/
ea_apply_normalization_tofile.m
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ea_apply_normalization_tofile.m
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function ea_apply_normalization_tofile(options,from,to,useinverse,interp,ref)
% this function applies lead-dbs normalizations to nifti files.
% currently just used to generate patient specific atlases,i.e., from MNI
% space to native space
if ischar(from)
from = {from};
end
if ischar(to)
to = {to};
end
if ~exist('interp', 'var')
interp=4;
end
if ~exist('ref', 'var')
ref='';
end
json = loadjson(options.subj.norm.log.method);
if ischar(interp)
if strcmp(interp,'auto') % only works if one image supplied
interp=detinterp(from,contains(json.method, {'ANTs','EasyReg'}));
end
end
if contains(json.method, {'ANTs','EasyReg'})
ea_ants_apply_transforms(options, from, to, useinverse, ref, '', interp);
elseif contains(json.method, 'FNIRT')
if useinverse
% In case inverse transformation using FSL, make sure the input has
% exactly the same affine matrix as the template.
for i=1:length(from)
ea_imcalc(from{i}, [ea_space, options.primarytemplate, '.nii'], '', interp);
end
end
ea_fsl_apply_normalization(options, from,to, useinverse, ref, '', interp);
elseif contains(json.method, 'SPM')
for i=1:length(from)
if strcmp(from{i}(end-2:end),'.gz')
wasgz = 1;
[~, fn] = fileparts(from{i});
copyfile(from{i}, [tempdir, fn, '.gz']);
gunzip([tempdir, fn, '.gz']);
from{i} = [tempdir, fn];
else
wasgz = 0;
end
refIsGz = 0;
% ATTENTION: when using PUSH method, transforming from native space
% to template space should use the INVERSE transformation,
% transforming from template space to native space should use
% FORWARD transformation.
usepush=1;
if useinverse
if isempty(ref)
ref = options.subj.preopAnat.(options.subj.AnchorModality).coreg;
elseif endsWith(ref, '.gz')
refIsGz = 1;
gunzip(ref);
ref = strrep(ref, '.gz', '');
end
if usepush
matlabbatch{1}.spm.util.defs.comp{1}.def = {[options.subj.norm.transform.forwardBaseName, 'spm.nii']};
matlabbatch{1}.spm.util.defs.out{1}.push.fnames = from(i);
matlabbatch{1}.spm.util.defs.out{1}.push.weight = {''};
matlabbatch{1}.spm.util.defs.out{1}.push.savedir.saveusr = {fileparts(to{i})};
matlabbatch{1}.spm.util.defs.out{1}.push.fov.file = {ref};
matlabbatch{1}.spm.util.defs.out{1}.push.preserve = 0;
matlabbatch{1}.spm.util.defs.out{1}.push.fwhm = [0.5 0.5 0.5];
matlabbatch{1}.spm.util.defs.out{1}.push.prefix = '';
else
matlabbatch{1}.spm.util.defs.comp{1}.def = {[options.subj.norm.transform.inverseBaseName, 'spm.nii']};
matlabbatch{1}.spm.util.defs.out{1}.pull.fnames = from(i);
matlabbatch{1}.spm.util.defs.out{1}.pull.savedir.saveusr = {fileparts(to{i})};
matlabbatch{1}.spm.util.defs.out{1}.pull.interp = interp;
matlabbatch{1}.spm.util.defs.out{1}.pull.mask = 1;
matlabbatch{1}.spm.util.defs.out{1}.pull.fwhm = [0.5 0.5 0.5];
matlabbatch{1}.spm.util.defs.out{1}.pull.prefix = '';
end
spm_jobman('run',{matlabbatch});
clear matlabbatch
else
if isempty(ref)
ref = [ea_space, options.primarytemplate, '.nii'];
elseif endsWith(ref, '.gz')
refIsGz = 1;
gunzip(ref);
ref = strrep(ref, '.gz', '');
end
if usepush
matlabbatch{1}.spm.util.defs.comp{1}.def = {[options.subj.norm.transform.inverseBaseName, 'spm.nii']};
matlabbatch{1}.spm.util.defs.out{1}.push.fnames = from(i);
matlabbatch{1}.spm.util.defs.out{1}.push.weight = {''};
matlabbatch{1}.spm.util.defs.out{1}.push.savedir.saveusr = {fileparts(to{i})};
matlabbatch{1}.spm.util.defs.out{1}.push.fov.file = {ref};
matlabbatch{1}.spm.util.defs.out{1}.push.preserve = 0;
matlabbatch{1}.spm.util.defs.out{1}.push.fwhm = [0.5 0.5 0.5];
matlabbatch{1}.spm.util.defs.out{1}.push.prefix = '';
else
matlabbatch{1}.spm.util.defs.comp{1}.def = {[options.subj.norm.transform.forwardBaseName, 'spm.nii']};
matlabbatch{1}.spm.util.defs.out{1}.pull.fnames = from(i);
matlabbatch{1}.spm.util.defs.out{1}.pull.savedir.saveusr = {fileparts(to{i})};
matlabbatch{1}.spm.util.defs.out{1}.pull.interp = interp;
matlabbatch{1}.spm.util.defs.out{1}.pull.mask = 1;
matlabbatch{1}.spm.util.defs.out{1}.pull.fwhm = [0.5 0.5 0.5];
matlabbatch{1}.spm.util.defs.out{1}.pull.prefix = '';
end
spm_jobman('run',{matlabbatch});
clear matlabbatch
end
pth = fileparts(to{i});
[~, fn, ext] = fileparts(from{i});
if strcmp(to{i}(end-2:end),'.gz')
to{i} = to{i}(1:end-3);
gzip_output = 1;
else
gzip_output = 0;
end
movefile(fullfile(pth, ['sw', fn, ext]), to{i});
if refIsGz
gzip(ref);
delete(ref);
end
if gzip_output
gzip(to{i});
delete(to{i});
end
if wasgz
ea_delete([tempdir, fn, '.gz']);
ea_delete([tempdir, fn]);
end
end
end
function interp=detinterp(from,ants)
if length(from)>1
ea_error('Auto detection only implemented for single images.')
end
nii=ea_load_nii(from{1});
outs=unique(nii.img(:));
if ants
interp='LanczosWindowedSinc'; % default
else
interp=1;
end
if length(outs)<3
if ants
interp='GenericLabel';
else
interp=0;
end
end
if length(outs)<100 % likely labeling file
if outs==round(outs) % integers only, pretty much certainly labeling file
if ants
interp='GenericLabel';
else
interp=0;
end
end
end