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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Hi Hanneke,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>it occured to me to change x and y when I
clicked around in the mri presented to me by vt_voulmesegment (it shows up when
cfg.coordsys is not specified). I noticed that a voxel that had index [i j k]
in the neuromag GUI had index [j i k] in this image. But when you specify the
fiducials manually in fieldtrip, I don’t think you have to worry about
that. You could try not to swap x and y coordinates and comment out
cfg.coordsys in the segmentation part. In the picture that comes up, do the
axes go through the fiducials (y through nas)? If so, the alignment is correct.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>To my mind, the big helmet in your picture
could mean that the sensor positions are given in cm and the headmodel vertices
in m. What happens if you multiply headmodel.pos by 10?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Best,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>jan<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>Von:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
fieldtrip-bounces@donders.ru.nl [mailto:fieldtrip-bounces@donders.ru.nl] <b><span
style='font-weight:bold'>Im Auftrag von </span></b>Hanneke van Dijk<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Freitag, 15. April 2011
11:34<br>
<b><span style='font-weight:bold'>An:</span></b> <st1:PersonName w:st="on">Email
discussion list for the FieldTrip project</st1:PersonName><br>
<b><span style='font-weight:bold'>Betreff:</span></b> Re: [FieldTrip] I think
you solved the problem</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Dear Jan and Jan-Mathijs,<br>
<br>
Thanks for working on this problem! I'm testing it for data recorded with the
'old' neuromag 122 system. I'm using the script that Jan attached to a previous
e-mail, and the fieldtrip version that was released yesterday. The first
question that I have is: <br>
<br>
What to do if you don't have fiducial information from the neuromag software? I
could use ft_volume_realign with cfg.method = 'interactive' and point the
fiducials out and swap the y and x axes. But in what coordinate system am I
then, and in what coordinate system should I move on? <br>
<br>
second,<br>
<br>
My 'vol' , headmodel, seems to end up in a factor 10 (or more(?)) smaller unit
then the grid and grad. You can't even see it in the headmodelplot (it is a
small dot somewhere in the middle). I don't know what happened there.<br>
<br>
third,<br>
<br>
If you look at the picture I attached the grid is not in the centre of the
helmet (pic1 from the top down), and very low (pic2 looking from the left). I
don't know how to solve that. I at least think the subject was not in the
helmet that way!<br>
<br>
Groetjes Hanneke<br>
<br>
--------------------------------------------------<br>
Dr. Hanneke van Dijk<br>
Institut für Klinische Neurowissenschaften und Medizinische Psychologie<br>
Gebäude-Nr.: 23.02<br>
Ebene: 03 Zimmer-Nr.: 47<br>
Tel.: +49 211-81-13074<br>
Mail : <a href="mailto:hanneke.vandijk@med.uni-duesseldorf.de">hanneke.vandijk@med.uni-duesseldorf.de</a><br>
<a
href="http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html">http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html</a><o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Thu, Apr 14, 2011 at 9:31 AM, <<a
href="mailto:Jan.Hirschmann@med.uni-duesseldorf.de">Jan.Hirschmann@med.uni-duesseldorf.de</a>>
wrote:<o:p></o:p></span></font></p>
<div link=blue vlink=blue>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Dear Jan-Mathijs,</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>sure, I will do that. I have tested one head model with
ft_dipole_simulation and beamforming and it looks good (at least when I
simulate two conditions and subtract sources the right location comes out). So
I guess we (and maybe others) will use the new procedure now.</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Best,</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>jan</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center>
</span></font></div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;font-weight:
bold'>Von:</span></font></b><font size=2 face=Tahoma><span style='font-size:
10.0pt;font-family:Tahoma'> <a href="mailto:fieldtrip-bounces@donders.ru.nl"
target="_blank">fieldtrip-bounces@donders.ru.nl</a> [mailto:<a
href="mailto:fieldtrip-bounces@donders.ru.nl" target="_blank">fieldtrip-bounces@donders.ru.nl</a>]
<b><span style='font-weight:bold'>Im Auftrag von </span></b>jan-mathijs
schoffelen<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Mittwoch, 13. April 2011
16:57<br>
<b><span style='font-weight:bold'>An:</span></b> <st1:PersonName w:st="on">Email
discussion list for the FieldTrip project</st1:PersonName><br>
<b><span style='font-weight:bold'>Betreff:</span></b> Re: [FieldTrip] I think
you solved the problem</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Dear Jan,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>No problem. Thanks
for the script. If you feel up to it, you are kindly invited to update the
documentation on the fieldtrip wiki as well. If I recall correctly, at some
point Hanneke added some documentation about how to create MNI-based dipole
grids for neuromag data. A lot of the intermediate steps have now become
obsolete and this part of the wiki can be substantially cleaned.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Thanks,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>Jan-Mathijs<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'>On Apr 13, 2011,
at 2:31 PM, <<a href="mailto:Jan.Hirschmann@med.uni-duesseldorf.de"
target="_blank">Jan.Hirschmann@med.uni-duesseldorf.de</a>> <<a
href="mailto:Jan.Hirschmann@med.uni-duesseldorf.de" target="_blank">Jan.Hirschmann@med.uni-duesseldorf.de</a>>
wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<span style='word-spacing:0px'>
<div link=blue vlink=blue>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Dear Jan-Mathijs,</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>I think we solved the problem. Everthing is like you said in the
first place. ft_volumerealign and ft_volumesegment should be called with
cfg.coordsys=’neuromag’. The only thing that was wrong is that for
the voxel coordinates read from the Neuromag GUI x and y should be swapped. For
anyone interested I attach a script that is meant to be easy-to-use for
beginners.</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Thank you very much for your time!</span></font><o:p></o:p></p>
</div>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
color=black face="Times New Roman"><span style='font-size:12.0pt;color:black'>
<hr size=2 width="100%" align=center>
</span></font></div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:black;font-weight:bold'>Von:</span></font></b><font size=2 color=black
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;color:black'> <a
href="mailto:fieldtrip-bounces@donders.ru.nl" target="_blank">fieldtrip-bounces@donders.ru.nl</a>
[<a href="mailto:fieldtrip-bounces@donders.ru.nl" target="_blank">mailto:fieldtrip-bounces@donders.ru.nl</a>] <b><span
style='font-weight:bold'>Im Auftrag von </span></b>jan-mathijs schoffelen<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Dienstag, 12. April
2011 21:18<br>
<b><span style='font-weight:bold'>An:</span></b> <st1:PersonName w:st="on">Email
discussion list for the FieldTrip project</st1:PersonName><br>
<b><span style='font-weight:bold'>Betreff:</span></b> Re: [FieldTrip] I
think you solved the problem</span></font><o:p></o:p></p>
</div>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Dear Jan,</span></font><o:p></o:p></p>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>I suspect that your mri, as it comes out of ft_read_mri is already
coregistered in neuromag space. After your realignment and after replacing
mri.transform with real_mri.transform, the coordinate axes in your pic1 look
strange. This I think causes the 'dropped pocket change'. </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>What happens if you skip the ft_volumerealign step and call
ft_volumesegment directly on the mri (with cfg.coordsys = 'neuromag', or, for
what it's worth, without cfg.coordsys; in this case you will be able to verify
the coordinate system)?</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Alternatively, if this doesn't work, could you replace
mri.transform by eye(4) prior to calling ft_volumerealign and ft_volumesegment
(both with cfg.coordsys = 'neuromag' and no further tampering with
transformation matrices?).</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Thanks</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>JM</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Apr 12, 2011, at 8:49 PM, <<a
href="mailto:Jan.Hirschmann@med.uni-duesseldorf.de" target="_blank">Jan.Hirschmann@med.uni-duesseldorf.de</a>>
<<a href="mailto:Jan.Hirschmann@med.uni-duesseldorf.de" target="_blank">Jan.Hirschmann@med.uni-duesseldorf.de</a>>
wrote:</span></font><o:p></o:p></p>
</div>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
<br>
</span></font><o:p></o:p></p>
</div>
<span style='word-spacing:0px'>
<div link=blue vlink=blue>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>Dear Jan-Mathijs,</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>sorry, I think I was a bit too enthusiastic when
I said everything worked out wonderfully. It worked only once. After an
afternoon of confusion I concluded that on my first try I must have misspelled
cfg.coordsys=’neuromag’ on my calls to ft_volumerealign and
ft_volumesegment. In fact, the segmentation looks really bad with these
settings. What works for me is written underneath:</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>mri = ft_read_mri('….fif');</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>hdr=ft_read_header('…fif');</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>mri.anatomy=double(mri.anatomy);</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>%this is taken from the Neuromag GUI for MRI-MEG Integration</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg=[];</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.fiducial.rpa=[136.35 142.80
31.96];</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.fiducial.nas=[47.84 101.80 100.10];</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.fiducial.lpa=[139.22 146.17 162.69];</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>%go from neuromag voxel to neuromag head coordinates</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.coordsys='neuromag';</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.method='fiducial';</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>real_mri=ft_volumerealign(cfg,mri);</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>%taking real_mri with its coordsys field will not work, so I take
mri</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>mri.transform=real_mri.transform;</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg
= [];</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.keepintermediate = 'no';</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.write = 'no';</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>segmentedmri = ft_volumesegment(cfg, mri);</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>Before segmentation the function shows some kind
of brain (pic 1). When segmentation is done the segmented brain looks good (pic
2) but the brain does not fit the helmet (pic 3). It is looking at its feet as
if it dropped some pocket change. Do you know what is going on?</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>Thanks,</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>jan</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
color=black face="Times New Roman"><span style='font-size:12.0pt;color:black'>
<hr size=2 width="100%" align=center>
</span></font></div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:black;font-weight:bold'>Von:</span></font></b><font size=2 color=black
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;color:black'> <a
href="mailto:fieldtrip-bounces@donders.ru.nl" target="_blank">fieldtrip-bounces@donders.ru.nl</a> [<a
href="mailto:fieldtrip-bounces@donders.ru.nl" target="_blank">mailto:fieldtrip-bounces@donders.ru.nl</a>] <b><span
style='font-weight:bold'>Im Auftrag von </span></b>jan-mathijs schoffelen<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Dienstag, 12. April
2011 12:11<br>
<b><span style='font-weight:bold'>An:</span></b> <st1:PersonName w:st="on">Email
discussion list for the FieldTrip project</st1:PersonName><br>
<b><span style='font-weight:bold'>Betreff:</span></b> Re: [FieldTrip] I
think you solved the problem</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Dear Jan,</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Apart from not being properly aligned, the segmentation looks a
bit strange to me. I suspect that not everything went well here ;o).</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Could you try the following:</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>specify cfg.coordsys = 'neuromag', both in your call to
ft_volumerealign and in your call to ft_volumesegment. The cfg.coordinates for
ft_volumesegment has to be removed (actually it is a deprecated option). The
idea now is that mri-structures in fieldtrip can have a coordsys field, which
allows for more transparent use of the different head coordinate system
conventions. This takes away the need for intermediately coregistering the MRI
in 'ctf'-convention, and would also take away your need to call headcoordinates
later on.</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Best wishes,</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Jan-Mathijs</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Apr 12, 2011, at 11:07 AM, <<a
href="mailto:Jan.Hirschmann@med.uni-duesseldorf.de" target="_blank">Jan.Hirschmann@med.uni-duesseldorf.de</a>>
<<a href="mailto:Jan.Hirschmann@med.uni-duesseldorf.de" target="_blank">Jan.Hirschmann@med.uni-duesseldorf.de</a>>
wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
<br>
<br>
</span></font><o:p></o:p></p>
</div>
</div>
<span style='word-spacing:0px'>
<div link=blue vlink=blue>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>Dear fieldtrip experts,</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>I have two questions regarding head model
creation. As noted on this thread, the volumesegment function was updated and I
tested it for our Neuromag data. The segmentation is performed, but
unfortunately it is not aligned with the MRI in my case. Here is the code I am
using, the fieldtrip is from 9<sup>th</sup> April 2011.</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>%read mri</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>mri
= ft_read_mri(subject_files.fiff_mri);</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>mri.anatomy=double(mri.anatomy);</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>%these are the fiducials for this subject taken from the Neuromag
GUI for coregistration</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg=[];</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.fiducial.rpa=[136.35 142.80
31.96];</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.fiducial.nas=[47.84 101.80 100.10];</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.fiducial.lpa=[139.22 146.17 162.69];</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>%define the head coordinate system according to CTF conventions</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.method='fiducial';</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>real_mri=ft_volumerealign(cfg,mri);</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>%segment</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg
= [];</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.template =
'/data/apps/spm/spm8/templates/T1.nii';</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.coordinates = 'ctf';</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.keepintermediate = 'no';</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>segmentedmri = ft_volumesegment(cfg,
real_mri);</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>%plot white matter</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>test=segmentedmri;</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>test.anatomy=real_mri.anatomy;</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg=[];</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>cfg.funparameter='white';</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>ft_sourceplot(cfg,test); %see attached picture</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>The other issue regards back-transformation from
CTF to Neuromag coordinates, which is necessary to make the head model fit the
sensors. My idea was to create an appropriate transformation matrix like this.</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>cd
/net/avidya/storage/home/jan/fieldtrip-20110409/private</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>ctfmat=headcoordinates(nas,lpa,rpa,'ctf');</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>nmmat=headcoordinates(nas,lpa,rpa,'neuromag');</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>ctf_to_nm=nmmat/ctfmat;</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>And then to use it on the head model to bring it
back into Neuromag coordinates:</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>%create single shell, realistic headmodel</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>cfg
= [];</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>hdm
= ft_prepare_singleshell(cfg,segmentedmri);</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>% transformation of headmodel into Neuromag space</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>hdm.bnd.pnt=warp_apply(ctf_to_nm,hdm.bnd.pnt,'homogeneous');</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>Does this survive a sanity check?</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>Best regards and thanks a lot,</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'>Jan</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span lang=EN-US style='font-size:10.0pt;
font-family:Arial;color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
color=black face="Times New Roman"><span style='font-size:12.0pt;color:black'>
<hr size=2 width="100%" align=center>
</span></font></div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><b><font
size=2 color=black face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;
color:black;font-weight:bold'>Von:</span></font></b><font size=2 color=black
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma;color:black'> <a
href="mailto:fieldtrip-bounces@donders.ru.nl" target="_blank">fieldtrip-bounces@donders.ru.nl</a> [<a
href="mailto:fieldtrip-bounces@donders.ru.nl" target="_blank">mailto:fieldtrip-bounces@donders.ru.nl</a>] <b><span
style='font-weight:bold'>Im Auftrag von </span></b>Jen Whitman<br>
<b><span style='font-weight:bold'>Gesendet:</span></b> Montag, 28. Februar
2011 22:32<br>
<b><span style='font-weight:bold'>An:</span></b> <st1:PersonName w:st="on">Email
discussion list for the FieldTrip project</st1:PersonName><br>
<b><span style='font-weight:bold'>Betreff:</span></b> [FieldTrip] I think
you solved the problem</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>I just checked, and when I re-ran my segmentation script with the
new Fieldtrip in order to use an spm8 template image, coordinates got reversed.
When I take out the calls to flipdim, they look fine (see attached
screenshots). That certainly explains the meaningless results I was getting!<br>
<br>
Thanks for figuring that out,<br>
<br>
Jen</span></font><o:p></o:p></p>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Mon, Feb 28, 2011 at 12:36 PM, jan-mathijs schoffelen <<a
href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>>
wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Hi Jen,</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>At first glance I have a comment on your script. You may need to
explicitly check the alignment of your segmented volume and the original
anatomy. A while a go some changes were made to ft_volumesegment, taking away
the need to do the flipdim(flipdim... operations. I have posted this on
the discussion list last January, but you may not have noticed. </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Anyway, if you now have used a recent version of FieldTrip for
your segmentation both the location of your dipole grid, and the volume
conductor model will not be adequately coregistered with the data, which may
lead to funky results to begin with. That's most likely not related to the
filetype in which the volumes are saved for later use.</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Best wishes,</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color="#888888" face="Times New Roman"><span style='font-size:12.0pt;
color:#888888'>Jan-Mathijs</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Feb 28, 2011, at 8:59 PM, Jen Whitman wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
<br>
<br>
<br>
</span></font><o:p></o:p></p>
</div>
</div>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Hello Jan, <br>
<br>
When calling volumesegment, I specified 'ctf' as the coordinate system. The
function I wrote to call volumesegment and prepare_singleshell for each subject
and save the results is pasted below, with a couple of comments added for
clarity.<br>
Over the weekend I tried specifying the coordinate system in the call to
ft_volumenormalise as 'ctf' rather than 'spm', and commented out all the lines
that said cfg.spmversion = 'spm8'; before calling a function. However, that
created worse results, as each plot involved stripes of activation and empty
voxels, suggesting that 'ctf' was not the correct coordinate system to specify.<br>
<br>
Thanks for the attached script. Looking in that the comments in that, I suspect
that the solution to my problems will be to specify my filetype as nifti_img
rather than nifti. I'll let you know how that goes.<br>
<br>
Jen<br>
<br>
------------------------------------------------------------------------------------------------------------<br>
% the variable subj is simply a string consisting of a subject number (e.g.
's05') which can be a folder name or part of a filename<br>
function [vol mri segmentedmri
segmentedmriF]=call_volume_segment_function_spm8(subj)<br>
cfg.spmversion = 'spm8';<br>
cfg.template = '/home/woodwardlab/spm8/templates/EPI.nii';<br>
%cfg.template='/home/common/matlab/spm2/templates/T1.mnc'; <br>
<a href="http://cfg.name" target="_blank">cfg.name</a>=[subj '_volseg'];<br>
cfg.write='yes';<br>
cfg.smooth='no'; <br>
cfg.coordinates='ctf'; <br>
mri=read_mri([subj '/mri/' subj 'head.mri']); % made with CTF mriConverter and
mriViewer software, after fiducials were marked<br>
segmentedmri = volumesegment(cfg, mri);<br>
segmentedmriF = segmentedmri;<br>
segmentedmriF.gray = flipdim(flipdim(flipdim(segmentedmriF.gray,3),2),1);<br>
segmentedmriF.white = flipdim(flipdim(flipdim(segmentedmriF.white,3),2),1);<br>
segmentedmriF.csf =
flipdim(flipdim(flipdim(segmentedmriF.csf,3),2),1);<br>
segmentedmriF.transform = mri.transform;<br>
segmentedmriF.anatomy = mri.anatomy;<br>
cfg = [];<br>
cfg.spmversion = 'spm8';<br>
vol = prepare_singleshell(cfg, segmentedmriF);<br>
eval(['save ' subj '/meg/mrisegmented.mat mri segmentedmri segmentedmriF vol'])<br>
<br>
<br>
<br>
<br>
</span></font><o:p></o:p></p>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Sat, Feb 26, 2011 at 5:26 AM, jan-mathijs schoffelen <<a
href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>>
wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Dear Jen,</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>I do not manage to reproduce your issue, when only focussing on
the ft_volumewrite and visualization part of your pipeline. See attached
script, and yet an updated version of ft_volumewrite which you need to
(hopefully) draw the same conclusion as I did.</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Yet, I only now realize that your question may pertain to the
entire pipeline. It could be that something is going wrong there. </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>I only see now that in the part of your script of which you
reported that it gave 'good' results, you specify cfg.coordinates = 'ctf'
before calling ft_volumenormalise. I assume this is correct, because the
coordinate system your source-reconstructed data lives in, is according to the
CTF-convention, and not according to the SPM-convention. On the other hand, the
template for the spatial normalization lives in the SPM-coordinate system. In
order for the spatial normalization to work OK, Fieldtrip tries to convert from
one coordinate system to the other (once again, this is appropriate behaviour),
before doing the actual normalization. It seems that at least in the script you
sent along, in the final (not working version), you specified cfg.coordinates =
'spm' prior to calling ft_volumenormalise. This is probably wrong.</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Another important point that should be mentioned, is that the
coordinate systems in which the functional data and the anatomical data live
should be the same for the ft_sourceinterpolate to make sense. In other words,
if your source reconstructed images are defined on a 3D grid of positions in
CTF-space, the mri.transform of your anatomy should describe a transformation
from voxel to CTF-space.</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>I think you may want to revisit step by step this part of the
pipeline; I don't think the problem lies in the writing.</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>A final possibility of course is that Mricron is misbehaving...</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Best,</span></font><o:p></o:p></p>
</div>
</div>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color="#888888" face="Times New Roman"><span style='font-size:12.0pt;
color:#888888'>Jan-Mathijs</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
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<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color="#888888" face="Times New Roman"><span style='font-size:12.0pt;
color:#888888'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
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<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color="#888888" face="Times New Roman"><span style='font-size:12.0pt;
color:#888888'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
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<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color="#888888" face="Times New Roman"><span style='font-size:12.0pt;
color:#888888'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
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<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Feb 25, 2011, at 9:44 PM, Jen Whitman wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
<br>
<br>
<br>
</span></font><o:p></o:p></p>
</div>
</div>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Hi Jan,<br>
<br>
I tried re-running the analysis with the new script you sent me, and the latest
version of fieldtrip (since I needed ft_get_opt as well), but the spm8 images
being written are still producing flawed results. It's the same problem as I
mentioned briefly in my previous post. I am not getting any error messages when
writing these images. Rather, my problem is that the spm8 and spm2 results from
the same data ought to be identical when viewed in mricron, but they're far
from it. When I use mricron to look at the results from the spm8-format images,
combined across participants to create a t-image, I just get a single 'blob'
spanning roughly half the brain. In contrast, when I used spm2-format
previously on the same data, the t-image was much more meaningful; a posterior
alpha power decrease in a set of regions corresponding to the 'task-positive
network' (a network found in the results of an fMRI version of my experiment,
and widely reported in the fMRI literature). <br>
<br>
This failure to replicate the spm2 results when using spm8 images from the same
data leads me to suspect that something is wrong with the coordinates for spm8
format. However, after experimenting extensively with different cfg options I
still haven't identified the problem. If I my structural MRIs have been saved
to .mri files using CTF's MRIConverter program, which cfg options, particularly
for coordinates, template images, and filetypes, should I specify before
calling the ft_volumesegment, ft_prepare_singleshell, ft_sourceinterpolate,
ft_volumenormalise, and ft_volumewrite functions? Or should I be calling a different
set of functions now?<br>
<br>
Thanks again for your help,<br>
<br>
Jen</span></font><o:p></o:p></p>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Thu, Feb 24, 2011 at 10:07 AM, Jen Whitman <<a
href="mailto:jenwhitman@gmail.com" target="_blank">jenwhitman@gmail.com</a>>
wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Great, thanks!<br>
<br>
I'll start the analysis with your new script today and will let you know how it
works out.<br>
</span></font><font color="#888888"><span style='color:#888888'><br>
Jen</span></font><o:p></o:p></p>
<div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Thu, Feb 24, 2011 at 4:44 AM, jan-mathijs schoffelen <<a
href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>>
wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<blockquote style='border:none;border-left:solid windowtext 3.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt;
border-color:-moz-use-text-color -moz-use-text-color -moz-use-text-color windowtext'>
<div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Dear Jen,</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>I managed to reproduce your problem. The code was rather buggy and
indeed ft_volumewrite did not behave as it should have. I now fixed it in the
code and it should run fine now. Please find the updated file attached. It will
be available on our ftp-server as of tonight. Please note that I updated the
documentation, and changed the names of some of the options a bit. If you want
to save your data in analyze-format, you should specify cfg.filetype =
'analyze_spm'. If you specify cfg.filetype = 'nifti', it should write out a
volume to nifti-format, using SPM8.</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Best wishes,</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color="#888888" face="Times New Roman"><span style='font-size:12.0pt;
color:#888888'>Jan-Mathijs</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color="#888888" face="Times New Roman"><span style='font-size:12.0pt;
color:#888888'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color="#888888" face="Times New Roman"><span style='font-size:12.0pt;
color:#888888'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
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</div>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Feb 23, 2011, at 7:44 PM, Jen Whitman wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
Dear Jan,<br>
<br>
Thanks for the quick reply. Yes, I have tried it out quite a few times now,
experimenting with different settings in the cfgs. Below I'll paste the code
I've been using to write images - first the code that successfully created spm2
images that produced good results, then the code used for creating nifti format
images from the same data. The comments in this second part are at this point a
bit of a maze of cfg options I've been changing back & forth. Any
insights/suggestions regarding how to set up my cfgs to make this work would be
greatly appreciated.<br>
<br>
Jen<br>
<br>
<br>
%%%%%%%% this code generated spm2-compatible images which did work (producing
results that made sense).<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
<br>
sourcetemp.avg.pow = (sourcetemp.avg.pow -
sourcePre.avg.pow) ./ sourcePre.avg.pow;<br>
<br>
cfg = [];<br>
cfg.downsample = 2;<br>
sourcetempInt = sourceinterpolate(cfg, sourcetemp , mri);<br>
<br>
% projecting the plot onto a surface...<br>
cfg = [];<br>
cfg.coordinates = 'ctf';<br>
cfg.template =
'/home/common/matlab/spm2/templates/T1.mnc'; %this template is in MNI
coordinates<br>
sourcetempIntN = volumenormalise(cfg, sourcetempInt);<br>
<br>
filename=[subj 'run' int2str(r) 'cond' int2str(cond) '_'
int2str(f) 'HzWin' int2str(win) 'width750ms'];<br>
cfg=[];<br>
cfg.parameter = 'avg.pow'; % string,
describing the functional data to be processed, e.g. 'pow', 'coh' or 'nai'<br>
cfg.filename = [filename
'.img']; %'testimageoutput_alphafreq'; % filename without the extension<br>
cfg.filetype = 'spm';
%'analyze', 'spm', 'vmp' or 'vmr'<br>
cfg.coordinates = 'spm'; %'spm, 'ctf' or empty
for interactive (default = [])<br>
cfg.datatype = 'double'; %'float'; %'double'; %'bit1',
'uint8', 'int16', 'int32', 'float' or 'double'<br>
<br>
volumewrite(cfg, sourcetempIntN)<br>
<br>
<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<br>
%%%%% this code below hasn't worked yet...<br>
<br>
% I added cfg.spmversion = 'spm8';<br>
% in the cfgs for the calls to ft_prepare_leadfield and ft_sourceanalysis,<br>
% and in the call to prepare_singleshell after calling volumesegment<br>
<br>
% I've also ensured that spm8 is the only spm version in my path, even in<br>
% the fieldtrip/external folder, and ensured that spm8 is installed properly<br>
% (files compiled correctly, etc..)<br>
<br>
sourcetemp.avg.pow = (sourcetemp.avg.pow -
sourcePre.avg.pow) ./ sourcePre.avg.pow;<br>
<br>
filename=[subj 'run' int2str(r) 'cond' int2str(cond) '_'
int2str(f) 'Hzspm8_FIXv9_Win' int2str(win) 'width750ms.img'];<br>
<br>
cfg = [];<br>
% cfg.coordinates = 'spm'; % changed for version
5<br>
% cfg.spmversion = 'spm8'; % changed for version 5<br>
cfg.downsample = 4;<br>
sourcetempInt = ft_sourceinterpolate(cfg, sourcetemp , mri);<br>
<br>
<br>
% projecting the plot onto a surface...<br>
cfg = [];<br>
%cfg.coordinates = 'spm'; % changed for version 5<br>
%cfg.coordinates = 'ctf'; % changed for version 5<br>
cfg.coordinates = 'spm'; % changed back to spm for version 9<br>
cfg.downsample = 4;<br>
%cfg.spmversion = 'spm8'; % changed for version 6 (because
this gets specified in volumewrite)<br>
cfg.template = 'Hmatrix/mask.nii.nii'; % basically
equivalent to using spm8/templates/EPI.nii, except that mask.nii (produced from
fmri data) has the desired voxel size<br>
% <a href="http://cfg.name" target="_blank">cfg.name</a> =
[filename]; % changed for version 6<br>
%cfg.write= 'yes'; % changed for version 6 (when this was
set to 'yes' there was no subsequent call to volumewrite)<br>
cfg.write= 'no'; % changed for version 6<br>
sourcetempIntN = ft_volumenormalise(cfg, sourcetempInt);<br>
<br>
% this whole cfg and function call added for version 6 <br>
cfg=[];<br>
% cfg.parameter =
string, describing the functional data to be processed, e.g. 'pow', 'coh' or
'nai'<br>
% cfg.filename = filename without the
extension<br>
% cfg.filetype = 'analyze', 'spm',
'vmp' or 'vmr'<br>
% cfg.vmpversion = 1 or 2 (default) version of
the vmp-format to use<br>
% cfg.coordinates = 'spm, 'ctf' or empty for
interactive (default = [])<br>
cfg.parameter='pow';<br>
cfg.filename=filename; <br>
cfg.filetype = 'spm';<br>
cfg.spmversion = 'SPM8'; % capitalized after first error
message from vers 6<br>
% cfg.dataformat='nifti'; % added after first error message
from vers 6<br>
% commented out after 2nd error message from vers 6<br>
%cfg.vmpversion=2; % this is a filetype, like spm, so don't
need to specify unless cfg.filetyp='vmp' <br>
cfg.coordinates='spm';<br>
ft_volumewrite(cfg,sourcetempIntN);<br>
<br>
<br>
<br>
<br>
<br>
<br>
</span></font><o:p></o:p></p>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>On Wed, Feb 23, 2011 at 7:50 AM, jan-mathijs schoffelen <<a
href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>>
wrote:</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Dear Jen,<br>
<br>
I notice that indeed in the documentation section of ft_write_volume there is a
FIXME behind nifti. Yet, nifti format seems to be supported by ft_write_volume
(at least in a recent version of fieldtrip). Did you try it at all (and ran
into problems) or were you held back by the FIXME statement? Could you just try
it out using a recent fieldtrip function?<br>
<br>
Thanks and best wishes<br>
<br>
Jan-Mathijs</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
<br>
<br>
On Feb 23, 2011, at 2:21 AM, Jen Whitman wrote:</span></font><o:p></o:p></p>
</div>
</div>
<blockquote style='border:none;border-left:solid windowtext 3.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-top:5.0pt;margin-right:0cm;margin-bottom:5.0pt;
border-color:-moz-use-text-color -moz-use-text-color -moz-use-text-color windowtext'>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;margin-bottom:12.0pt'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Hello,<br>
<br>
While writing beamformed images to spm2 format in a previous version of
fieldtrip (now lost due to a computer crash), I was able to get nice-looking
results; networks of brain regions consistent with existing literature. When I
try to write images from the same dataset and the same analysis to spm8 format,
my results (t-images computed across subjects) end up being single clusters
spanning large sections of the brain (e.g. a 'blob' spanning all of one
hemisphere but not the other). Unfortunately, some aspects of my planned data
analyses cannot be performed on spm2 images, so I have to find a way of writing
to successfully to nifti format.<br>
<br>
I just noticed that in the comments in the ft_write_volume function, which I am
calling via ft_volumewrite, it says 'FIXME' next to nifti under the list of
supported dataformats. Is there by any chance a patch out there for writing
nifti images?<br>
<br>
Thanks!</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>_______________________________________________<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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
</div>
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</div>
</blockquote>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
Dr. J.M. (Jan-Mathijs) Schoffelen<br>
Donders Institute for Brain, Cognition and Behaviour,<br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The Netherlands<br>
<a href="mailto:J.Schoffelen@donders.ru.nl" target="_blank">J.Schoffelen@donders.ru.nl</a><br>
Telephone: 0031-24-3614793<br>
<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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
</div>
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<div>
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<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
</div>
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</div>
</blockquote>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div><span style='word-spacing:0px'>
<div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Dr. J.M. (Jan-Mathijs) Schoffelen </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Donders Institute for Brain, Cognition and
Behaviour, <br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The Netherlands</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><a href="mailto:J.Schoffelen@donders.ru.nl"
target="_blank">J.Schoffelen@donders.ru.nl</a></span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Telephone: 0031-24-3614793</span></font><o:p></o:p></p>
</div>
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</div>
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<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'></span> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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</div>
</div>
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</div>
</div>
</div>
</span>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
</span></span>_______________________________________________<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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
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<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Dr. J.M. (Jan-Mathijs) Schoffelen </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Donders Institute for Brain, Cognition and Behaviour, <br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The Netherlands</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><a href="mailto:J.Schoffelen@donders.ru.nl" target="_blank">J.Schoffelen@donders.ru.nl</a></span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'>Telephone: 0031-24-3614793</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
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<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
_______________________________________________<br>
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<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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div><span style='word-spacing:0px'><span style='word-spacing:0px'>
<div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Dr. J.M. (Jan-Mathijs) Schoffelen </span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Donders Institute for Brain, Cognition and
Behaviour, <br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The Netherlands</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><a href="mailto:J.Schoffelen@donders.ru.nl"
target="_blank">J.Schoffelen@donders.ru.nl</a></span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Telephone: 0031-24-3614793</span></font><o:p></o:p></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'></span></span> </span></font><o:p></o:p></p>
</div>
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</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'><br>
_______________________________________________<br>
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target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
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<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><misalignment.png></span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>_______________________________________________<br>
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target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><span style='word-spacing:0px'><span style='word-spacing:
0px'>Dr. J.M. (Jan-Mathijs) Schoffelen </span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Donders Institute for Brain, Cognition and
Behaviour, <br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The Netherlands</span></font><o:p></o:p></p>
</div>
</div>
</div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><a href="mailto:J.Schoffelen@donders.ru.nl"
target="_blank">J.Schoffelen@donders.ru.nl</a></span></font><o:p></o:p></p>
</div>
</div>
</div>
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<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Telephone: 0031-24-3614793</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
</div>
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<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
</div>
</span>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'></span><pic1.png><pic2.png><pic3.png></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>_______________________________________________<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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'> </span></font><o:p></o:p></p>
</div>
<div>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><span style='word-spacing:0px'><span style='word-spacing:
0px'>Dr. J.M. (Jan-Mathijs) Schoffelen </span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Donders Institute for Brain, Cognition and
Behaviour, <br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The Netherlands</span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><a href="mailto:J.Schoffelen@donders.ru.nl"
target="_blank">J.Schoffelen@donders.ru.nl</a></span></font><o:p></o:p></p>
</div>
</div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Telephone: 0031-24-3614793</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 color=black face="Times New Roman"><span style='font-size:12.0pt;
color:black'></span> </span></font><o:p></o:p></p>
</div>
</span>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><headmodel_with_neuromag.m></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>_______________________________________________<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"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
<div>
<div>
<div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><span style='word-spacing:0px'><span style='word-spacing:
0px'>Dr. J.M. (Jan-Mathijs) Schoffelen </span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Donders Institute for Brain, Cognition and
Behaviour, <br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The Netherlands</span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'><a href="mailto:J.Schoffelen@donders.ru.nl"
target="_blank">J.Schoffelen@donders.ru.nl</a></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=4 color=black face=Helvetica><span style='font-size:13.5pt;font-family:
Helvetica;color:black'>Telephone: 0031-24-3614793</span></font><o:p></o:p></p>
</div>
</div>
</div>
</div>
</span>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=3 face="Times New Roman"><span style='font-size:12.0pt'> <o:p></o:p></span></font></p>
</span>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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