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Dear Vitória,
<div class="moz-forward-container">
<div><br>
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<div>The short answer to your question would be:</div>
<div><br>
</div>
<div>If in subsequent steps you do planar gradient transformation
or data visualization it's safe to replace the grad. If in
subsequent steps you want to do sourceanalysis, it's not safe to
replace the grad.</div>
<div><br>
</div>
<div>Reason: essential information that is needed for a correct
forward computation (i.e. construction of the leadfields) is
removed by replacing the grad. This information is represented
in grad.tra. The explanation would be a bit technical, and it
has been our intention for a while to document this on the
FT-wiki as a FAQ, but we didn't get to it yet. For visualization
and planar gradient transformation, only the grad.chanpos is
needed, and this is correctly represented in an 'earlier-stage'
grad-structure.</div>
<div><br>
</div>
<div>Note that we have made some changes just this past week that
actually addresses this NaN-issue. It will not work on
backprojected data (i.e. data that has gone through
ft_componentanalysis, followed by ft_rejectcomponent), but if
you grab the most recent FT version and do ft_rejectcomponent, I
believe the grad.chanpos will be reconstructed without NaNs. I
haven't tried it myself, but rumour has it that this is the
case.</div>
<div><br>
</div>
<div>Would you be interested in contributing to the documentation,
let me know...</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div>%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%</div>
<div><br>
<div>
<div>On Oct 5, 2013, at 4:26 AM, Vitória Magalhães Piai wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Hi FT-ers,<br>
<br>
It took me a while to find some older posts that would
answer my question, and this thread almost did the whole
job:<br>
<a moz-do-not-send="true"
href="http://mailman.science.ru.nl/pipermail/fieldtrip/2013-July/006779.html">http://mailman.science.ru.nl/pipermail/fieldtrip/2013-July/006779.html</a><br>
<a moz-do-not-send="true"
href="http://mailman.science.ru.nl/pipermail/fieldtrip/2013-July/006788.html">http://mailman.science.ru.nl/pipermail/fieldtrip/2013-July/006788.html</a><br>
<br>
Like Alex, I figured out that it was the ICA that left my
grad.chanpos with NaNs only, and like Haiteng, I thought
just replacing the grad field with a pre-ICA grad field
would be one way to go.<br>
But just like Alex I was wondering whether this is the
right way to go: "however, it feels somewhat dangerous to
perform such "dirty" fixes, since that grad info is
probably removed for a certain reason. We are oblivious to
its impact subsequent steps like planar transform and
source reconstruction."<br>
Talking to a knowledgeable colleague yesterday about this
issue, he also had his question marks. But I don't see any
follow-up on Alex's remark (I guess he further discussed
this with colleagues while drinking coffee at the DCCN
kitchen...! :-)<br>
SS<br>
So I still don't know the answer and maybe some other
people may want to know it as well in the future.<br>
<br>
Any opinion on whether it's safe to use pre-ICA grad
information for subsequent planar transformation and
source analyses?<br>
Thanks a lot, Vitória<br>
<br>
-- <br>
** Please consider the environment - do you really need to
print? **<br>
<br>
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</blockquote>
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<div>Jan-Mathijs Schoffelen,
MD PhD </div>
<div><br>
</div>
<div>Donders Institute for
Brain, Cognition and
Behaviour, <br>
Centre for Cognitive
Neuroimaging,<br>
Radboud University
Nijmegen, The Netherlands</div>
<div><br>
</div>
<div>Max Planck Institute
for Psycholinguistics,</div>
<div>Nijmegen, The
Netherlands</div>
<div><br>
</div>
<div><a
moz-do-not-send="true"
href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div>
<div>Telephone:
+31-24-3614793</div>
<div><br>
</div>
<div><a
moz-do-not-send="true"
href="http://www.hettaligebrein.nl">http://www.hettaligebrein.nl</a></div>
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