[FieldTrip] errors replicating Salzburg Fieldtrip tutorial

Irene Varela Leniz irene.varela at alumni.mondragon.edu
Thu May 23 08:55:26 CEST 2019 

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
>
>
>
>
> 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
>>
>>
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>> https://doi.org/10.1371/journal.pcbi.1002202
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>>
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