hmri_create_comm_adjust.m

function [M,R] = hmri_create_comm_adjust(option,Ref,Other,Nits,doshear,Template)

% This function is a version of comm_adjust.m customized for T1 like
% images, i.e. MT images. Now it is necessary to define as input parameter
% the Template to be used for the commisure adjustment.
%
%% Lester Melie-Garcia
% LREN, CHUV.
% Lausanne, December 6th, 2016

if option,
    switch nargin
        case 1, Nits = 2; doshear = 0;
            %Modality = input('modality of image?: ','s');
            Ref = myselect(Inf,'image','select file to adust',sel,wd,'.*','1');
            Other = myselect(Inf,'image','select other files to adust','',pwd,'.*','1');
            if isempty(Other), filenames = Ref; else
                filenames = unique(strvcat(Ref,Other),'rows'); %#ok<*FPARK>
            end
        case 2,
            %Modality = input('modality of image?: ','s');
            Other = myselect(Inf,'image','select other files to adust','',pwd,'.*','1');
            if isempty(Other), filenames = Ref; else
                filenames = unique(strvcat(Ref,Other),'rows');
            end
        case 3, Nits = 2; doshear = 0;
            Other = myselect(Inf,'image','select other files to adust','',pwd,'.*','1');
            if isempty(Other), filenames = Ref; else
                filenames = unique(strvcat(Ref,Other),'rows');
            end
        case 4, Nits = 2; doshear = 0;
            filenames = unique(strvcat(Ref,Other),'rows');
        case 5, doshear = 0;
            filenames = unique(strvcat(Ref,Other),'rows');
        case 6, doshear = logical(doshear);
            filenames = unique(strvcat(Ref,Other),'rows');
        otherwise, error('too or few inputs!')
    end
else
    switch nargin
        case 2, Nits = 2; doshear = 0; filenames = Ref; %Modality = 'T1';
        case 3, Nits = 2; doshear = 0; filenames = Ref;
        case 4, Nits = 2; doshear = 0;
            filenames = unique(strvcat(Ref,Other),'rows');
        case 5, doshear = 0;
            filenames = unique(strvcat(Ref,Other),'rows');
        case 6, doshear = logical(doshear);
            filenames = unique(strvcat(Ref,Other),'rows');
        otherwise, error('too or few inputs!')
    end
end
sep = 8./[1 2 4*ones(1,Nits)];
%Tmp = sprintf('%s//templates//%s.nii',spm('Dir'),Modality);
if ~exist('Template','var')
    Template = fullfile(spm('Dir'),'canonical','avg152T1.nii');
end;
flags = struct('WG'      ,[]    ,...
    'WF'      ,[]    ,...
    'sep'     ,8     ,...
    'regtype' ,'mni' ,...
    'globnorm',0);

VRef = spm_smoothto8bit(spm_vol(Ref),8);
VTmp = spm_smoothto8bit(spm_vol(Template),0);
%VTmp = spm_smoothto8bit(spm_vol(Tmp),0);
VRef.pinfo(1:2,:) = VRef.pinfo(1:2,:)/spm_global(VRef);
VTmp.pinfo(1:2,:) = VTmp.pinfo(1:2,:)/spm_global(VTmp);

[M,scal] = spm_affreg(VTmp,VRef,flags,eye(4));
for i = 2:Nits,
    flags.sep = sep(i);
    [M,scal] = spm_affreg(VTmp,VRef,flags,M,scal); %VTmp.mat\M*VRef.mat
end
if doshear
    R = M; 
else
    [A,B,C] = svd(M(1:3,1:3)); R = A*C'; %#ok<ASGLU>
    R(:,4) = R*(M(1:3,1:3)\M(1:3,4)); R(4,4) = 1;
end

spm_progress_bar('Init',size(filenames,1),'Reorient to AC-PC line','volumes completed');
for i = 1:size(filenames,1),
    spm_get_space(deblank(filenames(i,:)),...
        R*spm_get_space(deblank(filenames(i,:))));
    spm_progress_bar('Set',i);
end
spm_progress_bar('Clear');

end