leaddbs/ea_compat_data.m at develop · SachsLab/leaddbs · GitHub

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if strcmp(ea_getspace,'MNI_ICBM_2009b_NLIN_ASYM')
    if exist([ea_getearoot,'templates',filesep,'mni_hires_t1.nii'],'file');
        try movefile([ea_getearoot,'templates'], [ea_getearoot,'templates_temp']); end
        try mkdir([ea_getearoot,'templates',filesep,'space',filesep]); end

        try movefile([ea_getearoot,'templates_temp'],[ea_getearoot,'templates',filesep,'space',filesep,ea_getspace]); end % do not use ea_space in this line since wont be defined and result in error.
        try movefile([ea_getearoot,'atlases'],[ea_space,'atlases']); end

        try movefile([ea_space,'mni_hires_t1.nii'],[ea_space,'t1.nii']); end
        try movefile([ea_space,'mni_hires_t2.nii'],[ea_space,'t2.nii']); end
        try movefile([ea_space,'mni_hires_pd.nii'],[ea_space,'pd.nii']); end
        try movefile([ea_space,'mni_hires_fa.nii'],[ea_space,'fa.nii']); end
        try movefile([ea_space,'mni_hires_bb.nii'],[ea_space,'bb.nii']); end
        try movefile([ea_space,'mni_hires_c1mask.nii'],[ea_space,'c1mask.nii']); end
        try movefile([ea_space,'mni_hires_c2mask.nii'],[ea_space,'c2mask.nii']); end
        try movefile([ea_space,'TPM_2009b.nii'],[ea_space,'TPM.nii']); end
        try movefile([ea_space,'mni_hires_distal.nii'],[ea_space,'atlas.nii']); end
        try movefile([ea_space,'mni_wires.mat'],[ea_space,'wires.mat']); end
    end

    if ~exist([ea_space,'ea_space_def.mat'],'file')
        try spacedef=ea_gendefspacedef; end
        try save([ea_space,'ea_space_def.mat'],'spacedef'); end

    end

    if exist([ea_space,'distal.nii'],'file')
        try movefile( [ea_space,'distal.nii'],[ea_space,'atlas.nii']); end
    end

    if exist([ea_space,'TPM_Lorio_Draganski.nii'],'file')
        try movefile([ea_space,'TPM_Lorio_Draganski.nii'],[ea_getearoot,'templates',filesep,'TPM_Lorio_Draganski.nii']); end
    end

    if exist([ea_space,'electrode_contacts'],'dir')
        try movefile( [ea_space,'electrode_contacts'],[ea_getearoot,'templates']); end
    end

    if exist([ea_space,'electrode_models'],'dir')
        try movefile( [ea_space,'electrode_models'],[ea_getearoot,'templates']); end
    end

    % remove square bracket from folder name
    folders = ea_regexpdir([ea_space, 'atlases'], '\[.*\]/$', 0);
    for i=1:length(folders)
        oldfolder = folders{i}(1:end-1);
        newfolder = regexprep(oldfolder,'(.*) \[(.*)\]', '$1 - $2');
        movefile(oldfolder, newfolder)
    end

    % remove square bracket from file name
    files = ea_regexpdir([ea_space, 'labeling'], '\[.*\]', 0);
    for i=1:length(files)
        oldfile = files{i};
        newfile = regexprep(oldfile,'\[(.*)\]', '- $1');
        movefile(oldfile, newfile)
    end
end

if ~exist([ea_getearoot,'spacedefinitions'],'dir')
    prefs=ea_prefs;
    if exist([prefs.lc.datadir,'spacedefinitions'], 'dir')
        try movefile([prefs.lc.datadir,'spacedefinitions'], [ea_getearoot,'templates']); end
    elseif exist([ea_getearoot,'spacedefinitions'], 'dir')
        try movefile([ea_getearoot,'spacedefinitions'], [ea_getearoot,'templates']); end
    end
end