[FieldTrip] errors replicating Salzburg Fieldtrip tutorial
Irene Varela Leniz
irene.varela at alumni.mondragon.edu
Thu May 23 11:37:10 CEST 2019
Dear Tzvetan,
El jue., 23 may. 2019 a las 9:22, Tzvetan Popov (<
tzvetan.popov at uni-konstanz.de>) escribió:
> Dear Irene,
> This is not going to work.
> 1. The headmodel is expressed in units of ‘m’ and aligned to the 4D/bti
> MEG coordinates. This has nothing to do with your EEG electrode positions.
> 2. As you already anticipated the type of headmodel is not appropriate for
> EEG source analysis.
>
> I recommend the following:
> 1. Work out the tutorial with the provided data.
> 2. Go thru it again and try to internalize the order of the analysis steps.
> 3. Switch to an EEG source analysis tutorial. Use the provided data there
> and try to understand the key differences. For example here:
> http://www.fieldtriptoolbox.org/workshop/natmeg/dipolefitting/
> Or also here
> http://www.fieldtriptoolbox.org/workshop/aarhus/beamformingerf/
> 4. Go back and try to merge the two tutorials to reflect your needs.
>
> Good luck
> Tzvetan
>
> Am 23.05.2019 um 08:55 schrieb Irene Varela Leniz <
> irene.varela at alumni.mondragon.edu>:
>
> Dear both,
>
> You are right. I thought I was working with the latest version but I did
> not know that another more recent one had been released on April 19th.
> Anyway, what I could see investigating inside the function is that they
> have changed the way to configure the cfg in the function, right?
>
> The function is not able to understand the cfg that I am configuring. I
> must mention that in my case, I am working with EEG, so for example the
> configuration of lcmv.reducerank I had to change it to 3. Anyway I get the
> following error related to the cfg:
>
> * cfg = [];*
>
>
>
>
>
>
>
> * cfg.label = data.label;
> cfg.elec = data.elec; cfg.vol
> = hdm; cfg.lcmv.reducerank = 3; % I am working with
> EEG data cfg.normalize = 'yes'
> cfg.grid = sourcemodel; [grid] =
> ft_prepare_leadfield(cfg);*
>
>
> *Error using ft_prepare_leadfield (line 110)*
>
> *It seems as if the first input argument is a FieldTrip data structure,
> while a cfg is expected*
>
>
> I also add information about how the data (EEG), the headmodel and the
> sourcemodel are:
>
> *hdm = *
>
> * struct with fields:*
>
> * bnd: [1×1 struct]*
>
> * type: 'singleshell'*
>
> * unit: 'm'*
>
> * cfg: [1×1 struct]*
>
>
> *sourcemodel = *
>
> * struct with fields:*
>
> * pos: [6426×3 double]*
>
> * dim: [17 21 18]*
>
> * unit: 'm'*
>
> * inside: [17×21×18 logical]*
>
> * cfg: [1×1 struct]*
>
>
>
>
>
>
>
>
>
>
> *data = struct with fields: hdr: [1×1 struct] trial:
> {1×69 cell} time: {1×69 cell} elec: [1×1 struct]
> fsample: 256 label: {128×1 cell} sampleinfo: [69×2 double]
> cfg: [1×1 struct]*
>
> On the other hand, if I'm working with EEG, do you think it makes sense to
> use files *standard_singleshell.mat*, *atlas ROI_MNI_V4.nii*, *mri.mat *and
> *hdm.mat* to create the leadfield? Do I need others for EEG?
>
> Thank you for your attention.
>
> Best wishes,
>
> Irene
>
>
> El mié., 22 may. 2019 a las 9:51, Schoffelen, J.M. (Jan Mathijs) (<
> jan.schoffelen at donders.ru.nl>) escribió:
>
>> You are not using the most recent fieldtrip code. See attached screenshot
>> for a section of ft_checkconfig (which I took from
>> https://github.com/fieldtrip/fieldtrip (utilities/ft_checkconfig.m)
>>
>> The error message in your earlier e-mail pointed to line 529.
>>
>> Jan-Mathijs
>>
>>
>>
>> <Screen Shot 2019-05-22 at 09.48.49.png>
>>
>> On 22 May 2019, at 09:42, Irene Varela Leniz <
>> irene.varela at alumni.mondragon.edu> wrote:
>>
>> Dear Shoffelen,
>>
>> I am working with last Fieldtrip and MATLAB version so I'm afraid that's
>> not the problem.
>>
>> Best wishes,
>>
>> Irene
>>
>> El mié., 22 may. 2019 a las 9:38, Schoffelen, J.M. (Jan Mathijs) (<
>> jan.schoffelen at donders.ru.nl>) escribió:
>>
>>> Hi Irene,
>>>
>>> Please check which version of the code you are using, and update to a
>>> more recent version to FieldTrip, and try again. The line + error you
>>> report does not match the ones in the current version of Fieldtrip.
>>>
>>> Best wishes,
>>> Jan-Mathijs
>>>
>>>
>>>
>>> On 22 May 2019, at 09:21, Irene Varela Leniz <
>>> irene.varela at alumni.mondragon.edu> wrote:
>>>
>>> Dear Fieldtripers,
>>>
>>> I am trying to replicate the well-known *tutorial:salzburg [FielTrip] (*
>>> http://old.fieldtriptoolbox.org/tutorial/salzburg). Anyway, I am
>>> getting some errors that I could not manage to solve. I would be really
>>> grateful if someone could lend me a hand.
>>>
>>> I am working on section called "Localizing auditory evoked fields using
>>> beamforming techniques in parceled brain space". I managed to compute
>>> the *sourcemode*l as explained in the tutorial without any problem. But
>>> now, when "Computing the leadfield" I get an error message related with *sourcemodel.inside
>>> *field, which makes it impossible for me to create the leadfield. The
>>> structure is the following:
>>>
>>> *sourcemodel = *
>>>
>>> * struct with fields:*
>>>
>>> * pos: [6426×3 double]*
>>>
>>> * dim: [17 21 18]*
>>>
>>> * unit: 'm'*
>>>
>>> * inside: [17×21×18 logical]*
>>>
>>> * cfg: [1×1 struct]*
>>>
>>>
>>> The structure for computing the leadfield:
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> * cfg = []; cfg.label =
>>> data.label; cfg.elec = data.elec;
>>> cfg.vol = hdm;
>>> cfg.lcmv.reducerank = 2; % I am working with EEG data
>>> cfg.grid = sourcemodel; [grid] =
>>> ft_prepare_leadfield(cfg)*
>>>
>>>
>>> An the error I get:
>>>
>>>
>>> Operands to the || and && operators must be convertible to logical
>>> scalar values.
>>>
>>>
>>> Error in ft_checkconfig (line 529)
>>>
>>> elseif isfield(cfg, 'grid') && isfield(cfg.grid, 'inside') &&
>>> any(cfg.grid.inside>1)
>>>
>>>
>>> Error in ft_prepare_leadfield (line 156)
>>>
>>> cfg = ft_checkconfig(cfg, 'inside2logical', 'yes');
>>>
>>> I think the error comes from the fact that *sourcemodel.inside* is a
>>> 3-dimensional logical array. The operation - any(cfg.grid.inside>1) does
>>> not output a logical scalar value because* sourcemodel.inside* is in 3
>>> dimensions.
>>> So far I have always worked with models whose inside parameter was of
>>> one dimension. Anyway, I'm not sure if this is the problem, please correct
>>> me if I'm wrong.
>>>
>>> Has anyone encountered this same problem, and does anyone know how to
>>> fix it?
>>>
>>> Thank you very much for your attention,
>>>
>>>
>>> Irene
>>>
>>>
>>> _______________________________________________
>>> fieldtrip mailing list
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>>> https://doi.org/10.1371/journal.pcbi.1002202
>>>
>>>
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>>> https://doi.org/10.1371/journal.pcbi.1002202
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