[FieldTrip] Issue in realigning MRI

bioeng.yoosofzadeh at gmail.com bioeng.yoosofzadeh at gmail.com
Wed May 2 00:00:51 CEST 2018

Dear FT experts,


I am not able to realign a T1 scan using the fiducial points and headshapes
of a 4D/BTI system, can anyone help me on this? The "interactive"
realignment helped a lot, but the end result was not perfect!


Here's what I have tried,:


individual_mri = ft_read_mri(mripath); % ..\MEG_4D\C-101_T1.nii

ft_sourceplot([], individual_mri);


cfg = [];

cfg.method = 'flip';

mri.coordsys = '4d';

individual_mri = ft_volumereslice(cfg, individual_mri);

ft_sourceplot([], individual_mri);

individual_mri = ft_convert_units(individual_mri, 'm');


headshape = ft_read_headshape(headpath); % ..\MEG_4D\hs_file

mri_fids = headshape.fid.pos;


cfg = [];

cfg.fiducial.nas = mri_fids(1,:);

cfg.fiducial.lpa = mri_fids(2,:);

cfg.fiducial.rpa = mri_fids(3,:);

cfg.coordsys = '4d';

cfg.method = 'fiducial';

mri_realigned = ft_volumerealign(cfg, individual_mri);


cfg = [];

cfg.coordsys = '4d';

cfg.headshape = headshape;

cfg.method = 'headshape';

mri_realigned = ft_volumerealign(cfg, individual_mri);


% check that the MRI is consistent after realignment

ft_determine_coordsys(mri_realigned, 'interactive', 'no');

hold on; 




Data can be found at,







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