<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear all,<div><br></div><div>Looking at the MNE toolbox code, I think the following could be done to get the SSP projection if wanted:</div><div><br></div><div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; color: rgb(44, 152, 51); ">%% do SSP projection on data</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; color: rgb(44, 152, 51); "><span style="color: #000000"> </span>%%%% added by stephan moratti to do SSP</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> <span style="color: #223cfb">for</span> k = 1:length(data.hdr.orig.projs)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> data.hdr.orig.projs(k).active = true;</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> <span style="color: #223cfb">end</span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> fprintf(1,<span style="color: #b14bf0">'%d projection items activated\n'</span>,length(data.hdr.orig.projs));</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> [proj,nproj] = mne_make_projector_info(data.hdr.orig);</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> data.hdr.orig.raw.proj = proj;</div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 18.0px Courier; min-height: 22.0px"> <br class="webkit-block-placeholder"></p><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; color: rgb(44, 152, 51); "><span style="color: #000000"> </span>% now apply to data</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> <span style="color: #223cfb">for</span> i = 1:length(data.trial)</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> data.trial{i} = proj*data.trial{i};</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; font: normal normal normal 18px/normal Courier; "> <span style="color: #223cfb">end</span></div><p style="margin: 0.0px 0.0px 0.0px 0.0px; font: 18.0px Courier; min-height: 22.0px"> <br class="webkit-block-placeholder"></p><div><br></div><div>However, I am not sure how to put them into the grad.tra field.</div><div><br></div><div>Best,</div><div><br></div><div>Stephan</div><div><br></div><div><div>El 04/06/2011, a las 00:09, Tony W. Wilson escribió:</div><br class="Apple-interchange-newline"><blockquote type="cite">Dear Michael, everyone,<div>I believe you are correct. Most Neuromag sites have SSP vectors computed for data acquisitions; some groups occasionally recompute these per subject. These acquisition SSP vectors are stored in the fif file, but not applied w/o user intervention. In addition, I believe the tag relating to these vectors is removed from the fif file if you apply (t)SSS (through Maxfilter). However, I am not totally certain because I have never tried to apply these SSP vectors after applying SSS. Regardless, during analysis I treat the motion corrected t(SSS) output files just like raw data files. ... It is also worth noting here that one can compute new sets of SSP vectors in the MNE software (not directly related to the data acquisition vectors) and save these with the fif file for later use. I am not sure if these SSP vectors can be used outside of the MNE software.</div>
<div><br></div><div>Tony<br></div><br><div class="gmail_quote">On Fri, Jun 3, 2011 at 4:05 PM, <span dir="ltr"><<a href="mailto:michael.wibral@web.de">michael.wibral@web.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
dear neuromag / fieldtrip community,<br>
<br>
just a small question so I can keep up with the dsicussion:<br>
I thought that (t)SSS would nor project in a classical sense, i.e. for activities from inside the head leadfields would not have to be corrected? at least this I have read on the neuromeg list. So in most respcts the data should be treated just like rawdata - with standard coil positions after the motion correction ?<br>
<br>
maybe someone can shed more light on this?<br>
<br>
michael<br>
<br>
-----Ursprüngliche Nachricht-----<br>
Von: "Alexandre Gramfort" <<a href="mailto:alexandre.gramfort@inria.fr">alexandre.gramfort@inria.fr</a>><br>
Gesendet: 03.06.11 15:30:25<br>
<div class="im">An: "Email discussion list for the FieldTrip project" <<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
Betreff: Re: [FieldTrip] combining magnetometers and planad gradiometers for analysis<br>
<br>
</div><div><div></div><div class="h5">>Hi everyone,<br>
><br>
> > I don't know enough about the elekta-software/mne-software to know what is<br>
> > happening to the data when the ssp vectors are computed, but once we know<br>
> > enough details it should be straightforward to build it into fieldtrip.<br>
><br>
> SSP vectors are stored in fif files and applied to data only if requested.<br>
><br>
> In a typical MNE workflow, the SSP vectors are no directly applied to the raw<br>
> file (avoid data duplication on disk) but rather to the noise covariance matrix<br>
> and consequently in the whitening matrix. When computing an inverse solution,<br>
> the whitening matrix is used on the data and the lead field, hence taking<br>
> into account the SSP vectors.<br>
><br>
> Hope this helps.<br>
><br>
> --<br>
> Alexandre Gramfort, PhD<br>
> <a href="mailto:gramfort@nmr.mgh.harvard.edu">gramfort@nmr.mgh.harvard.edu</a><br>
> Dept. of Radiology MGH Martinos Center / Harvard Medical School<br>
> <a href="http://www-sop.inria.fr/members/Alexandre.Gramfort/" target="_blank">http://www-sop.inria.fr/members/Alexandre.Gramfort/</a><br>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; font-size: medium; "><div><br class="Apple-interchange-newline">________________________________________________________</div><div>Stephan Moratti, PhD<br><br></div><div>see also: <a href="http://web.me.com/smoratti/">http://web.me.com/smoratti/</a><br><br></div><div>Universidad Complutense de Madrid</div><div>Facultad de Psicología</div><div>Departamento de Psicología Básica I</div><div>Campus de Somosaguas</div><div>28223 Pozuelo de Alarcón (Madrid)</div><div>Spain</div><div><br></div><div>and</div><div><br></div><div>Center for Biomedical Technology</div><div>Laboratory for Cognitive and Computational Neuroscience</div><div>Parque Científico y Tecnológico de la Universidad Politecnica de Madrid<br>Campus Montegancedo</div><div>28223 Pozuelo de Alarcón (Madrid)</div><div>Spain<br><br><br>email: <a href="mailto:smoratti@psi.ucm.es">smoratti@psi.ucm.es</a><br>Tel.: +34 679219982<br><br></div></span></div></span></div></span></div></span></div>
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