Error in latest version of Lead DBS – unable to find anatomy

[PhilipM]

Hi there, trying to work with the latest release. Unfortunately it seems unable to find my correctly named anatomical images in the subject folder:

Error using ea_assignpretra (line 16)
No anatomy information found!
Please put either anat_t2.nii, anat_t1.nii or anat_pd.nii into subject
folder.

I’ve tried putting back in the old ea_assignpretra.m from the previous version but that creates a heap of new errors.

I’ve got anat.nii anat_t1.nii and rpostop_ct in the subject folder, which are already coregistered and resliced.

Thanks for your help.

[ningfei]

Hi Philip,

First, if you have anat.nii and anat_t1.nii in the subject folder, and you can successfully run into ea_assignpretra, the anat.nii should have been automatically renamed to anat_t2.nii . Could you maybe set a breakpoint at Line 13 in ea_assignpretra, run it again, and paste the value of options.prefs.prenii_searchstring and pfcell here?

Best,
Ningfei

[andreashorn]

Hi Philip,

sorry to hear – adding to Ningfei’s comment, as announced in the newsletter, we changed the naming scheme of anat.nii to anat_t2.nii by default. Lead-DBS should however take care of this for compatibility reasons (i.e. rename anat.nii to anat_t2.nii) and it is weird that it didn’t work in your case.

It’d be awesome if you could follow Ningfei’s directions and paste the output here.

Best, Andy

[PhilipM]

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

[ningfei]

Hi Philip,

It’s really weird that dir([directory,options.prefs.prenii_searchstring]); return an empty cell. Could you check the value of directory and also paste here? If your images are under the directory folder, pfcell should not be empty as I see.

Best,
Ningfei

[PhilipM]

Ah, checking directory has solved the problem. I had renamed my folders with the suffix “v2.0” as I am re-running previous analyses and Matlab was confused by the decimal point. Sorry for the confusion and thanks for your assistance.

[ningfei]

No problem. Good to know you solved it :)

[Author]

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