function [ mri_aligned segmentedmri ] = pre_process_mri_for_ft( dicom_file_name )

%pre_process_mri_for_ft Summary of this function goes here
%   Pre process dicom series for ft analysis

%% Utiliser le z aussi !!!! sinon cerveau pas dans bon sens
mri=ft_read_mri(dicom_file_name);
cfg=[];
cfg.method = 'interactive' ;
cfg.coordsys = 'neuromag' ;

mri_aligned = ft_volumerealign(cfg,mri) ;

save('mri_aligned.mat', 'mri_aligned');

%% disp(mri)
%% disp(mri_aligned)

%% Segmentation
cfg           = [];
cfg.output    = 'brain';
segmentedmri  = ft_volumesegment(cfg, mri_aligned);
save('segmentedmri.mat', 'segmentedmri') ;


end