[FieldTrip] error when converting from spm to ft

Thu Nov 15 22:28:48 CET 2012

Note that Duncan's suggestions only make sense for a dataset with only one trial. Even then I'm not sure why he had problems with the output as it was but I can check.

Vladimir

On 15 Nov 2012, at 18:57, Zita Eva Patai <eva.patai at psy.ox.ac.uk> wrote:

> awesome! thank you Duncan:)
> 
> Thanks everyone for all the suggestions!!
> 
> On Thu, Nov 15, 2012 at 6:24 PM, Duncan Astle <Duncan.Astle at mrc-cbu.cam.ac.uk> wrote:
> Word up Zita,
> 
>  
> 
> Try this(replacing the filename for the file you want):
> 
>  
> 
> D1 = spm_eeg_load('/imaging/as05/EEG data/Load3Easy_TF/wmrtf_efMMspm8_raw_0001');
> 
> l3e1=D1.fttimelock;
> 
> l3e1.dimord='chan_freq_time';
> 
> l3e1.powspctrm = squeeze(D1.fttimelock.powspctrm);
> 
>  
> 
> Extra tip: you first need to separate your conditions such that you have an SPM file for each subject for each condition……..
> 
>  
> 
> Let me know how you get on,
> 
> D.
> 
> ________________________________________________
> 
> Dr. Duncan Astle,
> 
> Programme Leader Track,
> 
> British Academy Research Fellow,
> 
> MRC Cognition and Brain Sciences Unit,
> 
> Chaucer Road,
> 
> Cambridge.
> 
> Duncan.Astle at mrc-cbu.cam.ac.uk
> 
>  
> 
> From: fieldtrip-bounces at science.ru.nl [mailto:fieldtrip-bounces at science.ru.nl] On Behalf Of Zita Eva Patai
> Sent: 15 November 2012 17:04
> To: FieldTrip discussion list
> Subject: Re: [FieldTrip] error when converting from spm to ft
> 
>  
> 
> Dear Jörn,
> 
>  
> 
> Thank you for the quick reply. I will try your suggestion!
> 
>  
> 
> Many thanks,
> 
> z
> 
> On Thu, Nov 15, 2012 at 2:55 PM, "Jörn M. Horschig" <jm.horschig at donders.ru.nl> wrote:
> 
> Dear Zita,
> 
> The function seems to convert the function not correctly to a freq datastructure - it seems more like raw data to me.
> 
> 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.
> 
> I don't use SPM so no clue if there is a better way than doing it manually.
> 
> Best,
> Jörn
> 
> 
> 
> On 11/14/2012 6:32 PM, Zita Eva Patai wrote:
> 
> Hello FT-ers
> 
>  
> 
> 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)
> 
>  
> 
> 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...
> 
>  
> 
> Thank you!
> 
> zita
> 
>  
> 
> *********************
> 
> >> D = spm_eeg_load
> 
> SPM M/EEG data object
> 
> Type: evoked
> 
> Transform: TF
> 
> 8 conditions
> 
> 326 channels
> 
> 20 frequencies
> 
> 501 samples/trial
> 
> 8 trials
> 
> Sampling frequency: 250 Hz
> 
> Loaded from file  C:\Users\Eva Z Patai\Documents\MATLAB\epoched_data\tf\rmtf_rs01_timecorr.mat
> 
>  
> 
> Use the syntax D(channels, frequencies, samples, trials) to access the data
> 
> Type "methods('meeg')" for the list of methods performing other operations with the object
> 
> Type "help meeg/method_name" to get help about methods
> 
>  
> 
> >> data = spm2ft(D)
> 
>  
> 
> mapping condition label "11" to condition code 1
> 
> mapping condition label "12" to condition code 2
> 
> mapping condition label "21" to condition code 3
> 
> mapping condition label "22" to condition code 4
> 
> mapping condition label "31" to condition code 5
> 
> mapping condition label "32" to condition code 6
> 
> mapping condition label "41" to condition code 7
> 
> mapping condition label "42" to condition code 8
> 
>  
> 
> data = 
> 
>  
> 
>       fsample: 250.0000
> 
>         label: {326x1 cell}
> 
>          time: {1x8 cell}
> 
>         trial: {1x8 cell}
> 
>     trialinfo: [8x1 double]
> 
>           cfg: [1x1 struct]
> 
>  
> 
>  
> 
> >> data2 = ft_checkdata(data, 'datatype', 'freq')
> 
>  
> 
> Warning: the data does not contain a trial definition, assuming that the trials are consecutive segments of a continuous recording 
> 
> > In utilities\private\warning_once at 81
> 
>   In utilities\private\fixsampleinfo at 54
> 
>   In ft_datatype_raw at 91
> 
>   In ft_checkdata at 170 
> 
> Error using ft_checkdata (line 288)
> 
> This function requires freq data as input.
> 
> 
> 
>  
> 
> --
> 
>  
> 
> Zita Patai
> 
> DPhil, Experimental Psychology
> 
> University of Oxford
> 
> bcl.psy.ox.ac.uk/people/zita-eva-patai/
> 
>  
> 
>  
> 
>  
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 
> 
> 
> -- 
> Jörn M. Horschig
> PhD Student
> Donders Institute for Brain, Cognition and Behaviour 
> Centre for Cognitive Neuroimaging
> Radboud University Nijmegen 
> Neuronal Oscillations Group
> FieldTrip Development Team
>  
> P.O. Box 9101
> NL-6500 HB Nijmegen
> The Netherlands
>  
> Contact:
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>  
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> 
> 
> 
>  
> 
> --
> 
>  
> 
> Zita Patai
> 
> DPhil, Experimental Psychology
> 
> University of Oxford
> 
> bcl.psy.ox.ac.uk/people/zita-eva-patai/
> 
>  
> 
>  
> 
> 
> _______________________________________________
> fieldtrip mailing list
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> 
> 
> 
> -- 
> 
> Zita Patai
> DPhil, Experimental Psychology
> University of Oxford
> bcl.psy.ox.ac.uk/people/zita-eva-patai/
> 
> 
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