:Author>
<o:Template>Normal</o:Template>
<o:LastAuthor>Saad Jbabdi</o:LastAuthor>
<o:Revision>14</o:Revision>
<o:Created>2007-05-01T12:19:00Z</o:Created>
<o:LastSaved>2007-05-01T12:41:00Z</o:LastSaved>
<o:Pages>4</o:Pages>
<o:Words>2419</o:Words>
<o:Characters>13789</o:Characters>
<o:Company>University of Oxford</o:Company>
<o:Lines>114</o:Lines>
<o:Paragraphs>27</o:Paragraphs>
<o:CharactersWithSpaces>16933</o:CharactersWithSpaces>
<o:Version>11.768</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Times New Roman";
panose-1:0 2 2 6 3 5 4 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Arial;
panose-1:0 2 11 6 4 2 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Courier New";
panose-1:0 2 7 3 9 2 2 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Geneva;
panose-1:0 2 11 5 3 3 4 4 4 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Tms Rmn";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Helv;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:swiss;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"MS Serif";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"MS Sans Serif";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:swiss;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"New York";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:System;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:swiss;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Wingdings;
panose-1:0 5 2 1 2 1 8 4 8 7;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"ï¼ï¼³ 明æœ";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:바탕;
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:宋体;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:新細明體;
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"ï¼ï¼³ ゴシック";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:Century;
panose-1:0 2 4 6 4 5 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Verdana;
panose-1:0 2 11 6 4 3 5 4 4 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Tahoma;
panose-1:0 2 11 6 4 3 5 4 4 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Monotype Sorts";
panose-1:0 1 1 6 1 1 1 1 1 1;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:Batang;
mso-font-alt:바탕;
mso-font-charset:129;
mso-generic-font-family:roman;
mso-font-pitch:variable;
mso-font-signature:-1342176593 1775729915 48 0 524447 0;}
@font-face
{font-family:"Lucida Grande";
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Abadi MT Condensed Extra Bold";
panose-1:0 2 11 10 6 3 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Abadi MT Condensed Light";
panose-1:0 2 11 3 6 3 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Academy Engraved LET";
panose-1:0 2 0 0 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"American Typewriter";
panose-1:0 2 9 6 4 2 0 4 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"American Typewriter Condensed";
panose-1:0 2 9 6 6 2 0 4 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"American Typewriter Light";
panose-1:0 2 9 3 4 2 0 4 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Andale Mono";
panose-1:0 2 11 5 9 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Apple Chancery";
panose-1:0 3 2 7 2 4 5 6 6 5;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Arial Black";
panose-1:0 2 11 10 4 2 1 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Arial Narrow";
panose-1:0 2 11 5 6 2 2 2 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Arial Rounded MT Bold";
panose-1:0 2 15 7 4 3 5 4 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bank Gothic";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Baskerville;
panose-1:0 2 2 5 2 7 4 1 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Baskerville Old Face";
panose-1:0 2 2 6 2 8 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Baskerville Semibold";
panose-1:0 2 2 7 2 7 4 0 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bauhaus 93";
panose-1:0 4 3 9 5 2 11 2 2 12;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bell MT";
panose-1:0 2 2 5 3 6 3 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bernard MT Condensed";
panose-1:0 2 5 8 6 6 9 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Big Caslon";
panose-1:0 2 0 6 3 9 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Blackmoor LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"BlairMdITC TT-Medium";
panose-1:0 0 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni Ornaments ITC TT";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo ITC TT-Bold";
panose-1:0 0 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo ITC TT-Book";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo ITC TT-BookIta";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo OS ITC TT-Bold";
panose-1:0 0 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo OS ITC TT-Book";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo OS ITC TT-BookIt";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo SC ITC TT-Book";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Book Antiqua";
panose-1:0 2 4 6 2 5 3 5 3 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bookman Old Style";
panose-1:0 2 5 6 4 5 5 5 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bordeaux Roman Bold LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bradley Hand ITC TT-Bold";
panose-1:0 0 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Braggadocio;
panose-1:0 4 3 11 7 13 11 2 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Britannic Bold";
panose-1:0 2 11 9 3 6 7 3 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Brush Script MT";
panose-1:0 3 6 8 2 4 4 6 7 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Calisto MT";
panose-1:0 2 4 6 3 5 5 5 3 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Century Gothic";
panose-1:0 2 11 5 2 2 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Century Schoolbook";
panose-1:0 2 4 6 4 5 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Chalkboard;
panose-1:0 3 5 6 2 4 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Chalkboard Bold";
panose-1:0 3 5 6 2 4 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Cochin;
panose-1:0 2 0 6 3 2 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Colonna MT";
panose-1:0 4 2 8 5 6 2 2 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Comic Sans MS";
panose-1:0 3 15 7 2 3 3 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Cooper Black";
panose-1:0 2 8 9 4 4 3 11 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Copperplate;
panose-1:0 2 0 5 4 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Copperplate Gothic Bold";
panose-1:0 2 14 7 5 2 2 6 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Copperplate Gothic Light";
panose-1:0 2 14 5 7 2 2 6 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Copperplate Light";
panose-1:0 2 0 6 4 3 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Cracked;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Curlz MT";
panose-1:0 4 4 4 4 5 7 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Desdemona;
panose-1:0 4 2 5 5 2 14 3 4 5;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Didot;
panose-1:0 2 0 5 3 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Edwardian Script ITC";
panose-1:0 3 3 3 2 4 7 7 13 8;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Engravers MT";
panose-1:0 2 9 7 7 8 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Euclid;
panose-1:0 2 2 5 3 6 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Extra";
panose-1:0 2 5 5 2 0 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Fraktur";
panose-1:0 3 1 6 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Math One";
panose-1:0 5 5 6 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Math Two";
panose-1:0 2 5 6 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Symbol";
panose-1:0 2 5 1 2 1 7 6 2 5;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euphemia UCAS";
panose-1:0 2 11 5 3 4 1 2 2 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euphemia UCAS Bold";
panose-1:0 2 11 8 3 4 1 2 2 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euphemia UCAS Italic";
panose-1:0 2 11 5 3 4 1 2 2 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Eurostile;
panose-1:0 2 11 5 4 2 2 2 5 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Footlight MT Light";
panose-1:0 2 4 6 2 6 3 10 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Futura;
panose-1:0 2 11 6 2 2 2 4 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Futura Condensed";
panose-1:0 2 11 5 6 2 2 4 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Garamond;
panose-1:0 2 2 4 4 3 3 1 1 8;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Geeza Pro";
panose-1:0 2 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Geeza Pro Bold";
panose-1:0 2 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Georgia;
panose-1:0 2 4 5 2 5 4 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Gill Sans";
panose-1:0 2 11 5 2 2 1 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Gill Sans Light";
panose-1:0 2 11 3 2 2 1 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Gill Sans Ultra Bold";
panose-1:0 2 11 10 2 2 1 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Gloucester MT Extra Condensed";
panose-1:0 2 3 8 8 2 6 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Goudy Old Style";
panose-1:0 2 2 5 2 5 3 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Guitar Pro 5";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Haettenschweiler;
panose-1:0 2 11 7 6 4 9 2 6 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Handwriting - Dakota";
panose-1:0 2 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Harrington;
panose-1:0 4 4 5 5 5 10 2 2 7;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue";
panose-1:0 2 0 5 3 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue Black Condensed";
panose-1:0 2 0 10 6 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue Bold Condensed";
panose-1:0 2 0 8 6 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue Light";
panose-1:0 2 0 4 3 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue UltraLight";
panose-1:0 2 0 2 6 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Herculanum;
panose-1:0 2 0 5 5 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Hoefler Text";
panose-1:0 2 3 6 2 5 5 6 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Hoefler Text Ornaments";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:Impact;
panose-1:0 2 11 8 6 3 9 2 5 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Imprint MT Shadow";
panose-1:0 4 2 6 5 6 3 3 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:InaiMathi;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Jazz LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Kino MT";
panose-1:0 4 3 7 5 13 12 2 2 7;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Blackletter";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Bright";
panose-1:0 2 4 6 2 5 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Calligraphy";
panose-1:0 3 1 1 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Fax";
panose-1:0 2 6 6 2 5 5 5 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Handwriting";
panose-1:0 3 1 1 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Sans";
panose-1:0 2 11 6 2 3 5 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Sans Typewriter";
panose-1:0 2 11 5 9 3 5 4 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Marker Felt";
panose-1:0 2 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Matura MT Script Capitals";
panose-1:0 3 2 8 2 6 6 2 7 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Mistral;
panose-1:0 3 9 7 2 3 4 7 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Modern No\. 20";
panose-1:0 2 7 7 4 7 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Mona Lisa Solid ITC TT";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Monaco;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Monotype Corsiva";
panose-1:0 3 1 1 1 1 2 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"MT Extra";
panose-1:0 5 5 1 2 1 2 5 2 2;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"News Gothic MT";
panose-1:0 2 11 5 4 2 2 3 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Onyx;
panose-1:0 4 5 6 2 8 7 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Optima;
panose-1:0 2 0 5 3 6 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Optima ExtraBlack";
panose-1:0 2 0 11 3 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Palatino;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Papyrus;
panose-1:0 2 11 6 2 4 2 0 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Party LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Perpetua Titling MT";
panose-1:0 2 2 5 2 6 5 5 2 8;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Plantagenet Cherokee";
panose-1:0 2 2 0 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Playbill;
panose-1:0 4 5 6 3 10 6 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"PortagoITC TT";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Princetown LET";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Rockwell;
panose-1:0 2 6 6 3 2 2 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Rockwell Extra Bold";
panose-1:0 2 6 9 3 4 5 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Santa Fe LET";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Savoye LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"SchoolHouse Cursive B";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"SchoolHouse Printed A";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Skia;
panose-1:0 2 13 5 2 2 2 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Snell Roundhand";
panose-1:0 2 0 6 3 8 0 0 9 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Snell Roundhand Black";
panose-1:0 2 0 10 4 9 0 0 9 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Snell Roundhand Bold";
panose-1:0 2 0 8 3 9 0 0 9 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Stencil;
panose-1:0 4 4 9 5 13 8 2 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Stone Sans ITC TT-Bold";
panose-1:0 0 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Stone Sans ITC TT-Semi";
panose-1:0 0 0 6 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Stone Sans ITC TT-SemiIta";
panose-1:0 0 0 6 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Symbol Proportional BT";
panose-1:0 5 5 1 2 1 6 7 2 6;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Synchro LET";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Trebuchet MS";
panose-1:0 2 11 6 3 2 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Type Embellishments One LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Webdings;
panose-1:0 5 3 1 2 1 5 9 6 7;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"Wide Latin";
panose-1:0 2 10 10 7 5 5 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Wingdings 2";
panose-1:0 5 2 1 2 1 5 7 7 7;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"Wingdings 3";
panose-1:0 5 4 1 2 1 8 7 7 7;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"Zapf Dingbats";
panose-1:0 5 2 1 2 1 7 4 2 6;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:Zapfino;
panose-1:0 3 3 3 0 4 7 7 7 12;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Courier CE";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Geneva CE";
panose-1:0 2 11 5 3 3 4 4 4 2;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Helvetica CE";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:Krungthep;
panose-1:0 2 0 4 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Lucida Grande CE";
panose-1:0 2 11 6 0 4 5 2 2 2;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Monaco CE";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:Silom;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Times CE";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:Ayuthaya;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Charcoal CY";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Geneva CY";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Helvetica CY";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Lucida Grande CY";
panose-1:0 2 11 6 0 4 5 2 2 2;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Monaco CY";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:Sathu;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:Thonburi;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Times CY";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Apple LiGothic Medium";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"Apple LiSung Light";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:BiauKai;
panose-1:0 2 1 6 1 0 1 1 1 1;
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"儷宋 Pro";
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"儷黑 Pro";
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"GB18030 Bitmap";
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:Hei;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:Kai;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡ä»¿å®‹;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡é»‘体;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡æ¥·ä½“;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡å®‹ä½“;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡ç»†é»‘;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:"ï¼ï¼³ Ｐゴシック";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ï¼ï¼³ Ｐ明æœ";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:Osaka;
panose-1:0 2 11 6 0 0 0 0 0 0;
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:Osaka−ç‰å¹…;
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ヒラギノ角ゴ Pro W3";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ヒラギノ角ゴ Pro W6";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ヒラギノ角ゴ Std W8";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ヒラギノ丸ゴ Pro W4";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ãƒ’ãƒ©ã‚®ãƒŽæ˜Žæœ Pro W3";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ãƒ’ãƒ©ã‚®ãƒŽæ˜Žæœ Pro W6";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"\#PC명조";
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:"\#ê¶ì„œì²´";
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:"\#필기체";
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:"\#헤드ë¼ì¸A";
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:AppleGothic;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:AppleMyungjo;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:굴림;
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:TimesNewRomanPS-BoldMT;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:"Times New Roman";
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:TimesNewRomanPSMT;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:"Times New Roman";
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"MS Mincho";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:"ï¼ï¼³ 明æœ";
mso-font-charset:128;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:fixed;
mso-font-signature:1 134676480 16 0 131072 0;}
@font-face
{font-family:TimesNewRomanPS-ItalicMT;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:"Times New Roman";
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Times-Roman;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:Times;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331651 0 0 0 1 0;}
@font-face
{font-family:"MS PGothic";
mso-font-charset:128;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:Times-Italic;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:Times;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Times-Bold;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:Times;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:SimSun;
mso-font-alt:宋体;
mso-font-charset:134;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:3 135135232 16 0 262145 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-parent:"";
margin-right:0cm;
mso-margin-top-alt:auto;
mso-margin-bottom-alt:auto;
margin-left:0cm;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:Times;}
h3
{margin-right:0cm;
mso-margin-top-alt:auto;
mso-margin-bottom-alt:auto;
margin-left:0cm;
mso-pagination:widow-orphan;
mso-outline-level:3;
font-size:13.5pt;
font-family:Times;
font-weight:bold;}
h4
{margin-right:0cm;
mso-margin-top-alt:auto;
mso-margin-bottom-alt:auto;
margin-left:0cm;
mso-pagination:widow-orphan;
mso-outline-level:4;
font-size:12.0pt;
font-family:Times;
font-weight:bold;}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;
text-underline:single;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;
text-underline:single;}
p
{margin-right:0cm;
mso-margin-top-alt:auto;
mso-margin-bottom-alt:auto;
margin-left:0cm;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:Times;}
table.MsoNormalTable
{mso-style-parent:"";
font-size:10.0pt;
font-family:"Times New Roman";}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;
mso-header-margin:35.4pt;
mso-footer-margin:35.4pt;
mso-paper-source:0;}
div.Section1
{page:Section1;}
/* List Definitions */
@list l0
{mso-list-id:1984657773;
mso-list-type:hybrid;
mso-list-template-ids:956073462 67698689 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;}
@list l0:level1
{mso-level-number-format:bullet;
mso-level-text:ï‚·;
mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l1
{mso-list-id:2083598282;
mso-list-type:hybrid;
mso-list-template-ids:945746370 67698689 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;}
@list l1:level1
{mso-level-number-format:bullet;
mso-level-text:ï‚·;
mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1033"/>
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1"/>
</o:shapelayout></xml><![endif]-->
</head>
<body bgcolor=white background="fdt_images/fsl-bg.jpg" lang=EN-GB link=blue
vlink=blue style='tab-interval:36.0pt'>
<div class=Section1>
<h3><span lang=EN-US style='font-size:14.0pt'>PROBTRACKX - probabilistic
tracking with crossing fibres<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><br>
</span><span lang=EN-US style='font-size:11.0pt'>For details about
probabilistic tractography as implemented by FDT, look <a
href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">here</a>.
Briefly, FDT repetitively samples from the distributions on voxel-wise
diffusion directions, each time computing a streamline through these local
samples to generate a <em>probabilistic streamline</em> or a <em>sample</em>
from the distribution on the location of the true streamline. By taking many
such samples FDT is able to build up the posterior distribution on the
streamline location or the <em>connectivity distribution</em>. The major
difference with <a href="http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_probtrack.html">Probtrack</a>
is that the local samples have a more complex distribution. They can model
different diffusion directions, allowing to track finer pathways and resolve
crossing fibres in regions with complex fibre architecture. <o:p></o:p></span></p>
<p><span lang=EN-US style='font-size:11.0pt'>After BedpostX has been applied it
is possible to run tractography analyses using probtrackx.</span><span
lang=EN-US> Note that probtrackx can also be run after bedpost. In that case,
probtrackx simply samples from the single fibre orientation given by bedpost.<o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Using probtrackx in command line<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Probtrackx requires a set of mandatory arguments. The
optional arguments allow further specifications. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Below is a command for probtrackx with all possible arguments.
The bold faced arguments are mandatory. Click on each argument to have a
precise description. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>probtrackx<b> <span style='mso-tab-count:1'> </span>-s
<<a href="#basename">basename</a>> <span style='mso-tab-count:1'> </span>-m
<<a href="#mask">mask</a>> <span style='mso-tab-count:1'> </span>-x
<<a href="#seed">seed</a>></b></span><span lang=EN-US style='font-size:
11.0pt'> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--mode=<<a href="#mode">chosenMode</a>> <span
style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#opd">opd </a><span style="mso-spacerun:
yes"> </span><span style="mso-spacerun: yes"> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#os2t">os2t</a> <span style='mso-tab-count:
1'> </span>--targetmasks=<<a href="#targetmasks">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#omatrix2">omatrix2</a> <span
style='mso-tab-count:1'> </span>--lrmask=<<a
href="#lrmask">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>-o <<a href="#outputfile">outputfile</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--network<o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--waypoints=<<a href="#waypoints">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--seedref=<<a href="#seedref">filename</a>> <span
style='mso-tab-count:1'> </span>--xfm=<<a href="#xfm">transformation</a>>
<o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--dir=<<a href="#dir">directory</a>> <span
style='mso-tab-count:1'> </span>--<a
href="#forcedir">forcedir</a> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--stop=<<a href="#stop">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--avoid=<<a href="#rubbish">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'><a href="#nsamples">--nsamples=<n></a> <a
href="#cthr">--cthr=<n></a> <a href="#steplength">--steplength=<n></a>
--<a href="#loopcheck">loopcheck</a> --<a href="#usef">usef</a> --<a
href="#randfib">randfib</a> --<a href="#modeeuler">modeuler</a> --<a
href="#rseed">rseed</a> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#verbose">verbose</a> --<a href="#help">help</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Below you can find a few typical command lines.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<ul style='margin-top:0cm' type=disc>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question1">I want to see all the tracts
that go from my ROI<span style="mso-spacerun: yes"> </span>to the
rest of the brain</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question2">I want to use the high
resolution structural image (or the standard space image) to draw my ROIs</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question3">I want to segment an ROI
depending on its connections with another set of ROIs</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question4">I want to segment an ROI
into different parts having different connections with the rest of the
brain</a> <o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US style='font-size:
11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US style='font-size:
11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The output of probtrackx can be analysed further with:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<ul style='margin-top:0cm' type=disc>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l1 level1 lfo6;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:11.0pt'><a
href="http://www.fmrib.ox.ac.uk/fsl/fdt/find_the_biggest.html">find_the_biggest</a>
(for seed2target classification)<o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l1 level1 lfo6;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:11.0pt'>ccops (for matrix spectral clustering after using
the omatrix2 options)<o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Mandatory arguments<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>There are <b>three</b></span><span lang=EN-US
style='font-size:11.0pt'> compulsory arguments in probtrackx. Basically, the
algorithm needs to know the local <b>orientation distributions</b></span><span
lang=EN-US style='font-size:11.0pt'> (output of bedpostX), <b>the brain mask</b></span><span
lang=EN-US style='font-size:11.0pt'> (in order not to draw pathways outside it)
and a <b>seed region</b></span><span lang=EN-US style='font-size:11.0pt'> for
the probabilistic tractography. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=basename></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>-s <basename ><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><basename> is the prefix of the file containing
the orientation distribution given by bedpostX, which in general are of the
form (in the case of two fibres per voxel):<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_th1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_th2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_ph1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_ph2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_f1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_f2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>If the path to the directory where these files are
stored is <pathdir>, then the basename is <b><pathdir>/merged.</b></span><span
lang=EN-US style='font-size:11.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt;tab-stops:187.0pt'><a
name=mask></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>-m <mask><span style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Binary brain mask that can be computed with <a
href="http://www.fmrib.ox.ac.uk/fsl/bet">bet</a>. This mask MUST BE IN THE
DIFFUSION SPACE (i.e. same as the diffusion data). Usually, it is computed from
the nodif image, and is named <b>nodif_brain_mask.</b></span><span lang=EN-US
style='font-size:11.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt;tab-stops:313.0pt'><a
name=roi></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span><a name=seed></a>-x <seed> <span style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Region of the brain which serves as a seed for the
tractography. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>When using the simple <a href="#mode">mode</a>,
<seed> is a textfile with the coordinates of the seed voxels stored as
follows :<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_1<span style='mso-tab-count:1'> </span>y_1<span
style='mso-tab-count:1'> </span>z_1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_2<span style='mso-tab-count:1'> </span>y_2<span
style='mso-tab-count:1'> </span>z_2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>…<span style='mso-tab-count:1'> </span>…<span
style='mso-tab-count:1'> </span>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_n<span style='mso-tab-count:1'> </span>y_n<span
style='mso-tab-count:1'> </span>z_n<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>When using seedmask mode, <seed> is a 3D image
with non-zero values inside the seed voxels. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><seed> can also be a text file with multiple
seed volumes:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdir1/volume1.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdir2/volume2.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>…<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdirk/volumek.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The program will then compute all the pathways
connecting any pair of brain regions defined in the network. The option --network
must be turned on in this case.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>In all cases (text file or image file), you can use
either the diffusion space, or another space (e.g. structural, standard
spaces), provided the –<b><a href="#seedref">seedref</a></b></span><span
lang=EN-US style='font-size:11.0pt'> and –<b><a href="#xfm">xfm</a></b></span><span
lang=EN-US style='font-size:11.0pt'> options.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Optional arguments<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Choose your mode ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=mode></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--mode=<chosenMode><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>You can run probtrackx in two different modes:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>simple<span style='mso-tab-count:3'> </span>:
In case the seed is a textfile with voxel coordinates.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>seedmask (default)<span style='mso-tab-count:1'> </span>:
In case the seed is a 3D image file (or ascii file of multiple 3D image files)<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US>The
voxel coordinates as well as the seedmask can be in a different space than the
diffusion space (e.g. high resolution structural space or standard space),
provided the transformation that goes from this space to the diffusion space
(see the options --<a href="#seedref">seedref</a> and --<a href="#xfm">xfm</a>).</span><span
style='mso-ansi-language:EN-GB'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Choose your outputs ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=opd></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--opd<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>This option allows to output the pathway distribution
in <outputfile>. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=pd></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--pd<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Activate the distance correction option. : The output pathway
distribution is the sum of the lengths of the pathways that cross each voxel.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=os2t></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--os2t<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>This option allows to output the probability that each
individual voxel in the seed mask is connected to each of the target masks
(provided a target mask list).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The output are of the form:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_target1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_target2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_targetn<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Each of these files is a volume with non-zero values
only within the seed mask. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The value in each voxel of seed_to_target1 within the
seed mask is the number of tracts seeded from this voxel that arrived at
target1.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Running <a
href="http://www.fmrib.ox.ac.uk/fsl/fdt/find_the_biggest">find_the_biggest</a>
on these outputs gives a segmentation of the seed mask into parts connected to
the different targets.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a
name=targetmasks></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--targetmasks=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is either a 3D file with one target
mask, or a text file containing a list of target masks (with the full path) as
following:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/target1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/target2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/targetn<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><![if !supportEmptyParas]> <![endif]><o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=omatrix2></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>---omatrix2<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This option allows to ouput a filename, called<b>
fdt_matrix2</b></span><span lang=EN-US style='font-size:12.0pt'>, which is a
NxP matrix, where N is the number of voxels in the seed mask, and P is the
number of voxels in the rest of the brain mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The values stored in this matrix represent the
probability that each voxel in the seed mask is connected with each voxel of
the rest of the brain. This value depends on the choice of the option --<a
href="#pd">pd</a>.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This matrix is useful for seed classification based on
connectivity profile with the spectral reordering tool : ccops.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For computational and storage reasons, we recommend to
use a low resolution brain mask, (e.g. 5x5x5 mm^3). <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=lrmask></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--lrmask=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is a low resolution brain mask used
along with the --omatrix2 option<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>To create a low resolution mask, take a whole brain mask
(e.g. using bet), of the same image as the one on which the seeds have been
drawn, and subsample it with the command:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>flirt –i seed_brain_mask –ref seed_brain_mask
–applyisoxfm 5 –o lowresmask<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>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><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=outputfile></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>-o <outputfile><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This is the pathway probability distribution. By
default, this file is called fdt_paths.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The pathway distribution is in the same space as the
seed mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=mask2></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--mask2=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Add this option if you want to draw all the pathways
that go from the seed mask to a second region (drawn in mask2), and all the
pathways that go from this second region to the seed region.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>mask2 must be in the same space as the seed mask.<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=waypoints></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--waypoints=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Add this option if you want to track only the pathways
that happen to cross a (or a set of) region(s) in the brain. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is either a 3D file with a region
mask, or a text file with a list of 3D region masks along with their full path
as follows:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_1<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_2<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>…<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_n<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>The waypoint masks must all be in the same space as
the seed mask<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** For registration ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>When the seed mask is not in the diffusion space (i.e.
ROIs were drawn on the structural image, or in the standard space, coming from
FMRI group activation or some template), you must provide probtrackx with a <b>reference
image</b></span><span lang=EN-US style='font-size:12.0pt'> and a <b>transformation</b></span><span
lang=EN-US style='font-size:12.0pt'>.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=seedref></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--seedref=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is the name of an image in the same
space as the seed mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For example, struct_brain (if the seed space is the
structural space), or standard (if the seed space is the standard space).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=xfm></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>---xfm=<transformation><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><transformation> is a text file containing the
transformation matrix (as computed by <a
href="http://www.fmrib.ox.ac.uk/fsl/flirt">flirt</a>) from the seed space to
the diffusion space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For example :<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>str2diff.mat if the seed space is the structural
image.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>std2diff.mat if the seed space is the standard space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Miscellaneous arguments ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=verbose></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--verbose=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><n> varies from 0 (very few ouput comments) to 2
(a lot of comments) during the execution of probtrackx.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=help></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--help<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This prints out the help message providing a short
description of the different options.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=dir></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--dir=<directory><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Name of the directory which will contain all the
outputs (fdt_paths, fdt_matrix2, seed_to_targets etc.)<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=forcedir></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--forcedir<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Overwrites the ouput directory if there is already one
having the same name. By default, probtrackx will add “+†to an already
existing one.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=rubbish></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--avoid=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use this option if you want to exclude from the
pathway distribution all those pathways that go into a given region.
<filename> is a 3D mask of this region. This option is opposite to
waypoints. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=stop></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--stop=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use this option if you want to stop the pathways when
they enter a given region. <filename> is a 3D mask of this region. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Expert mode parameters ***</span><span lang=EN-US
style='font-size:12.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=nsamples></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--nsamples=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Number of sample pathways drawn per voxel of the seed
mask. The default value is 5000. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=cthr></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--cthr=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Threshold value for the cosine of the angle between
two successive steps during the tractography. The default value is 0.2
(corresponding to an angle of 78 degrees).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=nsteps></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--nsteps=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Maximum number of steps (default=2000). Using a step
length of 0.5mm, this corresponds to a distance of 1m.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=steplength></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--steplength=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Length of each step during the tractography. The
default value is 0.5 voxels (of the seed space).<span style="mso-spacerun:
yes"> </span>You may want to change this value depending on the voxel
size, or if the tractography is performed on different sized brain (e.g.
infants or animals).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=loopcheck></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--loopcheck<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This option removes the tracts that make a loop, which
can happen as the tractography is probabilistic. It slows down a bit the
computations.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=usef></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--usef<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use this option if you want the fractional anisotropic
volumes (stored in merged_fsamples) to influence the tractography. The tracts
stop if the anisotropy is lower than a random variable between 0 (low
anisotropy) and 1 (high anisotropy).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=randfib></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--randfib<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Select randomly the different fibre directions when
starting the tractography at one seed voxel. By default, the tractography start
from the leading direction (the one with highest fractional volume inside the
seed voxel).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=modeeuler></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--modeuler<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use modified Euler integration instead of standard
Euler. This is more accurate, but slightly slower.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=rseed></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--rseed<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Random variable generator. By default, the value of this
variable is fixed, which means that when repeating an experiment with the same
data, one gets EXACTELY the same results. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Command line examples<o:p></o:p></span></h3>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question1></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
see all the tracts that go from my seed<span style="mso-spacerun: yes">
</span>to the rest of the brain<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>A typical command when one wants to draw all the
pathways (in terms of probability distribution) that run from the seed mask is:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a>
--<a href="#opd">opd</a> <a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Below is the result with a seed in the internal
capsule.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question2></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
see only the tracts that go from an ROI to another (set of) ROIs <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Sometimes, one is only interested in the pathways that
connect one region to one or several others. For example, one can have the
internal capsule as a seed mask, and ask for the pathways that go to M1 in the
hand area and the face area, as well as to the cerebral peduncle. Here is a
typical command using the waypoints option:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a> <a
href="#waypoints">--waypoints=<listOfWaypoints></a> --<a href="#opd">opd</a>
<a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Below is the result. Note that the resulting pathways
are a subgroup of the pathways drawn in the first example, which include only
those that reach the waypoints.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question3></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
use the high resolution structural image (or the standard space image) to draw
my ROIs<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Sometime, one needs to draw the seed mask in a high
resolution image (for example, to finely delineate some structure), or on a standard
space image (e.g. to use group activations as a common seed mask for a group of
subjects). Here is a typical command using the structural as a seed space. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Note that the resulting pathways are also in the seed
space, but all the computations are done in the diffusion space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a> <a
href="#seedref">--seedref=struct</a> <a href="#xfm">--xfm=<subject>.bedpostX/xfms/str2diff.mat</a>
<a href="#opd">--opd</a> <a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question4></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
segment an ROI depending on its connections with another set of ROIs <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>One can use probtrackx to know which part of the seed
mask is more probably connected to each target region within a list. For
example, which part of the internal capsule is connected to the hand area, and
which part is connected to the face area ? <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>A typical command for doing that is:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s <subject>.bedpostX/merged</a>
<a href="#mask">–m <subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x
seed_mask</a><span style="mso-spacerun: yes"> </span><a href="#os2t">--os2t</a>
<a href="#targetmasks">--targetmasks=<listOfTargets></a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
segment an ROI into different parts having different connections with the rest
of the brain <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>As for the SMA/preSMA study, one can ask whether the
seed region is composed of two ore more parts having different connections with
the rest of the brain, i.e. participating in different structural networks.
Probtrackx allows one to output a matrix composed of the values of the
connections between each voxel in the seed mask with the rest of the brain
(taken at a low resolution for computational reason). <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Once this matrix calculated, one can une a spectral
reordering command (ccops) to see whether there are two or more clusters within
the seed mask. Here is a typical command: <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#mask">–s seed_mask</a><span
style="mso-spacerun: yes"> </span><a href="#omatrix2">--omatrix2</a> <a
href="#dir">--dir=<subject>.probtrackx</a> <a href="#lrmask">--lrmask=lowres_mask</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p align=center style='text-align:center'><span lang=EN-US><!--[if gte vml 1]><v:shapetype
id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
<v:stroke joinstyle="miter"/>
<v:formulas>
<v:f eqn="if lineDrawn pixelLineWidth 0"/>
<v:f eqn="sum @0 1 0"/>
<v:f eqn="sum 0 0 @1"/>
<v:f eqn="prod @2 1 2"/>
<v:f eqn="prod @3 21600 pixelWidth"/>
<v:f eqn="prod @3 21600 pixelHeight"/>
<v:f eqn="sum @0 0 1"/>
<v:f eqn="prod @6 1 2"/>
<v:f eqn="prod @7 21600 pixelWidth"/>
<v:f eqn="sum @8 21600 0"/>
<v:f eqn="prod @7 21600 pixelHeight"/>
<v:f eqn="sum @10 21600 0"/>
</v:formulas>
<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
<o:lock v:ext="edit" aspectratio="t"/>
</v:shapetype><v:shape id="_x0000_i1029" type="#_x0000_t75" style='width:495pt;
height:388pt'>
<v:imagedata src="fdt_probtrackx_files/image001.gif" o:title="fdt_probtrackx"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=495 height=388
src="fdt_probtrackx_files/image002.jpg" v:shapes="_x0000_i1029"><![endif]><o:p></o:p></span></p>
</div>
</body>
</html>
\ No newline at end of file
+<html xmlns:v="urn:schemas-microsoft-com:vml"
xmlns:o="urn:schemas-microsoft-com:office:office"
xmlns:w="urn:schemas-microsoft-com:office:word"
xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta name=Title content="FDT - FMRIB's Diffusion Toolbox - User Guide">
<meta name=Keywords content="">
<meta http-equiv=Content-Type content="text/html; charset=utf-8">
<meta name=ProgId content=Word.Document>
<meta name=Generator content="Microsoft Word 11">
<meta name=Originator content="Microsoft Word 11">
<link rel=File-List href="fdt_probtrackx_files/filelist.xml">
<link rel=Edit-Time-Data href="fdt_probtrackx_files/editdata.mso">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]-->
<title>FDT - FMRIB's Diffusion Toolbox - User Guide</title>
<!--[if gte mso 9]><xml>
<o:DocumentProperties>
<o:Author>Saad Jbabdi</o:Author>
<o:Template>Normal</o:Template>
<o:LastAuthor>Saad Jbabdi</o:LastAuthor>
<o:Revision>14</o:Revision>
<o:Created>2007-05-01T12:19:00Z</o:Created>
<o:LastSaved>2007-05-01T12:41:00Z</o:LastSaved>
<o:Pages>4</o:Pages>
<o:Words>2419</o:Words>
<o:Characters>13789</o:Characters>
<o:Company>University of Oxford</o:Company>
<o:Lines>114</o:Lines>
<o:Paragraphs>27</o:Paragraphs>
<o:CharactersWithSpaces>16933</o:CharactersWithSpaces>
<o:Version>11.768</o:Version>
</o:DocumentProperties>
<o:OfficeDocumentSettings>
<o:AllowPNG/>
</o:OfficeDocumentSettings>
</xml><![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:"Times New Roman";
panose-1:0 2 2 6 3 5 4 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Arial;
panose-1:0 2 11 6 4 2 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Courier New";
panose-1:0 2 7 3 9 2 2 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Geneva;
panose-1:0 2 11 5 3 3 4 4 4 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Tms Rmn";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Helv;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:swiss;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"MS Serif";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"MS Sans Serif";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:swiss;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"New York";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:System;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:77;
mso-generic-font-family:swiss;
mso-font-format:other;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Wingdings;
panose-1:0 5 2 1 2 1 8 4 8 7;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"ï¼ï¼³ 明æœ";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:바탕;
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:宋体;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:新細明體;
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"ï¼ï¼³ ゴシック";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:Century;
panose-1:0 2 4 6 4 5 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Verdana;
panose-1:0 2 11 6 4 3 5 4 4 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Tahoma;
panose-1:0 2 11 6 4 3 5 4 4 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Monotype Sorts";
panose-1:0 1 1 6 1 1 1 1 1 1;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:Batang;
mso-font-alt:바탕;
mso-font-charset:129;
mso-generic-font-family:roman;
mso-font-pitch:variable;
mso-font-signature:-1342176593 1775729915 48 0 524447 0;}
@font-face
{font-family:"Lucida Grande";
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Abadi MT Condensed Extra Bold";
panose-1:0 2 11 10 6 3 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Abadi MT Condensed Light";
panose-1:0 2 11 3 6 3 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Academy Engraved LET";
panose-1:0 2 0 0 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"American Typewriter";
panose-1:0 2 9 6 4 2 0 4 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"American Typewriter Condensed";
panose-1:0 2 9 6 6 2 0 4 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"American Typewriter Light";
panose-1:0 2 9 3 4 2 0 4 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Andale Mono";
panose-1:0 2 11 5 9 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Apple Chancery";
panose-1:0 3 2 7 2 4 5 6 6 5;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Arial Black";
panose-1:0 2 11 10 4 2 1 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Arial Narrow";
panose-1:0 2 11 5 6 2 2 2 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Arial Rounded MT Bold";
panose-1:0 2 15 7 4 3 5 4 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bank Gothic";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Baskerville;
panose-1:0 2 2 5 2 7 4 1 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Baskerville Old Face";
panose-1:0 2 2 6 2 8 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Baskerville Semibold";
panose-1:0 2 2 7 2 7 4 0 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bauhaus 93";
panose-1:0 4 3 9 5 2 11 2 2 12;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bell MT";
panose-1:0 2 2 5 3 6 3 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bernard MT Condensed";
panose-1:0 2 5 8 6 6 9 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Big Caslon";
panose-1:0 2 0 6 3 9 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Blackmoor LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"BlairMdITC TT-Medium";
panose-1:0 0 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni Ornaments ITC TT";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo ITC TT-Bold";
panose-1:0 0 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo ITC TT-Book";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo ITC TT-BookIta";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo OS ITC TT-Bold";
panose-1:0 0 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo OS ITC TT-Book";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo OS ITC TT-BookIt";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bodoni SvtyTwo SC ITC TT-Book";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Book Antiqua";
panose-1:0 2 4 6 2 5 3 5 3 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bookman Old Style";
panose-1:0 2 5 6 4 5 5 5 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bordeaux Roman Bold LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Bradley Hand ITC TT-Bold";
panose-1:0 0 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Braggadocio;
panose-1:0 4 3 11 7 13 11 2 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Britannic Bold";
panose-1:0 2 11 9 3 6 7 3 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Brush Script MT";
panose-1:0 3 6 8 2 4 4 6 7 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Calisto MT";
panose-1:0 2 4 6 3 5 5 5 3 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Century Gothic";
panose-1:0 2 11 5 2 2 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Century Schoolbook";
panose-1:0 2 4 6 4 5 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Chalkboard;
panose-1:0 3 5 6 2 4 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Chalkboard Bold";
panose-1:0 3 5 6 2 4 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Cochin;
panose-1:0 2 0 6 3 2 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Colonna MT";
panose-1:0 4 2 8 5 6 2 2 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Comic Sans MS";
panose-1:0 3 15 7 2 3 3 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Cooper Black";
panose-1:0 2 8 9 4 4 3 11 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Copperplate;
panose-1:0 2 0 5 4 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Copperplate Gothic Bold";
panose-1:0 2 14 7 5 2 2 6 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Copperplate Gothic Light";
panose-1:0 2 14 5 7 2 2 6 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Copperplate Light";
panose-1:0 2 0 6 4 3 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Cracked;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Curlz MT";
panose-1:0 4 4 4 4 5 7 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Desdemona;
panose-1:0 4 2 5 5 2 14 3 4 5;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Didot;
panose-1:0 2 0 5 3 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Edwardian Script ITC";
panose-1:0 3 3 3 2 4 7 7 13 8;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Engravers MT";
panose-1:0 2 9 7 7 8 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Euclid;
panose-1:0 2 2 5 3 6 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Extra";
panose-1:0 2 5 5 2 0 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Fraktur";
panose-1:0 3 1 6 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Math One";
panose-1:0 5 5 6 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Math Two";
panose-1:0 2 5 6 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euclid Symbol";
panose-1:0 2 5 1 2 1 7 6 2 5;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euphemia UCAS";
panose-1:0 2 11 5 3 4 1 2 2 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euphemia UCAS Bold";
panose-1:0 2 11 8 3 4 1 2 2 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Euphemia UCAS Italic";
panose-1:0 2 11 5 3 4 1 2 2 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Eurostile;
panose-1:0 2 11 5 4 2 2 2 5 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Footlight MT Light";
panose-1:0 2 4 6 2 6 3 10 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Futura;
panose-1:0 2 11 6 2 2 2 4 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Futura Condensed";
panose-1:0 2 11 5 6 2 2 4 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Garamond;
panose-1:0 2 2 4 4 3 3 1 1 8;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Geeza Pro";
panose-1:0 2 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Geeza Pro Bold";
panose-1:0 2 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Georgia;
panose-1:0 2 4 5 2 5 4 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Gill Sans";
panose-1:0 2 11 5 2 2 1 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Gill Sans Light";
panose-1:0 2 11 3 2 2 1 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Gill Sans Ultra Bold";
panose-1:0 2 11 10 2 2 1 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Gloucester MT Extra Condensed";
panose-1:0 2 3 8 8 2 6 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Goudy Old Style";
panose-1:0 2 2 5 2 5 3 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Guitar Pro 5";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Haettenschweiler;
panose-1:0 2 11 7 6 4 9 2 6 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Handwriting - Dakota";
panose-1:0 2 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Harrington;
panose-1:0 4 4 5 5 5 10 2 2 7;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue";
panose-1:0 2 0 5 3 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue Black Condensed";
panose-1:0 2 0 10 6 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue Bold Condensed";
panose-1:0 2 0 8 6 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue Light";
panose-1:0 2 0 4 3 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Helvetica Neue UltraLight";
panose-1:0 2 0 2 6 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Herculanum;
panose-1:0 2 0 5 5 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Hoefler Text";
panose-1:0 2 3 6 2 5 5 6 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Hoefler Text Ornaments";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:Impact;
panose-1:0 2 11 8 6 3 9 2 5 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Imprint MT Shadow";
panose-1:0 4 2 6 5 6 3 3 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:InaiMathi;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Jazz LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Kino MT";
panose-1:0 4 3 7 5 13 12 2 2 7;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Blackletter";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Bright";
panose-1:0 2 4 6 2 5 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Calligraphy";
panose-1:0 3 1 1 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Fax";
panose-1:0 2 6 6 2 5 5 5 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Handwriting";
panose-1:0 3 1 1 1 1 1 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Sans";
panose-1:0 2 11 6 2 3 5 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Lucida Sans Typewriter";
panose-1:0 2 11 5 9 3 5 4 3 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Marker Felt";
panose-1:0 2 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Matura MT Script Capitals";
panose-1:0 3 2 8 2 6 6 2 7 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Mistral;
panose-1:0 3 9 7 2 3 4 7 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Modern No\. 20";
panose-1:0 2 7 7 4 7 5 5 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Mona Lisa Solid ITC TT";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Monaco;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Monotype Corsiva";
panose-1:0 3 1 1 1 1 2 1 1 1;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"MT Extra";
panose-1:0 5 5 1 2 1 2 5 2 2;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"News Gothic MT";
panose-1:0 2 11 5 4 2 2 3 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Onyx;
panose-1:0 4 5 6 2 8 7 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Optima;
panose-1:0 2 0 5 3 6 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Optima ExtraBlack";
panose-1:0 2 0 11 3 0 0 0 2 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Palatino;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Papyrus;
panose-1:0 2 11 6 2 4 2 0 2 3;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Party LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Perpetua Titling MT";
panose-1:0 2 2 5 2 6 5 5 2 8;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Plantagenet Cherokee";
panose-1:0 2 2 0 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Playbill;
panose-1:0 4 5 6 3 10 6 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"PortagoITC TT";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Princetown LET";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Rockwell;
panose-1:0 2 6 6 3 2 2 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Rockwell Extra Bold";
panose-1:0 2 6 9 3 4 5 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Santa Fe LET";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Savoye LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"SchoolHouse Cursive B";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"SchoolHouse Printed A";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Skia;
panose-1:0 2 13 5 2 2 2 4 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Snell Roundhand";
panose-1:0 2 0 6 3 8 0 0 9 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Snell Roundhand Black";
panose-1:0 2 0 10 4 9 0 0 9 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Snell Roundhand Bold";
panose-1:0 2 0 8 3 9 0 0 9 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Stencil;
panose-1:0 4 4 9 5 13 8 2 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Stone Sans ITC TT-Bold";
panose-1:0 0 0 7 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Stone Sans ITC TT-Semi";
panose-1:0 0 0 6 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Stone Sans ITC TT-SemiIta";
panose-1:0 0 0 6 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Symbol Proportional BT";
panose-1:0 5 5 1 2 1 6 7 2 6;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Synchro LET";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Trebuchet MS";
panose-1:0 2 11 6 3 2 2 2 2 2;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Type Embellishments One LET";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Webdings;
panose-1:0 5 3 1 2 1 5 9 6 7;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"Wide Latin";
panose-1:0 2 10 10 7 5 5 5 2 4;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Wingdings 2";
panose-1:0 5 2 1 2 1 5 7 7 7;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"Wingdings 3";
panose-1:0 5 4 1 2 1 8 7 7 7;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:"Zapf Dingbats";
panose-1:0 5 2 1 2 1 7 4 2 6;
mso-font-charset:2;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:0 0 256 0 -2147483648 0;}
@font-face
{font-family:Zapfino;
panose-1:0 3 3 3 0 4 7 7 7 12;
mso-font-charset:0;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"Courier CE";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Geneva CE";
panose-1:0 2 11 5 3 3 4 4 4 2;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Helvetica CE";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:Krungthep;
panose-1:0 2 0 4 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Lucida Grande CE";
panose-1:0 2 11 6 0 4 5 2 2 2;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Monaco CE";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:Silom;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:"Times CE";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:88;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:83886080 0 0 0 2 0;}
@font-face
{font-family:Ayuthaya;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Charcoal CY";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Geneva CY";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Helvetica CY";
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Lucida Grande CY";
panose-1:0 2 11 6 0 4 5 2 2 2;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Monaco CY";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:Sathu;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:Thonburi;
panose-1:0 0 0 4 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Times CY";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:89;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16908288 0 0 0 4 0;}
@font-face
{font-family:"Apple LiGothic Medium";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"Apple LiSung Light";
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:BiauKai;
panose-1:0 2 1 6 1 0 1 1 1 1;
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"儷宋 Pro";
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"儷黑 Pro";
mso-font-charset:81;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 134479873 0 1048576 0;}
@font-face
{font-family:"GB18030 Bitmap";
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:Hei;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:Kai;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡ä»¿å®‹;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡é»‘体;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡æ¥·ä½“;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡å®‹ä½“;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:åŽæ–‡ç»†é»‘;
mso-font-charset:80;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 235143169 0 262144 0;}
@font-face
{font-family:"ï¼ï¼³ Ｐゴシック";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ï¼ï¼³ Ｐ明æœ";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:Osaka;
panose-1:0 2 11 6 0 0 0 0 0 0;
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:Osaka−ç‰å¹…;
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ヒラギノ角ゴ Pro W3";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ヒラギノ角ゴ Pro W6";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ヒラギノ角ゴ Std W8";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ヒラギノ丸ゴ Pro W4";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ãƒ’ãƒ©ã‚®ãƒŽæ˜Žæœ Pro W3";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"ãƒ’ãƒ©ã‚®ãƒŽæ˜Žæœ Pro W6";
mso-font-charset:78;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:"\#PC명조";
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:"\#ê¶ì„œì²´";
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:"\#필기체";
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:"\#헤드ë¼ì¸A";
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:AppleGothic;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:AppleMyungjo;
panose-1:0 2 0 5 0 0 0 0 0 0;
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:굴림;
mso-font-charset:79;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 103022593 0 524288 0;}
@font-face
{font-family:TimesNewRomanPS-BoldMT;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:"Times New Roman";
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:TimesNewRomanPSMT;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:"Times New Roman";
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:"MS Mincho";
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:"ï¼ï¼³ 明æœ";
mso-font-charset:128;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:fixed;
mso-font-signature:1 134676480 16 0 131072 0;}
@font-face
{font-family:TimesNewRomanPS-ItalicMT;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:"Times New Roman";
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Times-Roman;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:Times;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331651 0 0 0 1 0;}
@font-face
{font-family:"MS PGothic";
mso-font-charset:128;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:16777216 0 117702657 0 131072 0;}
@font-face
{font-family:Times-Italic;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:Times;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:Times-Bold;
panose-1:0 0 0 0 0 0 0 0 0 0;
mso-font-alt:Times;
mso-font-charset:77;
mso-generic-font-family:roman;
mso-font-format:other;
mso-font-pitch:auto;
mso-font-signature:50331648 0 0 0 1 0;}
@font-face
{font-family:SimSun;
mso-font-alt:宋体;
mso-font-charset:134;
mso-generic-font-family:auto;
mso-font-pitch:variable;
mso-font-signature:3 135135232 16 0 262145 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{mso-style-parent:"";
margin-right:0cm;
mso-margin-top-alt:auto;
mso-margin-bottom-alt:auto;
margin-left:0cm;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:Times;}
h3
{margin-right:0cm;
mso-margin-top-alt:auto;
mso-margin-bottom-alt:auto;
margin-left:0cm;
mso-pagination:widow-orphan;
mso-outline-level:3;
font-size:13.5pt;
font-family:Times;
font-weight:bold;}
h4
{margin-right:0cm;
mso-margin-top-alt:auto;
mso-margin-bottom-alt:auto;
margin-left:0cm;
mso-pagination:widow-orphan;
mso-outline-level:4;
font-size:12.0pt;
font-family:Times;
font-weight:bold;}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;
text-underline:single;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;
text-underline:single;}
p
{margin-right:0cm;
mso-margin-top-alt:auto;
mso-margin-bottom-alt:auto;
margin-left:0cm;
mso-pagination:widow-orphan;
font-size:10.0pt;
font-family:Times;}
table.MsoNormalTable
{mso-style-parent:"";
font-size:10.0pt;
font-family:"Times New Roman";}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;
mso-header-margin:35.4pt;
mso-footer-margin:35.4pt;
mso-paper-source:0;}
div.Section1
{page:Section1;}
/* List Definitions */
@list l0
{mso-list-id:1984657773;
mso-list-type:hybrid;
mso-list-template-ids:956073462 67698689 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;}
@list l0:level1
{mso-level-number-format:bullet;
mso-level-text:ï‚·;
mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
@list l1
{mso-list-id:2083598282;
mso-list-type:hybrid;
mso-list-template-ids:945746370 67698689 67698691 67698693 67698689 67698691 67698693 67698689 67698691 67698693;}
@list l1:level1
{mso-level-number-format:bullet;
mso-level-text:ï‚·;
mso-level-tab-stop:36.0pt;
mso-level-number-position:left;
text-indent:-18.0pt;
font-family:Symbol;}
-->
</style>
<!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1033"/>
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1"/>
</o:shapelayout></xml><![endif]-->
</head>
<body bgcolor=white background="fdt_images/fsl-bg.jpg" lang=EN-GB link=blue
vlink=blue style='tab-interval:36.0pt'>
<div class=Section1>
<h3><span lang=EN-US style='font-size:14.0pt'>PROBTRACKX - probabilistic
tracking with crossing fibres<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><br>
</span><span lang=EN-US style='font-size:11.0pt'>For details about
probabilistic tractography as implemented by FDT, look <a
href="http://www.fmrib.ox.ac.uk/analysis/techrep/tr03tb1/tr03tb1/">here</a>.
Briefly, FDT repetitively samples from the distributions on voxel-wise
diffusion directions, each time computing a streamline through these local
samples to generate a <em>probabilistic streamline</em> or a <em>sample</em>
from the distribution on the location of the true streamline. By taking many
such samples FDT is able to build up the posterior distribution on the
streamline location or the <em>connectivity distribution</em>. The major
difference with <a href="http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_probtrack.html">Probtrack</a>
is that the local samples have a more complex distribution. They can model
different diffusion directions, allowing to track finer pathways and resolve
crossing fibres in regions with complex fibre architecture. <o:p></o:p></span></p>
<p><span lang=EN-US style='font-size:11.0pt'>After BedpostX has been applied it
is possible to run tractography analyses using probtrackx.</span><span
lang=EN-US> Note that probtrackx can also be run after bedpost. In that case,
probtrackx simply samples from the single fibre orientation given by bedpost.<o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Using probtrackx in command line<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Probtrackx requires a set of mandatory arguments. The
optional arguments allow further specifications. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Below is a command for probtrackx with all possible arguments.
The bold faced arguments are mandatory. Click on each argument to have a
precise description. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>probtrackx<b> <span style='mso-tab-count:1'> </span>-s
<<a href="#basename">basename</a>> <span style='mso-tab-count:1'> </span>-m
<<a href="#mask">mask</a>> <span style='mso-tab-count:1'> </span>-x
<<a href="#seed">seed</a>></b></span><span lang=EN-US style='font-size:
11.0pt'> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--mode=<<a href="#mode">chosenMode</a>> <span
style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#opd">opd </a><span style="mso-spacerun:
yes"> </span><span style="mso-spacerun: yes"> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#os2t">os2t</a> <span style='mso-tab-count:
1'> </span>--targetmasks=<<a href="#targetmasks">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#omatrix2">omatrix2</a> <span
style='mso-tab-count:1'> </span>--lrmask=<<a
href="#lrmask">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>-o <<a href="#outputfile">outputfile</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--network<o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--waypoints=<<a href="#waypoints">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--seedref=<<a href="#seedref">filename</a>> <span
style='mso-tab-count:1'> </span>--xfm=<<a href="#xfm">transformation</a>>
<o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--dir=<<a href="#dir">directory</a>> <span
style='mso-tab-count:1'> </span>--<a
href="#forcedir">forcedir</a> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--stop=<<a href="#stop">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--avoid=<<a href="#rubbish">filename</a>> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'><a href="#nsamples">--nsamples=<n></a> <a
href="#cthr">--cthr=<n></a> <a href="#steplength">--steplength=<n></a>
--<a href="#loopcheck">loopcheck</a> --<a href="#usef">usef</a> --<a
href="#randfib">randfib</a> --<a href="#modeeuler">modeuler</a> --<a
href="#rseed">rseed</a> <o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:36.0pt'><span lang=EN-US
style='font-size:11.0pt'>--<a href="#verbose">verbose</a> --<a href="#help">help</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Below you can find a few typical command lines.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<ul style='margin-top:0cm' type=disc>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question1">I want to see all the tracts
that go from my ROI<span style="mso-spacerun: yes"> </span>to the
rest of the brain</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question2">I want to use the high
resolution structural image (or the standard space image) to draw my ROIs</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question3">I want to segment an ROI
depending on its connections with another set of ROIs</a><o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l0 level1 lfo3;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:12.0pt'><a href="#question4">I want to segment an ROI
into different parts having different connections with the rest of the
brain</a> <o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US style='font-size:
11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US style='font-size:
11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The output of probtrackx can be analysed further with:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<ul style='margin-top:0cm' type=disc>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l1 level1 lfo6;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:11.0pt'><a
href="http://www.fmrib.ox.ac.uk/fsl/fdt/find_the_biggest.html">find_the_biggest</a>
(for seed2target classification)<o:p></o:p></span></li>
<li class=MsoNormal style='margin-top:0cm;margin-bottom:0cm;margin-bottom:
.0001pt;mso-list:l1 level1 lfo6;tab-stops:list 36.0pt'><span lang=EN-US
style='font-size:11.0pt'>ccops (for matrix spectral clustering after using
the omatrix2 options)<o:p></o:p></span></li>
</ul>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:18.0pt;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Mandatory arguments<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>There are <b>three</b></span><span lang=EN-US
style='font-size:11.0pt'> compulsory arguments in probtrackx. Basically, the
algorithm needs to know the local <b>orientation distributions</b></span><span
lang=EN-US style='font-size:11.0pt'> (output of bedpostX), <b>the brain mask</b></span><span
lang=EN-US style='font-size:11.0pt'> (in order not to draw pathways outside it)
and a <b>seed region</b></span><span lang=EN-US style='font-size:11.0pt'> for
the probabilistic tractography. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=basename></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>-s <basename ><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><basename> is the prefix of the file containing
the orientation distribution given by bedpostX, which in general are of the
form (in the case of two fibres per voxel):<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_th1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_th2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_ph1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_ph2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_f1samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>merged_f2samples<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>If the path to the directory where these files are
stored is <pathdir>, then the basename is <b><pathdir>/merged.</b></span><span
lang=EN-US style='font-size:11.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt;tab-stops:187.0pt'><a
name=mask></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>-m <mask><span style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Binary brain mask that can be computed with <a
href="http://www.fmrib.ox.ac.uk/fsl/bet">bet</a>. This mask MUST BE IN THE
DIFFUSION SPACE (i.e. same as the diffusion data). Usually, it is computed from
the nodif image, and is named <b>nodif_brain_mask.</b></span><span lang=EN-US
style='font-size:11.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt;tab-stops:313.0pt'><a
name=roi></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span><a name=seed></a>-x <seed> <span style='mso-tab-count:1'> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Region of the brain which serves as a seed for the
tractography. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>When using the simple <a href="#mode">mode</a>,
<seed> is a textfile with the coordinates of the seed voxels stored as
follows :<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_1<span style='mso-tab-count:1'> </span>y_1<span
style='mso-tab-count:1'> </span>z_1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_2<span style='mso-tab-count:1'> </span>y_2<span
style='mso-tab-count:1'> </span>z_2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>…<span style='mso-tab-count:1'> </span>…<span
style='mso-tab-count:1'> </span>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>x_n<span style='mso-tab-count:1'> </span>y_n<span
style='mso-tab-count:1'> </span>z_n<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>When using seedmask mode, <seed> is a 3D image
with non-zero values inside the seed voxels. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><seed> can also be a text file with multiple
seed volumes:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdir1/volume1.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdir2/volume2.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>…<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>pathdirk/volumek.nii.gz<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The program will then compute all the pathways
connecting any pair of brain regions defined in the network. The option --network
must be turned on in this case.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>In all cases (text file or image file), you can use
either the diffusion space, or another space (e.g. structural, standard
spaces), provided the –<b><a href="#seedref">seedref</a></b></span><span
lang=EN-US style='font-size:11.0pt'> and –<b><a href="#xfm">xfm</a></b></span><span
lang=EN-US style='font-size:11.0pt'> options.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Optional arguments<o:p></o:p></span></h3>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Choose your mode ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=mode></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--mode=<chosenMode><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>You can run probtrackx in two different modes:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>simple<span style='mso-tab-count:3'> </span>:
In case the seed is a textfile with voxel coordinates.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>seedmask (default)<span style='mso-tab-count:1'> </span>:
In case the seed is a 3D image file (or ascii file of multiple 3D image files)<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US>The
voxel coordinates as well as the seedmask can be in a different space than the
diffusion space (e.g. high resolution structural space or standard space),
provided the transformation that goes from this space to the diffusion space
(see the options --<a href="#seedref">seedref</a> and --<a href="#xfm">xfm</a>).</span><span
style='mso-ansi-language:EN-GB'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Choose your outputs ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=opd></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--opd<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>This option allows to output the pathway distribution
in <outputfile>. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=pd></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun: yes">
</span>--pd<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>Activate the distance correction option. : The output pathway
distribution is the sum of the lengths of the pathways that cross each voxel.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=os2t></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--os2t<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>This option allows to output the probability that each
individual voxel in the seed mask is connected to each of the target masks
(provided a target mask list).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'>The output are of the form:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_target1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_target2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:11.0pt'><b>seed_to_targetn<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Each of these files is a volume with non-zero values
only within the seed mask. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The value in each voxel of seed_to_target1 within the
seed mask is the number of tracts seeded from this voxel that arrived at
target1.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Running <a
href="http://www.fmrib.ox.ac.uk/fsl/fdt/find_the_biggest">find_the_biggest</a>
on these outputs gives a segmentation of the seed mask into parts connected to
the different targets.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a
name=targetmasks></a><span lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--targetmasks=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is either a 3D file with one target
mask, or a text file containing a list of target masks (with the full path) as
following:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/target1<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/target2<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>…<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><full_path_dir>/targetn<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b><![if !supportEmptyParas]> <![endif]><o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=omatrix2></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>---omatrix2<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This option allows to ouput a filename, called<b>
fdt_matrix2</b></span><span lang=EN-US style='font-size:12.0pt'>, which is a
NxP matrix, where N is the number of voxels in the seed mask, and P is the
number of voxels in the rest of the brain mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The values stored in this matrix represent the
probability that each voxel in the seed mask is connected with each voxel of
the rest of the brain. This value depends on the choice of the option --<a
href="#pd">pd</a>.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This matrix is useful for seed classification based on
connectivity profile with the spectral reordering tool : ccops.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For computational and storage reasons, we recommend to
use a low resolution brain mask, (e.g. 5x5x5 mm^3). <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=lrmask></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--lrmask=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is a low resolution brain mask used
along with the --omatrix2 option<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>To create a low resolution mask, take a whole brain mask
(e.g. using bet), of the same image as the one on which the seeds have been
drawn, and subsample it with the command:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>flirt –i seed_brain_mask –ref seed_brain_mask
–applyisoxfm 5 –o lowresmask<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>fslmaths lowresmask –thr 0.5 –bin lowresmask<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><span style="mso-spacerun: yes"> </span><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=outputfile></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>-o <outputfile><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This is the pathway probability distribution. By
default, this file is called fdt_paths.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>The pathway distribution is in the same space as the
seed mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=mask2></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--mask2=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Add this option if you want to draw all the pathways
that go from the seed mask to a second region (drawn in mask2), and all the
pathways that go from this second region to the seed region.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>mask2 must be in the same space as the seed mask.<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=waypoints></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--waypoints=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Add this option if you want to track only the pathways
that happen to cross a (or a set of) region(s) in the brain. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is either a 3D file with a region
mask, or a text file with a list of 3D region masks along with their full path
as follows:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_1<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_2<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>…<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><full_path_dir>/waypoints_n<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><b>The waypoint masks must all be in the same space as
the seed mask<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** For registration ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>When the seed mask is not in the diffusion space (i.e.
ROIs were drawn on the structural image, or in the standard space, coming from
FMRI group activation or some template), you must provide probtrackx with a <b>reference
image</b></span><span lang=EN-US style='font-size:12.0pt'> and a <b>transformation</b></span><span
lang=EN-US style='font-size:12.0pt'>.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=seedref></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--seedref=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><filename> is the name of an image in the same
space as the seed mask.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For example, struct_brain (if the seed space is the
structural space), or standard (if the seed space is the standard space).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=xfm></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>---xfm=<transformation><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><transformation> is a text file containing the
transformation matrix (as computed by <a
href="http://www.fmrib.ox.ac.uk/fsl/flirt">flirt</a>) from the seed space to
the diffusion space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>For example :<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>str2diff.mat if the seed space is the structural
image.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>std2diff.mat if the seed space is the standard space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Miscellaneous arguments ***<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=verbose></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--verbose=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><n> varies from 0 (very few ouput comments) to 2
(a lot of comments) during the execution of probtrackx.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=help></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--help<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This prints out the help message providing a short
description of the different options.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=dir></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--dir=<directory><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Name of the directory which will contain all the
outputs (fdt_paths, fdt_matrix2, seed_to_targets etc.)<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=forcedir></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--forcedir<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Overwrites the ouput directory if there is already one
having the same name. By default, probtrackx will add “+†to an already
existing one.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=rubbish></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--avoid=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use this option if you want to exclude from the
pathway distribution all those pathways that go into a given region.
<filename> is a 3D mask of this region. This option is opposite to
waypoints. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=stop></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--stop=<filename><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use this option if you want to stop the pathways when
they enter a given region. <filename> is a 3D mask of this region. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>*** Expert mode parameters ***</span><span lang=EN-US
style='font-size:12.0pt'><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=nsamples></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--nsamples=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Number of sample pathways drawn per voxel of the seed
mask. The default value is 5000. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=cthr></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--cthr=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Threshold value for the cosine of the angle between
two successive steps during the tractography. The default value is 0.2
(corresponding to an angle of 78 degrees).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=nsteps></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--nsteps=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Maximum number of steps (default=2000). Using a step
length of 0.5mm, this corresponds to a distance of 1m.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=steplength></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--steplength=<n><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Length of each step during the tractography. The
default value is 0.5 voxels (of the seed space).<span style="mso-spacerun:
yes"> </span>You may want to change this value depending on the voxel
size, or if the tractography is performed on different sized brain (e.g.
infants or animals).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=loopcheck></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--loopcheck<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>This option removes the tracts that make a loop, which
can happen as the tractography is probabilistic. It slows down a bit the
computations.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=usef></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--usef<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use this option if you want the fractional anisotropic
volumes (stored in merged_fsamples) to influence the tractography. The tracts
stop if the anisotropy is lower than a random variable between 0 (low
anisotropy) and 1 (high anisotropy).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=randfib></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--randfib<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Select randomly the different fibre directions when
starting the tractography at one seed voxel. By default, the tractography start
from the leading direction (the one with highest fractional volume inside the
seed voxel).<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><a name=modeeuler></a><span
lang=EN-US style='font-size:12.0pt;font-family:Symbol'>·</span><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--modeuler<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Use modified Euler integration instead of standard
Euler. This is more accurate, but slightly slower.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt;font-family:Symbol'>·</span><a name=rseed></a><span
lang=EN-US style='font-size:12.0pt'><span style="mso-spacerun:
yes"> </span>--rseed<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Random variable generator. By default, the value of this
variable is fixed, which means that when repeating an experiment with the same
data, one gets EXACTELY the same results. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<div class=MsoNormal align=center style='margin:0cm;margin-bottom:.0001pt;
text-align:center'><span lang=EN-US>
<hr size=2 width="100%" align=center>
</span></div>
<h3><span lang=EN-US style='font-size:14.0pt'>Command line examples<o:p></o:p></span></h3>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question1></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
see all the tracts that go from my seed<span style="mso-spacerun: yes">
</span>to the rest of the brain<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>A typical command when one wants to draw all the
pathways (in terms of probability distribution) that run from the seed mask is:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a>
--<a href="#opd">opd</a> <a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Below is the result with a seed in the internal
capsule.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question2></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
see only the tracts that go from an ROI to another (set of) ROIs <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Sometimes, one is only interested in the pathways that
connect one region to one or several others. For example, one can have the
internal capsule as a seed mask, and ask for the pathways that go to M1 in the
hand area and the face area, as well as to the cerebral peduncle. Here is a
typical command using the waypoints option:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a> <a
href="#waypoints">--waypoints=<listOfWaypoints></a> --<a href="#opd">opd</a>
<a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Below is the result. Note that the resulting pathways
are a subgroup of the pathways drawn in the first example, which include only
those that reach the waypoints.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question3></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
use the high resolution structural image (or the standard space image) to draw
my ROIs<o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Sometime, one needs to draw the seed mask in a high
resolution image (for example, to finely delineate some structure), or on a standard
space image (e.g. to use group activations as a common seed mask for a group of
subjects). Here is a typical command using the structural as a seed space. <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Note that the resulting pathways are also in the seed
space, but all the computations are done in the diffusion space.<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x seed_mask</a> <a
href="#seedref">--seedref=struct</a> <a href="#xfm">--xfm=<subject>.bedpostX/xfms/str2diff.mat</a>
<a href="#opd">--opd</a> <a href="#pd">--pd=1</a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><a name=question4></a><![if !supportLists]><span
lang=EN-US style='font-size:13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
segment an ROI depending on its connections with another set of ROIs <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>One can use probtrackx to know which part of the seed
mask is more probably connected to each target region within a list. For
example, which part of the internal capsule is connected to the hand area, and
which part is connected to the face area ? <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'>A typical command for doing that is:<o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:13.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s <subject>.bedpostX/merged</a>
<a href="#mask">–m <subject>.bedpostX/nodif_brain_mask</a> <a href="#seed">–x
seed_mask</a><span style="mso-spacerun: yes"> </span><a href="#os2t">--os2t</a>
<a href="#targetmasks">--targetmasks=<listOfTargets></a> <a href="#dir">--dir=<subject>.probtrackx</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin-top:0cm;margin-right:0cm;margin-bottom:0cm;
margin-left:36.0pt;margin-bottom:.0001pt;text-indent:-18.0pt;mso-list:l0 level1 lfo3;
tab-stops:list 36.0pt'><![if !supportLists]><span lang=EN-US style='font-size:
13.0pt;font-family:Symbol'>·<span style='font:7.0pt "Times New Roman"'>
</span></span><![endif]><span lang=EN-US style='font-size:13.0pt'><b>I want to
segment an ROI into different parts having different connections with the rest
of the brain <o:p></o:p></b></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>As for the SMA/preSMA study, one can ask whether the
seed region is composed of two ore more parts having different connections with
the rest of the brain, i.e. participating in different structural networks.
Probtrackx allows one to output a matrix composed of the values of the
connections between each voxel in the seed mask with the rest of the brain
(taken at a low resolution for computational reason). <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'>Once this matrix calculated, one can une a spectral
reordering command (ccops) to see whether there are two or more clusters within
the seed mask. Here is a typical command: <o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:12.0pt'><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US
style='font-size:14.0pt'>probtrackx <a href="#basename">–s
<subject>.bedpostX/merged</a> <a href="#mask">–m
<subject>.bedpostX/nodif_brain_mask</a> <a href="#mask">–s seed_mask</a><span
style="mso-spacerun: yes"> </span><a href="#omatrix2">--omatrix2</a> <a
href="#dir">--dir=<subject>.probtrackx</a> <a href="#lrmask">--lrmask=lowres_mask</a><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p class=MsoNormal style='margin:0cm;margin-bottom:.0001pt'><span lang=EN-US><![if !supportEmptyParas]> <![endif]><o:p></o:p></span></p>
<p align=center style='text-align:center'><span lang=EN-US><!--[if gte vml 1]><v:shapetype
id="_x0000_t75" coordsize="21600,21600" o:spt="75" o:preferrelative="t"
path="m@4@5l@4@11@9@11@9@5xe" filled="f" stroked="f">
<v:stroke joinstyle="miter"/>
<v:formulas>
<v:f eqn="if lineDrawn pixelLineWidth 0"/>
<v:f eqn="sum @0 1 0"/>
<v:f eqn="sum 0 0 @1"/>
<v:f eqn="prod @2 1 2"/>
<v:f eqn="prod @3 21600 pixelWidth"/>
<v:f eqn="prod @3 21600 pixelHeight"/>
<v:f eqn="sum @0 0 1"/>
<v:f eqn="prod @6 1 2"/>
<v:f eqn="prod @7 21600 pixelWidth"/>
<v:f eqn="sum @8 21600 0"/>
<v:f eqn="prod @7 21600 pixelHeight"/>
<v:f eqn="sum @10 21600 0"/>
</v:formulas>
<v:path o:extrusionok="f" gradientshapeok="t" o:connecttype="rect"/>
<o:lock v:ext="edit" aspectratio="t"/>
</v:shapetype><v:shape id="_x0000_i1029" type="#_x0000_t75" style='width:495pt;
height:388pt'>
<v:imagedata src="fdt_probtrackx_files/image001.gif" o:title="fdt_probtrackx"/>
</v:shape><![endif]--><![if !vml]><img border=0 width=495 height=388
src="fdt_probtrackx_files/image002.jpg" v:shapes="_x0000_i1029"><![endif]><o:p></o:p></span></p>
</div>
</body>
</html>
\ No newline at end of file
diff --git a/eddy_correct b/eddy_correct
index 7dc14801b1e77b8ed6ae3b2fb48956f13c0d419d..8dd7232ca257663f6ac6fea598737c64db953424 100644
--- a/eddy_correct
+++ b/eddy_correct
@@ -22,9 +22,9 @@ if [ `${FSLDIR}/bin/imtest $input` -eq 0 ];then
exit
fi
-avwroi $input $output $ref 1
+fslroi $input $output $ref 1
-avwsplit $input
+fslsplit $input
full_list=`${FSLDIR}/bin/imglob -oneperimage vol*`
for i in $full_list ; do
@@ -33,7 +33,7 @@ for i in $full_list ; do
${FSLDIR}/bin/flirt -in $i -ref $output -nosearch -o $i -paddingsize 1 >> ${output}.ecclog
done
-avwmerge -t $output $full_list
+fslmerge -t $output $full_list
/bin/rm vol*
diff --git a/facalc b/facalc
index 4c210ba73b5459bc6dacf7439dd4a1f8106361bc..3a844c1aba42d627e717ff8aaa3cfd3d56bc3585 100755
--- a/facalc
+++ b/facalc
@@ -25,15 +25,15 @@ exit
fi
-${FSLDIR}/bin/avwmaths ${bn}_L1 -add ${bn}_L2 -add ${bn}_L3 -div 3 tmpMD
-${FSLDIR}/bin/avwmaths ${bn}_L1 -sqr tmpL1sq
-${FSLDIR}/bin/avwmaths ${bn}_L2 -sqr tmpL2sq
-${FSLDIR}/bin/avwmaths ${bn}_L3 -sqr tmpL3sq
-${FSLDIR}/bin/avwmaths ${bn}_L1 -sub tmpMD -sqr tmpl1subsq
-${FSLDIR}/bin/avwmaths ${bn}_L2 -sub tmpMD -sqr tmpl2subsq
-${FSLDIR}/bin/avwmaths ${bn}_L3 -sub tmpMD -sqr tmpl3subsq
-${FSLDIR}/bin/avwmaths tmpL1sq -add tmpL2sq -add tmpL3sq denom
-${FSLDIR}/bin/avwmaths tmpl1subsq -add tmpl2subsq -add tmpl3subsq -mul 1.5 numer
-${FSLDIR}/bin/avwmaths numer -div denom -sqrt ${ob}_FA
+${FSLDIR}/bin/fslmaths ${bn}_L1 -add ${bn}_L2 -add ${bn}_L3 -div 3 tmpMD
+${FSLDIR}/bin/fslmaths ${bn}_L1 -sqr tmpL1sq
+${FSLDIR}/bin/fslmaths ${bn}_L2 -sqr tmpL2sq
+${FSLDIR}/bin/fslmaths ${bn}_L3 -sqr tmpL3sq
+${FSLDIR}/bin/fslmaths ${bn}_L1 -sub tmpMD -sqr tmpl1subsq
+${FSLDIR}/bin/fslmaths ${bn}_L2 -sub tmpMD -sqr tmpl2subsq
+${FSLDIR}/bin/fslmaths ${bn}_L3 -sub tmpMD -sqr tmpl3subsq
+${FSLDIR}/bin/fslmaths tmpL1sq -add tmpL2sq -add tmpL3sq denom
+${FSLDIR}/bin/fslmaths tmpl1subsq -add tmpl2subsq -add tmpl3subsq -mul 1.5 numer
+${FSLDIR}/bin/fslmaths numer -div denom -sqrt ${ob}_FA
${FSLDIR}/bin/imrm tmpMD tmpL1sq tmpL2sq tmpL3sq tmpl1subsq tmpl2subsq tmpl3subsq numer denom
diff --git a/ocmr_preproc b/ocmr_preproc
index 8584a1355363b6c988769cd938cb16fec9e7c58d..c391111ec0e135d195797d93f81a52715cb57663 100755
--- a/ocmr_preproc
+++ b/ocmr_preproc
@@ -19,16 +19,16 @@ nlp=`echo *lp2d_* |wc -w`
if [ $nep -gt 1 ];then
a1=`imglob -oneperimage images_?_*ep2d_*`
a2=`imglob -oneperimage images_??_*ep2d_*`
- avwmerge -t big4D $a1 $a2
+ fslmerge -t big4D $a1 $a2
elif [ $nlp -gt 1 ];then
a1=`imglob -oneperimage images_?_*lp2d_*`
a2=`imglob -oneperimage images_??_*lp2d_*`
- avwmerge -t big4D $a1 $a2
+ fslmerge -t big4D $a1 $a2
fi
#nslices=${1}
-#zsize=`avwval big4D dim3`
-#tsize=`avwval big4D dim4`
+#zsize=`fslval big4D dim3`
+#tsize=`fslval big4D dim4`
#tpts=`echo "10k $zsize $nslices /p "|dc -`
#afterdot=`echo $tpts | awk -F . '{print \$2}'`
#foo=`echo $afterdot|grep [123456798]`
@@ -37,15 +37,15 @@ fi
# exit 1
#fi
#tpts=`echo "$tpts \* $tsize" |bc"'
-#xsize=`avwval big4D dim1`
-#ysize=`avwval big4D dim2`
-#xvoxsize=`avwval big4D pixdim1`
-#yvoxsize=`avwval big4D pixdim2`
-#zvoxsize=`avwval big4D pixdim3`
-#datatype=`avwval big4D datatype`
+#xsize=`fslval big4D dim1`
+#ysize=`fslval big4D dim2`
+#xvoxsize=`fslval big4D pixdim1`
+#yvoxsize=`fslval big4D pixdim2`
+#zvoxsize=`fslval big4D pixdim3`
+#datatype=`fslval big4D datatype`
-#avwcreatehd $xsize $ysize $nslices $tpts $xvoxsize $yvoxsize $zvoxsize 0 0 0 0# $datatype big4D
+#fslcreatehd $xsize $ysize $nslices $tpts $xvoxsize $yvoxsize $zvoxsize 0 0 0 0# $datatype big4D
diff --git a/old_bedpost b/old_bedpost
index 89bff0389a241956d43bf100f2dfd05e7b0066f8..229eedc1b4e11de2ec5c27131671953b668ad249 100755
--- a/old_bedpost
+++ b/old_bedpost
@@ -151,16 +151,16 @@ mkdir -p ${subjdir}.bedpost/diff_slices
echo copying files to bedpost directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpost
${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpost
-${FSLDIR}/bin/avwmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpost/nodif_brain
+${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpost/nodif_brain
mkdir -p ${subjdir}.bedpost/logs
mkdir -p ${subjdir}.bedpost/logs/pid_${$}
-nslices=`${FSLDIR}/bin/avwval ${subjdir}/data dim3`
+nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
-${FSLDIR}/bin/avwslice ${subjdir}/data
-${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
+${FSLDIR}/bin/fslslice ${subjdir}/data
+${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask
#for parallel processing, the following need to be setup elsewhere
#FSLMACHINELIST="list of machines (can be duplicated for two processors etc.)"
@@ -198,12 +198,12 @@ done
##this will have to change..
echo "Merging outputs into 4D files"
-${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples`
-${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples`
-${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples`
-${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bedpost/mean_thsamples
-${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
-${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples
+${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples`
+${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples`
+${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples`
+${FSLDIR}/bin/fslmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bedpost/mean_thsamples
+${FSLDIR}/bin/fslmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
+${FSLDIR}/bin/fslmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpost/merged_thsamples ${subjdir}.bedpost/merged_phsamples ${subjdir}.bedpost/nodif_brain_mask ${subjdir}.bedpost/dyadic_vectors
diff --git a/old_bedpostX b/old_bedpostX
index 00e407c9a1ddf462c68f95eedd54eb69d10cb05c..ce72f25be72e4462125ecfab42d0dbe1932c6edb 100644
--- a/old_bedpostX
+++ b/old_bedpostX
@@ -171,16 +171,16 @@ mkdir -p ${subjdir}.bedpostX/diff_slices
echo copying files to bedpostX directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
-${FSLDIR}/bin/avwmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
+${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
mkdir -p ${subjdir}.bedpostX/logs
mkdir -p ${subjdir}.bedpostX/logs/pid_${$}
-nslices=`${FSLDIR}/bin/avwval ${subjdir}/data dim3`
+nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
-${FSLDIR}/bin/avwslice ${subjdir}/data
-${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
+${FSLDIR}/bin/fslslice ${subjdir}/data
+${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask
#for parallel processing, the following need to be setup elsewhere
#FSLMACHINELIST="list of machines (can be duplicated for two processors etc.)"
@@ -221,12 +221,12 @@ echo number of fibres $numfib
fib=1;
while [ $fib -le $numfib ];do
- ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
- ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
- ${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
- ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
- ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
- ${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
+ ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
+ ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
+ ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
+ ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
+ ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
+ ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpostX/merged_th${fib}samples ${subjdir}.bedpostX/merged_ph${fib}samples ${subjdir}.bedpostX/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}
diff --git a/post_xfibres b/post_xfibres
index f3b6ead860faaef0f2f042f4104f23509c86c386..c875482050f4f19dd684b48c884bcf9b69f9a3a3 100755
--- a/post_xfibres
+++ b/post_xfibres
@@ -20,13 +20,13 @@ numfib=`${FSLDIR}/bin/imglob -oneperimage *f*samples |wc -w`
echo "$numfib fibres"
fib=1;
-${FSLDIR}/bin/avwroi `${FSLDIR}/bin/imglob -oneperimage *f1samples` numfibs 0 1
-${FSLDIR}/bin/avwmaths numfibs -mul 0 numfibs
+${FSLDIR}/bin/fslroi `${FSLDIR}/bin/imglob -oneperimage *f1samples` numfibs 0 1
+${FSLDIR}/bin/fslmaths numfibs -mul 0 numfibs
while [ $fib -le $numfib ];do
echo $fib
- ${FSLDIR}/bin/avwmaths `${FSLDIR}/bin/imglob -oneperimage *f${fib}samples` -Tmean mean_f${fib}samples
- ${FSLDIR}/bin/avwmaths mean_f${fib}samples -thr $thresh -bin ${$}bin${fib}
- ${FSLDIR}/bin/avwmaths numfibs -add ${$}bin${fib} numfibs
+ ${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/imglob -oneperimage *f${fib}samples` -Tmean mean_f${fib}samples
+ ${FSLDIR}/bin/fslmaths mean_f${fib}samples -thr $thresh -bin ${$}bin${fib}
+ ${FSLDIR}/bin/fslmaths numfibs -add ${$}bin${fib} numfibs
${FSLDIR}/bin/make_dyadic_vectors `${FSLDIR}/bin/imglob -oneperimage *th${fib}samples` `${FSLDIR}/bin/imglob -oneperimage *ph${fib}samples` dyads${fib}
fib=`echo "$fib +1"|bc`;
done