[FieldTrip] ft_mergealgin: high residual variance?

Schoffelen, J.M. (Jan Mathijs) jan.schoffelen at donders.ru.nl
Thu Nov 1 09:23:11 CET 2018

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,


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<mailto: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);


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