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

You are here: Home1 / Forums2 / Support Forum (ARCHIVED – Please use Slack Channel instead)3 / Error in latest version of Lead DBS – unable to find anatomy4
Viewing 7 posts - 1 through 7 (of 7 total)
  • Author
    Posts
  • 12/27/2016 at 6:52 AM #1824
    PhilipM
    Participant

    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.

    12/27/2016 at 11:49 AM #1825
    ningfei
    Keymaster

    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

    12/27/2016 at 6:12 PM #1827
    andreashorn
    Keymaster

    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

    12/28/2016 at 5:49 AM #1829
    PhilipM
    Participant

    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

    12/28/2016 at 9:06 AM #1830
    ningfei
    Keymaster

    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

    12/28/2016 at 10:42 AM #1831
    PhilipM
    Participant

    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.

    12/28/2016 at 11:39 AM #1833
    ningfei
    Keymaster

    No problem. Good to know you solved it :)

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