[FieldTrip] Where to add a trialfun?
Ana Laura Diez Martini
diezmartini at gmail.com
Tue Sep 30 06:20:29 CEST 2014
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> 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> 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>
>> :
>>
>>> 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>
>>> 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>
>>>> > To: "FieldTrip discussion list" <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 > 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 >
>>>> > > To: "FieldTrip discussion list" < 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
>>>> > > 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
>>>> > +31-24-3668219
>>>> >
>>>> >
>>>> > neurobiologyoflanguage.com
>>>> > _______________________________________________
>>>> > fieldtrip mailing list
>>>> > fieldtrip at donders.ru.nl
>>>> > http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>> >
>>>> >
>>>> > _______________________________________________
>>>> > fieldtrip mailing list
>>>> > 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
>>>> +31-24-3668219
>>>>
>>>>
>>>> neurobiologyoflanguage.com
>>>> _______________________________________________
>>>> fieldtrip mailing list
>>>> fieldtrip at donders.ru.nl
>>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>>
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
>>> fieldtrip at donders.ru.nl
>>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
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>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
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