<div dir="ltr">Hi Jan-Mathijs,<div><br></div><div>Thanks for your quick reply. I will go through your comments one by one:</div><div><br></div><div>1. The plot shows the nai, and in stead of these straight vertical lines going even into the center of the brain, I expected to see blobs.</div>
<div>2. In the precomputed filters I have used the same lambda, I should remove the cfg from this part. I have used cfg.dics.lambda from 0.05 to 50 and as I said this only changes the 'power' but not the structure of the data.</div>
<div>3. About the cfg.vol. I have been fidling around with the units for quite some time, but this is the only way the functional data will not end up the size of a pea in the anatomical data. I think this has to do with ctf/neuromag/spm coordinate system differences that are not yet fixed in FieldTrip?</div>
<div><br></div><div>But it seems that there is no obvious thing that could be happening then? </div><div><br></div><div>Groetjes Hanneke</div><div><br></div><div><br></div><div><br></div><div><br></div></div><div class="gmail_extra">
<br><br><div class="gmail_quote">On Tue, Oct 22, 2013 at 3:13 PM, jan-mathijs schoffelen <span dir="ltr"><<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Hi Hanneke,<div><br></div><div>I don't know what you expect to see, but to me it is not clear what quantity you are visualizing here (given the units).</div>
<div>Also, note that when you put precomputed spatial filters in the cfg, the lambda specified for the second round of ft_sourceanalysis is not going to change the spatial structure of the result, because the spatial filters are fixed. Also, note that specifying '0.05%' leads to a very tiny regularization. I think that you wanted to specify '5%', which translates to 0.05 times the trace of the csd matrix. Also, even though the cfg.vol will not be used in the second round of ft_sourceanalysis (nor in the first one if you used precomputed leadfields) I don't see the point in fiddling around with the metric units (converting it to 'mm'), but then explicitly stating them to be in 'cm'. Did you not do this when actually computing the leadfields? I hope not.</div>
<div><br></div><div>Best,</div><div>Jan-Mathijs</div><div><br></div><div><br></div><div><br><div><div><div class="h5"><div>On Oct 22, 2013, at 3:02 PM, <<a href="mailto:Hanneke.vanDijk@med.uni-duesseldorf.de" target="_blank">Hanneke.vanDijk@med.uni-duesseldorf.de</a>> <<a href="mailto:Hanneke.vanDijk@med.uni-duesseldorf.de" target="_blank">Hanneke.vanDijk@med.uni-duesseldorf.de</a>> wrote:</div>
<br></div></div><blockquote type="cite"><span style="border-collapse:separate;font-family:Helvetica;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;font-size:medium"><div lang="EN-US" link="blue" vlink="purple">
<div><div class="h5"><div><div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="color:rgb(31,73,125);font-size:10pt;font-family:Arial,sans-serif;background-repeat:initial initial;background-image:initial">D</span><span style="color:rgb(34,34,34);font-size:10pt;font-family:Arial,sans-serif;background-repeat:initial initial;background-image:initial">ear all,</span><u></u><u></u></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">My data (that are recorded with a neuromag306 system) look vertically smeared after sourceanalysis (see attached picture). The sources look like columns. The location (when plotted with method 'surface') looks comparable to the sensor analysis so I am not worried about that. <u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">The noise projection (cfg.dics.lambda) is something that I have been playing around with, but other then 'nai amplitude' de- or increases, this does not change the sources 'verticallness'. This indicates to me that this might be the problem... <u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">I am wondering if any of you has an idea where I should look to find a solution. <u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">Further information:<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">I am using a mni-normalised headmodel such as described on the site: <a href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space" style="color:blue;text-decoration:underline" target="_blank"><span style="color:rgb(17,85,204)">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space</span></a> but adapted to the neuromag system (I will make changes to the specific site :-) ).<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">Then compute the fourier, and do sourceanalysis as follows:<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg = [];<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.method = 'dics';<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.grid = mni_grid;<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.grid.filter = source.avg.filter; % precomputed filter and leadfield to project all trials through the same filter<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.grid.leadfield = source.leadfield;<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.vol = ft_convert_units(mni_vol,'mm'); % this step is needed somehow...<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.vol.unit = 'cm';<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.frequency = 60;<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.latency = 3;<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.dics.projectnoise = 'yes';<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.dics.lambda = '0.05%';<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.dics.normalize = 'yes';<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.keeptrials = 'yes';<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">cfg.rawtrial = 'yes'; % project each single trial through the filter<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">s = ft_sourceanalysis(cfg, f);<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">Thanks in advance for any suggestion!<u></u><u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)"><u></u> <u></u></span></div>
<div style="margin-right:0cm;font-size:11pt;margin-left:0cm;margin-bottom:0.0001pt;font-family:Calibri,sans-serif;margin-top:0cm;background-image:initial"><span style="font-size:10pt;font-family:Arial,sans-serif;color:rgb(34,34,34)">Groetjes Hanneke<u></u><u></u></span></div>
<div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><u></u> <u></u></div><div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<u></u> <u></u></div><div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:9pt">__________________________________________<u></u><u></u></span></div>
<div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:9pt"><u></u> <u></u></span></div><div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif">
<span style="font-size:9pt">Hanneke van Dijk, PhD<u></u><u></u></span></div><div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span lang="DE" style="font-size:9pt"><a href="http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html" style="color:blue;text-decoration:underline" target="_blank"><span lang="EN-US">http://www.uniklinik-duesseldorf.de/deutsch/unternehmen/institute/KlinNeurowiss/Team/HannekevanDijk/page.html</span></a></span><span style="font-size:9pt"><u></u><u></u></span></div>
<div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:9pt">Institute for Clinical Neuroscience,<u></u><u></u></span></div>
<div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:9pt">Heinrich Heine Universit</span><span lang="DE" style="font-size:9pt">ä</span><span style="font-size:9pt">t D</span><span lang="DE" style="font-size:9pt">ü</span><span style="font-size:9pt">sseldorf, Germany<u></u><u></u></span></div>
<div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:9pt"><a href="mailto:Hanneke.vanDijk@med.uni-duesseldorf.de" style="color:blue;text-decoration:underline" target="_blank">Hanneke.vanDijk@med.uni-duesseldorf.de</a><u></u><u></u></span></div>
<div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:9pt">Tel. <a href="tel:%2B49%20%280%29%20211%2081%2013074" value="+492118113074" target="_blank">+49 (0) 211 81 13074</a> <u></u><u></u></span></div>
<div style="margin-top:0cm;margin-right:0cm;margin-left:0cm;margin-bottom:0.0001pt;font-size:11pt;font-family:Calibri,sans-serif"><span style="font-size:9pt">__________________________________________ <u></u><u></u></span></div>
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<div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div>
<div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl" target="_blank">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: <a href="tel:%2B31-24-3614793" value="+31243614793" target="_blank">+31-24-3614793</a></div>
<div><br></div><div><a href="http://www.hettaligebrein.nl" target="_blank">http://www.hettaligebrein.nl</a></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span>
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