[FieldTrip] error when converting from spm to ft

[Zita Eva Patai]

Great, thanks again!

On Fri, Nov 16, 2012 at 12:24 PM, Vladimir Litvak <litvak.vladimir at gmail.com
> wrote:

> 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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>
>
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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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