Thank you, I must have overlooked the newsletter about the re-naming. Regardless, still having difficulties – here is the information:
K>> pfcell
pfcell =
{}
K>> options.prefs.prenii_searchstring
ans =
anat_*.nii
And just in case it helps – here is the pasted ea_assignpretra:
function [options, presentfiles] = ea_assignpretra(options)
directory = [options.root,options.patientname,filesep];
presfiles=dir([directory,options.prefs.prenii_searchstring]);
pfcell = {presfiles.name}’;
% order the anatomical images in accordance with ‘prefs.prenii_order’
prenii_order = cellfun(@(x) strrep(options.prefs.prenii_searchstring,’*’,x), options.prefs.prenii_order, ‘UniformOutput’, 0);
[~,idx] = ismember(prenii_order, pfcell);
presentfiles = pfcell([nonzeros(idx)’,setdiff(1:numel(pfcell),nonzeros(idx))]);
if isempty(presentfiles)
ea_error([‘No anatomy information found!\nPlease put either ‘, …
prenii_order{1},’, ‘,prenii_order{2},’ or ‘,prenii_order{3},’ into subject folder.’], …
‘Error’, dbstack);
end
% set prenii_unnormalized
options.prefs.prenii_unnormalized = presentfiles{1};
% determine primary template
if any(idx)
options.primarytemplate = options.prefs.prenii_order{find(idx,1)};
else % could happen if neither T2, T1 or PD is present but only custom sequences are being used
options.primarytemplate = ‘t2’; % default T2.
end
