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<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US">Word up Zita,<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US">Try this(replacing the filename for the file you want):
<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US">D1 = spm_eeg_load(</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0;mso-fareast-language:EN-US">'/imaging/as05/EEG
data/Load3Easy_TF/wmrtf_efMMspm8_raw_0001'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US">);</span><span style="font-family:"Courier New";mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US">l3e1=D1.fttimelock;</span><span style="font-family:"Courier New";mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US">l3e1.dimord=</span><span style="font-size:10.0pt;font-family:"Courier New";color:#A020F0;mso-fareast-language:EN-US">'chan_freq_time'</span><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US">;</span><span style="font-family:"Courier New";mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:10.0pt;font-family:"Courier New";color:black;mso-fareast-language:EN-US">l3e1.powspctrm = squeeze(D1.fttimelock.powspctrm);</span><span style="font-family:"Courier New";mso-fareast-language:EN-US"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Extra tip: you first need to separate your conditions such that you have an SPM file for each subject for each condition……..<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Let me know how you get on,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">D.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">________________________________________________<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Dr. Duncan Astle,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Programme Leader Track,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">British Academy Research Fellow,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">MRC Cognition and Brain Sciences Unit,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Chaucer Road,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Cambridge.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Duncan.Astle@mrc-cbu.cam.ac.uk<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> fieldtrip-bounces@science.ru.nl [mailto:fieldtrip-bounces@science.ru.nl]
<b>On Behalf Of </b>Zita Eva Patai<br>
<b>Sent:</b> 15 November 2012 17:04<br>
<b>To:</b> FieldTrip discussion list<br>
<b>Subject:</b> Re: [FieldTrip] error when converting from spm to ft<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Dear Jörn,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Thank you for the quick reply. I will try your suggestion!<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Many thanks,<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">z<o:p></o:p></p>
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<p class="MsoNormal">On Thu, Nov 15, 2012 at 2:55 PM, "Jörn M. Horschig" <<a href="mailto:jm.horschig@donders.ru.nl" target="_blank">jm.horschig@donders.ru.nl</a>> wrote:<o:p></o:p></p>
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<div>
<p class="MsoNormal">Dear Zita,<br>
<br>
The function seems to convert the function not correctly to a freq datastructure - it seems more like raw data to me.<br>
<br>
freq data requires a .powspctrm field, which should be a matrix of observations x channels x freq x time. So you would need to use cell2mat on your .trial field. Probably you need to permute the dimensions to match this order. Additionally, you will need a
.dimord field which which should be 'rpt_chan_freq_time' and you need a .freq field that contains the frequencies in that matrix. Please first make sure that your trials actually have 3 dimensions, else something else in the conversion went wrong.<br>
<br>
I don't use SPM so no clue if there is a better way than doing it manually.<br>
<br>
Best,<br>
Jörn<o:p></o:p></p>
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<p class="MsoNormal"><br>
<br>
On 11/14/2012 6:32 PM, Zita Eva Patai wrote:<o:p></o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<div>
<p class="MsoNormal">Hello FT-ers <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">In the past i had no problem when converting my data from SPM (where i do preprocessing and averaging) to FT (where I do my cluster-stats and plotting)<o:p></o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Currently, I am using the new way to convert (previous version seems outdated 'nspm2ftrip') and I am hitting a wall: it says my data is not in the right format, ie: not freq data. But i know that it is...any advice would be much appreciated!
Not to mention is warns me my data is not epoched when it is indeed so...<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Thank you!<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">zita<o:p></o:p></p>
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<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">*********************<o:p></o:p></p>
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<div>
<div>
<p class="MsoNormal"><b>>> D = spm_eeg_load</b><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">SPM M/EEG data object<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Type: evoked<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Transform: TF<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">8 conditions<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">326 channels<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">20 frequencies<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">501 samples/trial<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">8 trials<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Sampling frequency: 250 Hz<o:p></o:p></p>
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<div>
<p class="MsoNormal">Loaded from file C:\Users\Eva Z Patai\Documents\MATLAB\epoched_data\tf\rmtf_rs01_timecorr.mat<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<div>
<p class="MsoNormal">Use the syntax D(channels, frequencies, samples, trials) to access the data<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Type "methods('meeg')" for the list of methods performing other operations with the object<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Type "help meeg/method_name" to get help about methods<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><b>>> data = spm2ft(D)</b><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">mapping condition label "11" to condition code 1<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">mapping condition label "12" to condition code 2<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">mapping condition label "21" to condition code 3<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">mapping condition label "22" to condition code 4<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">mapping condition label "31" to condition code 5<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">mapping condition label "32" to condition code 6<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">mapping condition label "41" to condition code 7<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">mapping condition label "42" to condition code 8<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">data = <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"> fsample: 250.0000<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> label: {326x1 cell}<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> time: {1x8 cell}<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> trial: {1x8 cell}<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> trialinfo: [8x1 double]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> cfg: [1x1 struct]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal"><b>>> data2 = ft_checkdata(data, 'datatype', 'freq')</b><o:p></o:p></p>
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<div>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording <o:p></o:p></p>
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<div>
<p class="MsoNormal">> In utilities\private\warning_once at 81<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> In utilities\private\fixsampleinfo at 54<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> In ft_datatype_raw at 91<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> In ft_checkdata at 170 <o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:red">Error using ft_checkdata (line 288)</span><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><span style="color:red">This function requires freq data as input.</span><o:p></o:p></p>
</div>
</div>
<div>
<p class="MsoNormal"><br clear="all">
<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Zita Patai<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">DPhil, Experimental Psychology<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">University of Oxford<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="http://bcl.psy.ox.ac.uk/people/zita-eva-patai/" target="_blank">bcl.psy.ox.ac.uk/people/zita-eva-patai/</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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</div>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>fieldtrip mailing list<o:p></o:p></pre>
<pre><a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><o:p></o:p></pre>
<pre><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></pre>
</blockquote>
<p class="MsoNormal"><br>
<br>
<br>
<o:p></o:p></p>
<pre>-- <o:p></o:p></pre>
<pre>Jörn M. Horschig<o:p></o:p></pre>
<pre>PhD Student<o:p></o:p></pre>
<pre>Donders Institute for Brain, Cognition and Behaviour <o:p></o:p></pre>
<pre>Centre for Cognitive Neuroimaging<o:p></o:p></pre>
<pre>Radboud University Nijmegen <o:p></o:p></pre>
<pre>Neuronal Oscillations Group<o:p></o:p></pre>
<pre>FieldTrip Development Team<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>P.O. Box 9101<o:p></o:p></pre>
<pre>NL-6500 HB Nijmegen<o:p></o:p></pre>
<pre>The Netherlands<o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Contact:<o:p></o:p></pre>
<pre>E-Mail: <a href="mailto:jm.horschig@donders.ru.nl" target="_blank">jm.horschig@donders.ru.nl</a><o:p></o:p></pre>
<pre>Tel: <a href="tel:%2B31-%280%2924-36-68493" target="_blank">+31-(0)24-36-68493</a><o:p></o:p></pre>
<pre>Web: <a href="http://www.ru.nl/donders" target="_blank">http://www.ru.nl/donders</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Visiting address:<o:p></o:p></pre>
<pre>Trigon, room 2.30<o:p></o:p></pre>
<pre>Kapittelweg 29<o:p></o:p></pre>
<pre>NL-6525 EN Nijmegen<o:p></o:p></pre>
<pre>The Netherlands<o:p></o:p></pre>
</div>
<p class="MsoNormal"><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></p>
</div>
<p class="MsoNormal"><br>
<br clear="all">
<o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<p class="MsoNormal">-- <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Zita Patai<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">DPhil, Experimental Psychology<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">University of Oxford<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><a href="http://bcl.psy.ox.ac.uk/people/zita-eva-patai/" target="_blank">bcl.psy.ox.ac.uk/people/zita-eva-patai/</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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