[FieldTrip] error when converting from spm to ft

[Vladimir Litvak]

Attached is a new version of fttimelock which outputs different versions of
the struct depending on the input and also allows selecting just subset of
the data to convert to FT. Duncan's fixes will not be necessary with it.
This will be included in next SPM8 update and in SPM12. You should put it
in @meeg directory in SPM.

Best,

Vladimir


On Fri, Nov 16, 2012 at 8:29 AM, Duncan Astle <
Duncan.Astle at mrc-cbu.cam.ac.uk> wrote:

>  I did it that way because the statistics options in fieldtrip need the
> data to be split into individual conditions for each subject (i.e. one
> average per condition per subject). Hence the one trial. ****
>
> ** **
>
> 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 *Vladimir Litvak
> *Sent:* 15 November 2012 21:29
>
> *To:* FieldTrip discussion list
> *Subject:* Re: [FieldTrip] error when converting from spm to ft****
>
>  ** **
>
> 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****
>
>  ****
>
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>
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>
> Contact:****
>
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>
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>
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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
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip****
>
>
>
> ****
>
> ** **
>
> -- ****
>
> ** **
>
> Zita Patai****
>
> DPhil, Experimental Psychology****
>
> University of Oxford****
>
> bcl.psy.ox.ac.uk/people/zita-eva-patai/****
>
> ** **
>
> ** **
>
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