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<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>Dear fieldtrip experts,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
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 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. <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'>%read mri<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'>mri
= ft_read_mri(subject_files.fiff_mri);<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'>mri.anatomy=double(mri.anatomy);<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'>%these are the fiducials for this subject taken
from the Neuromag GUI for coregistration <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'>cfg=[];<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'>cfg.fiducial.rpa=[136.35
142.80 31.96];<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'>cfg.fiducial.nas=[47.84
101.80 100.10];<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'>cfg.fiducial.lpa=[139.22
146.17 162.69];<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'>%define the head coordinate system
according to CTF conventions<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'>cfg.method='fiducial';<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'>real_mri=ft_volumerealign(cfg,mri);<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'>%segment <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'>cfg
= [];<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'>cfg.template
= '/data/apps/spm/spm8/templates/T1.nii';<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'>cfg.coordinates = 'ctf';<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'>cfg.keepintermediate = 'no';<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'>segmentedmri =
ft_volumesegment(cfg, real_mri);<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'>%plot white matter<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'>test=segmentedmri;<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'>test.anatomy=real_mri.anatomy;<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'>cfg=[];<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'>cfg.funparameter='white';<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'>ft_sourceplot(cfg,test); %see attached picture<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 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.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
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 lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>cd
/net/avidya/storage/home/jan/fieldtrip-20110409/private<o:p></o:p></span></font></p>
<p class=MsoNormal><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');<o:p></o:p></span></font></p>
<p class=MsoNormal><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');<o:p></o:p></span></font></p>
<p class=MsoNormal><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;<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
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 lang=EN-US
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 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:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
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 lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>%create single shell,
realistic headmodel<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>cfg
= [];<o:p></o:p></span></font></p>
<p class=MsoNormal><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);<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
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 lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>% transformation of
headmodel into Neuromag space<o:p></o:p></span></font></p>
<p class=MsoNormal><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');<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
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 lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>Does this survive a
sanity check?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
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 lang=EN-US
style='font-size:10.0pt;font-family:Arial;color:navy'>Best regards and thanks a
lot,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-US
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 lang=EN-US
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 lang=EN-US
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>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>
<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'>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<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 Mon, Feb 28, 2011 at 12:36 PM, jan-mathijs schoffelen <<a
href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>>
wrote:<o:p></o:p></span></font></p>
<div style='word-wrap: break-word'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi Jen,<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>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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. <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Best wishes,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><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><font size=3 color="#888888" face="Times New Roman"><span
style='font-size:12.0pt;color:#888888'>Jan-Mathijs<o:p></o:p></span></font></p>
</div>
<div>
<div>
<div>
<p class=MsoNormal><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><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><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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Feb 28, 2011, at 8:59 PM, Jen Whitman wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
<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'>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>
<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 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:<o:p></o:p></span></font></p>
<div style='word-wrap: break-word'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Dear Jen,<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>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Yet, I only now realize that your question may pertain to the entire
pipeline. It could be that something is going wrong there. <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>A final possibility of course is that Mricron is misbehaving...<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Best,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><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><font size=3 color="#888888" face="Times New Roman"><span
style='font-size:12.0pt;color:#888888'>Jan-Mathijs<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color="#888888" face="Times New Roman"><span
style='font-size:12.0pt;color:#888888'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color="#888888" face="Times New Roman"><span
style='font-size:12.0pt;color:#888888'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color="#888888" face="Times New Roman"><span
style='font-size:12.0pt;color:#888888'><o:p> </o:p></span></font></p>
</div>
</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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div style='word-wrap: break-word'>
<div>
<p class=MsoNormal><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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Feb 25, 2011, at 9:44 PM, Jen Whitman wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
<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'>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<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, Feb 24, 2011 at 10:07 AM, Jen Whitman <<a
href="mailto:jenwhitman@gmail.com" target="_blank">jenwhitman@gmail.com</a>>
wrote:<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'>Great, thanks!<br>
<br>
I'll start the analysis with your new script today and will let you know how it
works out.<br>
<font color="#888888"><span style='color:#888888'><br>
Jen</span></font><o:p></o:p></span></font></p>
<div>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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:<o:p></o:p></span></font></p>
</div>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<div>
<div>
<div style='word-wrap: break-word'>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Dear Jen,<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>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Best wishes,<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><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><font size=3 color="#888888" face="Times New Roman"><span
style='font-size:12.0pt;color:#888888'>Jan-Mathijs<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color="#888888" face="Times New Roman"><span
style='font-size:12.0pt;color:#888888'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 color="#888888" face="Times New Roman"><span
style='font-size:12.0pt;color:#888888'><o:p> </o:p></span></font></p>
</div>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</div>
<div style='word-wrap: break-word'>
<div>
<p class=MsoNormal><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><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Feb 23, 2011, at 7:44 PM, Jen Whitman wrote:<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>
</div>
<div>
<div>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><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>
<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 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:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>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<o:p></o:p></span></font></p>
<div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
<br>
<br>
On Feb 23, 2011, at 2:21 AM, Jen Whitman wrote:<o:p></o:p></span></font></p>
</div>
</div>
<blockquote style='border:none;border-left:solid #CCCCCC 1.0pt;padding:0cm 0cm 0cm 6.0pt;
margin-left:4.8pt;margin-right:0cm'>
<div>
<div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>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!<o:p></o:p></span></font></p>
</div>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>_______________________________________________<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><o:p></o:p></span></font></p>
</blockquote>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><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><o:p></o:p></span></font></p>
</div>
<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" 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><o:p></o:p></span></font></p>
</blockquote>
</div>
</div>
</div>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div><span style='word-spacing:0px'>
<div style='word-wrap: break-word'>
<div style='word-wrap: break-word'>
<div>
<p class=MsoNormal><font size=4 color=black face=Helvetica><span
style='font-size:13.5pt;font-family:Helvetica;color:black'>Dr. J.M.
(Jan-Mathijs) Schoffelen <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><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<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><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><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=4 color=black face=Helvetica><span
style='font-size:13.5pt;font-family:Helvetica;color:black'>Telephone:
0031-24-3614793<o:p></o:p></span></font></p>
</div>
</div>
</div>
</div>
</span>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</div>
</div>
</div>
<div>
<div>
<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" 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><o:p></o:p></span></font></p>
</div>
</div>
</blockquote>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<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" 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><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>
<div>
<div style='word-wrap: break-word'>
<div style='word-wrap: break-word'>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Dr. J.M. (Jan-Mathijs) Schoffelen <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Donders Institute for Brain, Cognition and Behaviour, <br>
Centre for Cognitive Neuroimaging,<br>
Radboud University Nijmegen, The Netherlands<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><a href="mailto:J.Schoffelen@donders.ru.nl" target="_blank">J.Schoffelen@donders.ru.nl</a><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Telephone: 0031-24-3614793<o:p></o:p></span></font></p>
</div>
</div>
</div>
</div>
<p class=MsoNormal><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><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" 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><o:p></o:p></span></font></p>
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12.0pt'><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><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>
<div><span style='word-spacing:0px'><span style='word-spacing:0px'>
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<p class=MsoNormal><font size=4 color=black face=Helvetica><span
style='font-size:13.5pt;font-family:Helvetica;color:black'>Dr. J.M.
(Jan-Mathijs) Schoffelen <o:p></o:p></span></font></p>
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<div>
<p class=MsoNormal><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<o:p></o:p></span></font></p>
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<div>
<p class=MsoNormal><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><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=4 color=black face=Helvetica><span
style='font-size:13.5pt;font-family:Helvetica;color:black'>Telephone:
0031-24-3614793<o:p></o:p></span></font></p>
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</div>
</span>
<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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</div>
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<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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