<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Philip,<div><br></div><div>many thanks for your suggestions. PDFs are ok, and so the seeds I think, because if I run track -inputmodel dt I get reasonable results. </div><div><br></div><div>But as I try this:</div><div><br></div><div><div>track -inputfile brainDT.Bdouble -schemefile direction.scheme -inputmodel bayesdirac_dt -seedfile mask -iterations 100 | procstreamlines -outputacm -header mask -outputroot bayes_</div></div><div><br></div><div>I get the error:</div><div><br></div><div><div>SEVERE: Exception in thread "main" class data.DataSourceException: End of file reached without completing voxel.</div></div><div><br></div><div>I have the latest software version. Any suggestions?</div><div><br></div><div>Many thanks again,</div><div><br></div><div>Silvia</div><div><br></div><div><br></div><div><br><div><div>On Mar 4, 2013, at 6:37 PM, Philip A Cook wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div>Hi, <br><br>A good first step is to look at the PDFs with pdview:<br><br> pdview -inputmodel pico -inputfile brainPICoPDFs.Bdouble -datadims <x> <y> <z><br><br>where x,y,z are the dimensions of your image. Check the orientations and concentration parameters are sensible. The image should resemble an FA image.<br><br>The next thing I would do is check the seeds are in the correct place. I usually check this by doing simple tracking first:<br><br> track -inputfile brainDT.Bdouble -inputmodel dt -seedfile mask | procstreamlines -outputacm -header mask -outputroot dt_streamline_<br><br>BTW, you can use the Bayesian tracking algorithm directly with track, skipping the PDF fitting process:<br><br> track -inputfile data.Bfloat -schemefile imaging.scheme -inputmodel bayesdirac_dt -seedfile mask -iterations 100 | procstreamlines -outputacm -header mask -outputroot bayes_<br><br><br><br>On Mar 4, 2013, at 4:00 AM, Silvia De Santis wrote:<br><br><blockquote type="cite">Hello,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I am trying to use pico to estimate the probability of connectivity between a bunch of voxels and I get inconsistent results, so I was seeking for help to understand what I am doing wrong. <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">cat brainDT.Bdouble | picopdfs -inputmodel dt -luts picoTable.dat > brainPICoPDFs.Bdouble<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">track -inputfile brainPICoPDFs.Bdouble -inputmodel pico -seedfile mask | procstreamlines -outputcp -outputroot results/ -seedfile mask <br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">brainDT.Bdouble is obtained with dtfit and looks ok<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">mask is an indexed mask of voxels (from 1 to n_voxels)<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">picoTable is obtained with dtlutgen<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I get .img files that basically contains white spots that are outside the brain, and since this is the first time I use camino I am really clueless.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Any kind of help would be greatly appreciated!<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Silvia<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">*****************************************************<br></blockquote><blockquote type="cite">Silvia De Santis<br></blockquote><blockquote type="cite">CUBRIC<br></blockquote><blockquote type="cite">School of Psychology<br></blockquote><blockquote type="cite">Cardiff University<br></blockquote><blockquote type="cite">Tel: 029 2087 0354<br></blockquote><blockquote type="cite">Fax: 029 2087 0339<br></blockquote><blockquote type="cite">Web: <a href="http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php">http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php</a><br></blockquote><blockquote type="cite">*****************************************************<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">*****************************************************<br></blockquote><blockquote type="cite">Silvia De Santis<br></blockquote><blockquote type="cite">CUBRIC<br></blockquote><blockquote type="cite">School of Psychology<br></blockquote><blockquote type="cite">Cardiff University<br></blockquote><blockquote type="cite">Tel: 029 2087 0354<br></blockquote><blockquote type="cite">Fax: 029 2087 0339<br></blockquote><blockquote type="cite">Web: <a href="http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php">http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php</a><br></blockquote><blockquote type="cite">*****************************************************<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">Camino-users mailing list<br></blockquote><blockquote type="cite"><a href="mailto:Camino-users@www.nitrc.org">Camino-users@www.nitrc.org</a><br></blockquote><blockquote type="cite"><a href="http://www.nitrc.org/mailman/listinfo/camino-users">http://www.nitrc.org/mailman/listinfo/camino-users</a><br></blockquote><br></div></blockquote></div><br><div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; -webkit-text-decorations-in-effect: none; "><div style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">*****************************************************</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Silvia De Santis<br>CUBRIC<br>School of Psychology<br>Cardiff University<br>Tel: 029 2087 0354<br>Fax: 029 2087 0339<br>Web: <a href="http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php">http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php</a></div><div style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">*****************************************************</div></span></div></div>
</div>
<br></div></div></blockquote></div><br><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><span class="Apple-style-span" style="orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; -webkit-text-decorations-in-effect: none; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; -webkit-text-decorations-in-effect: none; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="orphans: 2; text-align: -webkit-auto; text-indent: 0px; widows: 2; -webkit-text-decorations-in-effect: none; "><div style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">*****************************************************</div><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Silvia De Santis<br>CUBRIC<br>School of Psychology<br>Cardiff University<br>Tel: 029 2087 0354<br>Fax: 029 2087 0339<br>Web: <a href="http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php">http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php</a></div><div style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">*****************************************************</div></span></div></span></div></span></span>
</div>
<br></body></html>