<div dir="ltr"><div><div><div><div>Hi Erik<br><br></div>Just as FODs calculated using MRtrix 0.2 will appear slightly incorrect when viewed in the new version, any metrics derived from them will also be slightly incorrect. Furthermore, the nature and severity of the error will vary as a function of orientation.<br>
<br></div>If you have not yet seen it, there's a discussion on this topic on the relevant <a href="https://github.com/jdtournier/mrtrix3/wiki/Orthonormal-SH-basis">wiki page</a> (there's a couple of other pages there that might be worth having a look at, and the wiki should hopefully expand over time). If you first run <span style="font-family:courier new,monospace">shbasis</span> on your data with either the <span style="font-family:courier new,monospace">-force_new</span> or <span style="font-family:courier new,monospace">-force_native</span> option, then the FODs will be interpreted correctly by any command within the new software. Note that this does not mean that the FODs will be exactly as they would be if they were calculated in the new MRtrix command <span style="font-family:courier new,monospace">dwi2fod</span>; only that they will be correctly interpreted as they were produced by the 0.2 version command.<br>
<br></div>An important point regarding the <span style="font-family:courier new,monospace">shbasis</span> command is that it won't ruin your data if you accidentally run it on the same file multiple times; on subsequent attempts it will detect that the image data are already stored in the new orthonormal basis, and therefore will not modify the data any further.<br>
<br></div>Best regards<br>Rob<br></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br><br><span style="color:rgb(255,102,0)"><b>Robert Smith, Ph.D</b><br>Research Officer, Imaging Division</span><br>
<br>The Florey Institute of Neuroscience and Mental Health<br>Melbourne Brain Centre - Austin Campus<br>245 Burgundy Street<br>Heidelberg Vic 3084<br>Ph: +61 3 9035 7128<br>Fax: +61 3 9035 7301<br><a href="http://www.florey.edu.au/" target="_blank">www.florey.edu.au</a><br>
</div></div>
<br><br><div class="gmail_quote">On Mon, Jun 2, 2014 at 2:26 AM, Erik Ziegler <span dir="ltr"><<a href="mailto:erik.ziegler@ulg.ac.be" target="_blank">erik.ziegler@ulg.ac.be</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div dir="ltr">Hi Donald,
<div><br>
</div>
<div>As you've mentioned that the FOD basis is slightly different between versions, I was wondering if it was safe to use fod2metric on FODs from mrtrix 0.2? It is okay if I first use shbasis with -force_new?</div>
<div><br>
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<div>Thanks,</div>
<div><br>
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<div>Erik<br>
<div><br>
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<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On Tue, May 27, 2014 at 9:37 AM, Donald Tournier <span dir="ltr">
<<a href="mailto:jdtournier@gmail.com" target="_blank">jdtournier@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<p dir="ltr">Hi Ralf,</p>
<p dir="ltr">Currently it's not possible to view the FODs in volume render mode - I couldn't think of a way of rendering such a massive amount of information as a volume render - it's hard enough to absorb all that information in single-slice mode... The only
sensible way to do it would be to render the FODs on the clip planes, but then it doesn't really add much to the normal single-slice mode anyway...</p>
<p dir="ltr">And yes, of course it's possible to display the MRtrix3 generated FODs in the new viewer - although only in single-slice or ortho view. You can still display the MRtrix 0.2 FODs, but they will be subtly wrong since the definition of the SH basis
has changed slightly. You really need to watch out for that, the difference is so subtle that I can't tell which is which by eye - you need to use the shbasis app for this. Now that I think about it, I might need to emphasise this more strongly on the wiki...</p>
<p dir="ltr">Cheers,<br>
Donald</p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: <a href="tel:%2B44%20%280%2920%207188%207118%20ext%2053613" value="+442071887118" target="_blank">
+44 (0)20 7188 7118 ext 53613</a><br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a><br>
</p>
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<div class="gmail_quote">On 27 May 2014 07:46, "Luetzkendorf, Ralf" <<a href="mailto:Ralf.Luetzkendorf@med.ovgu.de" target="_blank">Ralf.Luetzkendorf@med.ovgu.de</a>> wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi MRTrix community,<br>
<br>
a quick question. Is it possible to show the FODs with MRTrix3 in the Volume View?<br>
I guess with the MRTrix3 calculated CSD it works, but does it work with the MRTrix 0.2 calculated CSDs / FODs?<br>
<br>
Ralf<br>
<br>
<br>
+++++++++++++++++++++++++++++++++++++++++++++++<br>
Ralf Lützkendorf<br>
Department for Biometry and Medical Informatics<br>
University of Magdeburg, Germany<br>
phone: <a href="tel:%2B49%20391%2067%2013546" value="+493916713546" target="_blank">
+49 391 67 13546</a><br>
fax: <a href="tel:%2B49%20391%2067%2013536" value="+493916713536" target="_blank">
+49 391 67 13536</a><br>
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