[FieldTrip] error when converting from spm to ft
Duncan Astle
Duncan.Astle at mrc-cbu.cam.ac.uk
Fri Nov 16 09:29:22 CET 2012
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<mailto: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<mailto: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<mailto:Duncan.Astle at mrc-cbu.cam.ac.uk>
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [mailto: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<mailto: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/<http://bcl.psy.ox.ac.uk/people/zita-eva-patai/>
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--
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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Tel: +31-(0)24-36-68493<tel:%2B31-%280%2924-36-68493>
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Zita Patai
DPhil, Experimental Psychology
University of Oxford
bcl.psy.ox.ac.uk/people/zita-eva-patai/<http://bcl.psy.ox.ac.uk/people/zita-eva-patai/>
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Zita Patai
DPhil, Experimental Psychology
University of Oxford
bcl.psy.ox.ac.uk/people/zita-eva-patai/<http://bcl.psy.ox.ac.uk/people/zita-eva-patai/>
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