[FieldTrip] ft_mergealgin: high residual variance?

[Maria Hakonen]

Dear FieldTrip experts,

Could the reason for the increased variance be that I have magnetometer
data?
However, the ft_megrealign and ft_prepare_headmodel don't have an option to
specify whether I have magnetometers or gradiometers.
Could you please let me know whether co-registration is needed before
ft_megrealign (it is not needed with maxfilter)?

Thank you already in advance!

Best,
Maria

pe 2. marrask. 2018 klo 8.37 Maria Hakonen (maria.hakonen at gmail.com)
kirjoitti:

> Hi Jan-Mathias!
>
> Thank you for the answer!
> I changed the units of gradiometers and head model to cm.
> This clearly decreased the residual variances.
> Also, singleshell seems to work better than localspheres.
>
> However, the transformation seems to still increase the residual variance
> a lot.
>
> Here are some examples:
> original -> template             RV 407.64 %
> original             -> original RV 9.85 %
> original -> template -> original RV 10.75 %
> realigning trial 706
> original -> template             RV 393.13 %
> original             -> original RV 9.00 %
> original -> template -> original RV 9.90 %
> realigning trial 707
> original -> template             RV 362.10 %
> original             -> original RV 8.33 %
> original -> template -> original RV 9.18 %
> realigning trial 708
> original -> template             RV 377.15 %
> original             -> original RV 9.43 %
> original -> template -> original RV 10.33 %
>
> The code is now as follows:
> load([data_path nameList{subj} '.mat']);
> grad = datafinal.grad;
> hs=ft_read_headshape([hdr_path nameList{subj} '/hs_file']);
>
> cfg           = [];
> cfg.method    = 'singlesphere';
> cfg.geom      = hs;
> cfg.grad      = grad;
> cfg.feedback  = true;
> vol  = ft_prepare_headmodel(cfg);
>
> vol = ft_convert_units(vol,'cm');
> grad = ft_convert_units(grad,'cm');
> cfg = [];
> cfg.template = template;
> cfg.inwardshift = 2.5;
> cfg.feedback ='no';
> cfg.vol =  vol;
> data = ft_megrealign(cfg, data);
>
> Best,
> Maria
>
> to 1. marrask. 2018 klo 10.35 Schoffelen, J.M. (Jan Mathijs) (
> jan.schoffelen at donders.ru.nl) kirjoitti:
>
>> Hi Maria,
>>
>> Are you sure about the units in your headmodel (and gradiometers)? Using
>> the value 1.0 as an inwardshift parameter suggests ‘cm’. Not sure what will
>> happen when by accident the hs_file is in ‘m’ (which, as far as I know, is
>> usually the case).
>>
>> Best wishes,
>>
>> Jan-Mathijs
>>
>> J.M.Schoffelen, MD PhD
>> Senior Researcher, VIDI-fellow - PI, language in interaction
>> Telephone: +31-24-3614793
>> Physical location: room 00.028
>> Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands
>>
>>
>>
>>
>> On 29 Oct 2018, at 13:33, Maria Hakonen <maria.hakonen at gmail.com> wrote:
>>
>> Dear FieldTrip experts,
>>
>> I have run ft_mergealign across subjects to align the head positions.
>> However, the residual variance between the original and the realigned data
>> seems to be high:
>>
>> original -> template             RV 21232.46 %
>> original             -> original RV 36.96 %
>> original -> template -> original RV 9579.95 %
>>
>> Could someone please let me know what would be the largest acceptable
>> change in the residual variance, and what should I do if the residual
>> variance is too high? Does the increase in residual variance mean that
>> there is a large shift in the head position?
>>
>> I have used ft_mergealign as follows:
>>
>> template = list of subjects (i.e. I want to calculate an average head
>> position over the subjects)
>>
>> grad = data.grad;
>> hs=ft_read_headshape([hdr_path nameList{subj} '/hs_file']);
>> vol = ft_headmodel_localspheres(hs,grad);
>>
>> cfg = [];
>> cfg.template = template;
>> cfg.inwardshift = 1.0;
>> cfg.vol =  vol;
>> data_aligned = ft_megrealign(cfg, data);
>>
>> Best,
>> Maria
>>
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>> https://doi.org/10.1371/journal.pcbi.1002202
>>
>>
>>
>>
>>
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>
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