<div dir="ltr"><div><div><div><div><div><div><div>Dear Britta,<br></div>I have been working with
the bias correction of my subject's MRI these days, and while working
extremely well for some of them, some others appear to be even worse
after correction.<br></div>I don't have much experience with MRI images, so maybe the combination of parameters that I am setting may be not optimal.<br></div>At
the moment, I am playing around with the Bias correction parameter
(from extremely light to no correction) and the FWHM bias (from 30mm to
150mm). <br></div>In the original images I can see some non-uniformity
in terms of contrast and usually they look quite smooth/low frequency to
me. After correction I can observe an improvement in the MRI images
themselves, but no improvement or even worsening in terms of not covered
surface in the source localization.<br></div>Do you have any suggestion
how to find some quantificable parameters to help me out in this
procedure? How can I quickly check whether the quality of the image is
enough to guarantee that the cortex is fully covered, without going
through the whole forward model production? Sometimes, even though the
grid is well positioned, I still have the aforementioned problem. <br><br></div>Best wishes,<br><br></div>Paolo<br></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Mar 18, 2016 at 3:35 PM, Paolo Belardinelli <span dir="ltr"><<a href="mailto:paolo.belardinelli@gmail.com" target="_blank">paolo.belardinelli@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><div><div><div><div><div>Dear Britta,<br></div>I was deeply involved in the processing and I forgot to update this post.<br></div>Thank you: it worked out!<br></div>Eliminating the bias from MRI images (using light/very light regularization) leads to more accurate grids and correct results.<br><br></div>Best,<br><br></div>Paolo<br><div><div><div><br><br></div></div></div></div><div class="HOEnZb"><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Thu, Feb 18, 2016 at 10:10 AM, Britta Westner <span dir="ltr"><<a href="mailto:britta.westner@uni-konstanz.de" target="_blank">britta.westner@uni-konstanz.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Dear Paolo,<br>
<br>
I experienced similar problems and found that correcting the field
bias in the participant's MRI (e.g. doing a "bias correction" with
SPM) can help. My explanation would be that the field bias either
leads to small inaccuracies in the segmentation and volume which
then "get visible" when warping the grid based on the non-segmented
MRI, or that the warping algorithm itself is affected by this bias.
Maybe you can give that a try!<br>
<br>
Hope this helps,<br>
Britta<div><div><br>
<br>
<br>
<br>
<div>Am 17.02.2016 um 20:20 schrieb Paolo
Belardinelli:<br>
</div>
</div></div><blockquote type="cite"><div><div>
<div dir="ltr">
<div>Dear Fieldtrippers,<br>
we are encountering a problem with a template model for source
reconstruction. In particular, we are warping (non linearly) a
template grid to the individual subject's MRI. <br>
</div>
<div>Doing that, it appears that the very top of the brain is
not fully covered by dipole locations.<br>
</div>
<div>We found that this issue has been already reported:<br>
<br>
<a href="http://www.fieldtriptoolbox.org/template/sourcemodel" target="_blank">http://www.fieldtriptoolbox.org/template/sourcemodel</a>
<br>
</div>
<div>
<div><br>
</div>
<div>Apparently, since March 7th 2013, this issue has been
fixed.<br>
</div>
<div>However we are using August 28th 2015 Fieldtrip version
and we are still dealing with the same issue.<br>
</div>
<div>Any suggestions?<br>
</div>
<div>Here are our code lines:<br>
<br>
cfg = [];<br>
cfg.grid.warpmni = 'yes';<br>
cfg.resolution = 6; % resolution of the template grid in mm<br>
cfg.grid.nonlinear = 'yes'; % use non linear normalization<br>
cfg.mri = mri_spm; % use subject's mri in mni coordinates<br>
cfg.grid.unit = 'mm';<br>
sourcemodel = ft_prepare_sourcemodel(cfg);<br>
<br>
</div>
<div>Thank you in advance.<br>
<br>
</div>
<div>Paolo <br>
</div>
<div><br>
<br>
<br>
<br>
</div>
<div>-- <br>
<div>
<div dir="ltr">
<div>--<br>
Paolo Belardinelli, PhD<br>
Neurology Department<br>
University Hospital Tuebingen<br>
Eberhard Karls University Tuebingen<br>
Hoppe-Seyler Str. 3<br>
D-72076 Tuebingen<br>
Tel: <a value="+4970712985894">+49
7071 / 29 80478</a><br>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
<br>
</div></div><pre>_______________________________________________
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</blockquote>
<br>
<br>
<pre cols="72">--
Britta Westner, M.Sc.
Neuroelectromagnetic Oscillations Laboratory
Fachbereich Psychologie
Universität Konstanz
Postfach 905
78457 Konstanz
Telefon: <a href="tel:%2B49-%280%297531-88-5703" value="+497531885703" target="_blank">+49-(0)7531-88-5703</a>
Fax: <a href="tel:%2B49-%280%297531-88-5709" value="+497531885709" target="_blank">+49-(0)7531-88-5709</a>
<a href="http://www.psychologie.uni-konstanz.de/nemo-lab" target="_blank">www.psychologie.uni-konstanz.de/nemo-lab</a></pre>
</div>
<br>_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br></blockquote></div><br><br clear="all"><br>-- <br><div><div dir="ltr"><div>--<br>Paolo Belardinelli, PhD<br>Neurology Department<br>
University Hospital Tuebingen<br>
Eberhard Karls University Tuebingen<br>
Hoppe-Seyler Str. 3<br>
D-72076 Tuebingen<br>
Tel: <a value="+4970712985894">+49 7071 / 29 80478</a><br><br></div></div></div>
</div>
</div></div></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><div>--<br>Paolo Belardinelli, PhD<br>Neurology Department<br>
University Hospital Tuebingen<br>
Eberhard Karls University Tuebingen<br>
Hoppe-Seyler Str. 3<br>
D-72076 Tuebingen<br>
Tel: <a value="+4970712985894">+49 7071 / 29 80478</a><br><br></div></div></div>
</div>