[FieldTrip] Where to add a trialfun?
"Jörn M. Horschig"
jm.horschig at donders.ru.nl
Wed Oct 1 16:03:38 CEST 2014
Hi Ana,
from the first call with eventtype = '?', the output says
> event type: 'trigger' with event values: 'DIN1' 'DIN2' 'DIN4' 'DIN8'
This means that there is one event type in our data, namely 'trigger',
and the only trigger values in your data are 'DIN1', 'DIN2', 'DIN4' and
'DIN8'. FieldTrip works that way that it passes on the cfg.trialdef
structure to the trialfun that is specified. In your particular case,
trialfun_bit2dec does not seem to have a very user-friendly error
message, but the error message means that whatever eventtype and
eventvalues you asked for, they are not present in your data. When
looking at what you define, you can probably easily spot that you ask
for cfg.trialdef.eventtype = 'STATUS'. However, checking back the output
that you created with '?', there is no event type 'STATUS' in your data.
Therefore, everything works fine with your trialfun. If you try
specifying the trialdef properly, everything should work fine.
A general advise when using an own trial fun and getting an error
message: Try your code without specifying cfg.trialfun first. Then
FieldTrip will use the standard trialfun, which should work if all your
cfg-settings are fine. If the standard trialfun runs without errors,
then your trialfun should do so too. If your trialfun, however, then
crashes, the error is most likely in the trialfun that you used, and not
in the cfg-settings. In your case, however, I am fairly certain that the
cfg-settings you specified were causing your problem.
I hope this helps.
Best,
Jörn
On 9/30/2014 10:27 PM, Ana Laura Diez Martini wrote:
> For a more simple check, when I try to read the events without the
> trialfun ( so it uses ft_trialfun_general by default) I get the
> original event values:
>
> >> cfg = [];
> >> cfg.dataset = '27CW1.RAW';
> >> cfg.trialdef.eventtype = '?';
> >> cfg=ft_definetrial(cfg);
>
> Warning: no trialfun was specified, using ft_trialfun_general
> > In ft_definetrial at 135
> evaluating trialfunction 'ft_trialfun_general'
> reading the events from '27CW1.RAW'
> the following events were found in the datafile
> event type: 'trigger' with event values: 'DIN1' 'DIN2' 'DIN4' 'DIN8'
> no trials have been defined yet, see FT_DEFINETRIAL for further help
> found 750 events
> created 0 trials
> the call to "ft_definetrial" took 4 seconds
>
> Then I try to use the trialfun, I get the same error
>
> >> cfg = [];
> >> cfg.dataset = '27CW1.RAW';
> >> cfg.trialfun = 'trialfun_bit2dec';
> >> cfg.trialdef.eventtype = '?';
> >> cfg=ft_definetrial(cfg);
> evaluating trialfunction 'trialfun_bit2dec'
>
> Attempted to access trl(:,1); index out of bounds because size(trl)=[0,0].
>
> Error in trialfun_bit2dec (line 66)
> idx = any(diff(trl(:,1),1,1),2);
>
> Error in ft_definetrial (line 169)
> trl = feval(cfg.trialfun, cfg);
>
> So there is something the trialfun_bit2dec does that events cannot be
> read anymore.
>
>
> On Mon, Sep 29, 2014 at 9:01 PM, Arjen Stolk <a.stolk8 at gmail.com
> <mailto:a.stolk8 at gmail.com>> wrote:
>
> Hi Ana Laura,
>
> Your 'trl' is empty, which it shouldn't be. So anytime you try to
> index an element in it, it will throw an error.
>
> Can you check what 'event.values' you find in your dataset? And
> compare those with any of the ones falling under the switch case
> statement? One way to do this, is to put a debug marker (red dot)
> at the 'end' of the first for-loop (judging from the wiki). Then
> check the value of event(i).value, and click the continue button
> to move on to the next. An alternative way is to put a debug
> marker after event = ft_read_event and to instantly check all
> values of event with "[event(:).value]".
>
> Goodluck,
> Arjen
>
> 2014-09-30 6:20 GMT+02:00 Ana Laura Diez Martini
> <diezmartini at gmail.com <mailto:diezmartini at gmail.com>>:
>
> This is my attempt of adapting the code for the new Fieldtrip
>
> % TRIAL DEFINITION
>
> cfg=[];
> cfg.dataset = 'myfile';
>
> hdr = ft_read_header( 'myfile');
> dat = ft_read_data('myfile');
> cfg.trialfun = 'trialfun_bit2dec';
> cfg.trialdef.eventtype = 'STATUS';
> cfg.trialdef.eventvalue = cgrmrk; % stimulus triggers
> cfg.trialdef.prestim = 0.2;
> cfg.trialdef.poststim = 1;
>
> cfg.reref = 'yes';
> cfg.refchannel = ['all'];
> cfg = ft_definetrial(cfg);
>
> again the error is:
>
> Attempted to access trl(:,1); index out of bounds because
> size(trl)=[0,0].
>
> Error in trialfun_bit2dec (line 66)
> idx = any(diff(trl(:,1),1,1),2);
>
> Error in ft_definetrial (line 169)
> trl = feval(cfg.trialfun, cfg);
>
> Error in process_ERP_1_fieldtrip (line 106)
> cfg = ft_definetrial(cfg);
>
>
>
> On Mon, Sep 29, 2014 at 12:11 PM, Ana Laura Diez Martini
> <diezmartini at gmail.com <mailto:diezmartini at gmail.com>> wrote:
>
> Dear Arjen and Nietzsche,
>
> I tried debugging with dbstop if error and cfg.debug =
> 'saveonerror' and matlab points to:
>
> % discard the repeated values
> idx = any(diff(trl(:,1),1,1),2);
> trl = trl(idx,:);
>
> It does seem it is not reading the events. When I read
> them with the raw data, they seem to be there, with the
> DIN prefix. Any idea?
>
> On Mon, Sep 29, 2014 at 8:57 AM, Arjen Stolk
> <a.stolk8 at gmail.com <mailto:a.stolk8 at gmail.com>> wrote:
>
> Hey Ana Laura,
>
> Seems from the error message you're getting
>
> "Attempted to access trl(:,1); index out of bounds
> because size(trl)=[0,0]."
>
> that none of the triggers were found in your event
> data. You might wanna check why this is happening, by
> debugging 'trialfun_bit2dec' on your input.
>
> Best,
> Arjen
>
>
>
> 2014-09-29 19:00 GMT+02:00 Ana Laura Diez Martini
> <diezmartini at gmail.com <mailto:diezmartini at gmail.com>>:
>
> Thank you again Nietzsche!!
>
> Yes, I was referring to trialfun_bit2dec. I
> followed your advice and I changed definetrial to
> ft_definetrial and I confirm the function was
> added to my paths. After doing this, the error I
> get is:
>
> Attempted to access trl(:,1); index out of bounds
> because size(trl)=[0,0].
>
> Error in trialfun_bit2dec (line 66)
> idx = any(diff(trl(:,1),1,1),2);
>
> Error in ft_definetrial (line 169)
> trl = feval(cfg.trialfun, cfg);
>
> Error in process_ERP_1_fieldtrip (line 95)
> cfg = ft_definetrial(cfg);
>
> This is again the trial definition part in which I
> think I added what I think are useless lines but I
> was just trying to make it run it.
>
> % TRIAL DEFINITION
> cfg=[];
> cfg.filename = ['myfolders/subject.RAW'];
> cfg.headerfile = ['myfolders/subject.RAW'];
> cfg.dataset = ['myfolders/subject.RAW'];
> cfg.trialfun = 'trialfun_bit2dec'; %% trialfun
> definition
> cfg.trialdef.eventtype = 'STATUS';
> cfg.trialdef.eventvalue = cgrmrk; % stimulus
> triggers
> cfg.trialdef.prestim = 0.2; % latency in seconds
> cfg.trialdef.poststim = 1; % latency in seconds
> cfg = ft_definetrial(cfg);
>
> trl = cfg.trl;
> cfg=[];
> cfg.dataset = ['myfolders/subject.RAW'];
> cfg.trl = trl;
> cfg.reref = 'yes';
> cfg.refchannel = ['all'];
>
> Unfortunately using this function is crucial to my
> analysis because I would like to use only
> Fieldtrip to analyse all my data. Thank you for
> taking all this time.
>
> On Sun, Sep 28, 2014 at 10:53 PM, Lam, Nietzsche
> <n.lam at fcdonders.ru.nl
> <mailto:n.lam at fcdonders.ru.nl>> wrote:
>
> Hi again Ana Laura,
>
> One other thing that I thought of was to make
> sure that the function "trialfun_bit2dec" is
> added to your paths in matlab, so that
> ft_definetrial can find this function.
>
> By updating your fieldtrip to the most recent
> version "trialfun_bit2dec" is *not* included.
> So you'll need to store that as a separate .m
> file in a location that can be accessed by the
> paths set in matlab.
>
> Nietzsche
>
> ----- Original Message -----
> > From: "Ana Laura Diez Martini"
> <diezmartini at gmail.com
> <mailto:diezmartini at gmail.com>>
> > To: "FieldTrip discussion list"
> <fieldtrip at science.ru.nl
> <mailto:fieldtrip at science.ru.nl>>
> > Sent: Saturday, 27 September, 2014 7:18:25 PM
> > Subject: Re: [FieldTrip] Where to add a
> trialfun?
> > Thank you Nietzsche!
> >
> >
> > I added it where you suggested and now this
> is the error I get:
> >
> >
> >
> > Error using feval
> > Invalid function name 'trialfun_bit2dec(cfg)'.
> >
> >
> > Error in definetrial (line 105)
> > trl = feval(cfg.trialfun, cfg);
> >
> >
> > Error in process_ERP_1_fieldtrip (line 97)
> > cfg = definetrial(cfg);
> >
> >
> > Something I was worried about is that I use
> an old version of
> > Fieldtrip for my scripts because I wrote
> them long ago and this
> > trialfun uses the new format (with
> 'ft_s',etc.). Could this affect it
> > in any way?
> >
> >
> > Thanks again!
> >
> >
> > On Fri, Sep 26, 2014 at 11:05 PM, Lam,
> Nietzsche <
> > n.lam at fcdonders.ru.nl
> <mailto:n.lam at fcdonders.ru.nl> > wrote:
> >
> >
> > Hi Ana Laura,
> >
> > In general, you need to determine which
> trial function (Trialfun) to
> > use when using definetrial (see this tutorial:
> >
> http://fieldtrip.fcdonders.nl/tutorial/preprocessing
> under "do the
> > trial definition for the fully incongruent
> (FIC) condition).
> >
> > Please try adding this: "cfg.trialfun =
> 'trialfun_bit2dec(cfg)". to
> > your code before calling definetrial (see
> below).
> >
> > % TRIAL DEFINITION
> > cfg=[];
> > cfg.filename = ['my/folders/', subject, '.RAW'];
> > cfg.headerfile = ['my/folders/', subject,
> '.RAW'];
> >
> > cfg.trialdef.eventtype = 'STATUS';
> > cfg.trialdef.eventvalue = cgrmrk;
> > cfg.trialdef.prestim = 0.2;
> > cfg.trialdef.poststim = 1;
> > cfg.trialdef.eventtype=?;
> > cfg.trialfun = 'trialfun_bit2dec(cfg) %%
> trialfun definition
> > cfg = definetrial(cfg);
> >
> >
> > As an addition note: based on your error
> message, it seemed that the
> > problem was in the function
> trialfun_bit2dec. However, from the code
> > you showed us, you haven't referenced/called
> this function. I was
> > wondering if the code you provide
> corresponded to the code that
> > created your error message? I'm guessing you
> ran [trl]
> > =trialfun_bit2dec(cfg) directly (i.e. not
> via definetrial). In which
> > case, it was looking for
> cfg.trialdef.eventtype. You can call
> > trialfun_bit2dec as long as you have all the
> relevant information in
> > the cfg (which is in the code you showed
> us). Hope this helps.
> >
> > Best,
> > Nietzsche
> >
> >
> >
> >
> >
> >
> > ----- Original Message -----
> > > From: "Ana Laura Diez Martini" <
> diezmartini at gmail.com
> <mailto:diezmartini at gmail.com> >
> > > To: "FieldTrip discussion list" <
> fieldtrip at science.ru.nl
> <mailto:fieldtrip at science.ru.nl> >
> > > Sent: Saturday, 27 September, 2014 2:42:21 AM
> > > Subject: [FieldTrip] Where to add a trialfun?
> > > Hello all! I'm having a simple problem. I
> want to add this trialfun:
> > >
> > >
> http://fieldtrip.fcdonders.nl/faq/how_can_i_transform_trigger_values_from_bits_to_decimal_representation_with_a_trialfun
> > >
> > >
> > >
> > > I get this error:
> > >
> > >
> > >
> > > Reference to non-existent field 'trialdef'.
> > >
> > >
> > > Error in trialfun_bit2dec (line 52)
> > > if strcmp(event(i).type,
> cfg.trialdef.eventtype)
> > >
> > >
> > > I'm quite sure it's because I'm not
> writing it in the correct part
> > > of
> > > my script. This is my trial definition
> part. Where should I add it
> > > and
> > > how should I write the line?
> > >
> > >
> > >
> > > % TRIAL DEFINITION
> > > cfg=[];
> > > cfg.filename = ['my/folders/', subject,
> '.RAW'];
> > > cfg.headerfile = ['my/folders/', subject,
> '.RAW'];
> > >
> > >
> > > cfg.trialdef.eventtype = 'STATUS';
> > > cfg.trialdef.eventvalue = cgrmrk;
> > > cfg.trialdef.prestim = 0.2;
> > > cfg.trialdef.poststim = 1;
> > > cfg.trialdef.eventtype=?;
> > >
> > >
> > > cfg = definetrial(cfg);
> > >
> > >
> > > trl = cfg.trl;
> > > cfg=[];
> > > cfg.dataset = ['my/folders/', subject,
> '.RAW'];
> > > cfg.trl = trl;
> > > cfg.reref = 'yes';
> > > cfg.refchannel = ['all'];
> > >
> > >
> > > THANKS!
> > >
> _______________________________________________
> > > fieldtrip mailing list
> > > fieldtrip at donders.ru.nl
> <mailto:fieldtrip at donders.ru.nl>
> > >
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> > --
> > Nietzsche H.L. Lam, MSc
> > PhD Candidate
> >
> > Max Planck Institute for Psycholinguistics
> > Wundtlaan 1, 6525 XD Nijmegen, The Netherlands
> >
> > Donders Institute for Brain, Cognition and
> Behaviour,
> > Centre for Cognitive Neuroimaging,
> > Kapittelweg 29, 6525EN Nijmegen, The Netherlands
> >
> > n.lam at fcdonders.ru.nl
> <mailto:n.lam at fcdonders.ru.nl>
> > +31-24-3668219 <tel:%2B31-24-3668219>
> >
> >
> > neurobiologyoflanguage.com
> <http://neurobiologyoflanguage.com>
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> <mailto:fieldtrip at donders.ru.nl>
> >
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> >
> >
> > _______________________________________________
> > fieldtrip mailing list
> > fieldtrip at donders.ru.nl
> <mailto:fieldtrip at donders.ru.nl>
> >
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
> --
> Nietzsche H.L. Lam, MSc
> PhD Candidate
>
> Max Planck Institute for Psycholinguistics
> Wundtlaan 1, 6525 XD Nijmegen, The Netherlands
>
> Donders Institute for Brain, Cognition and
> Behaviour,
> Centre for Cognitive Neuroimaging,
> Kapittelweg 29, 6525EN Nijmegen, The Netherlands
>
> n.lam at fcdonders.ru.nl
> <mailto:n.lam at fcdonders.ru.nl>
> +31-24-3668219 <tel:%2B31-24-3668219>
>
>
> neurobiologyoflanguage.com
> <http://neurobiologyoflanguage.com>
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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
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