Error: The logical indices contain a true value outside of the array bounds.

Hi all,

I have amended the code below slightly and it is now returning an error when it was working perfectly before, and I can't figure out why! Any advice greatly appreciated:

The logical indices contain a true value outside of the array bounds.

Error in LF_lesion_quant (line 44)

mean(F(I)); ...

clear, clc

addpath /Applications/freesurfer/7.3.2/matlab/

datadir = '';
d = dir([datadir filesep '*LF_Lesion_Mask.nii.gz']);
disp(['Found ' num2str(length(d)) ' Lesion Mask ' ]);
d = dir([datadir filesep '*LF_Contralateral_Mask.nii.gz']);
disp(['Found ' num2str(length(d)) ' Contralateral Mask ' ]);
d = dir([datadir filesep '*LF_DWI_Nonlinear_lncc5sx30vel_Coregistration.nii.gz']);
disp(['Found ' num2str(length(d)) ' LF DWI ' ]);
d = dir([datadir filesep '*LF_FLAIR.nii.gz']); 
disp(['Found ' num2str(length(d)) ' LF FLAIR ' ]);
resultspath = '';

Nd = numel(d);
data = cell(Nd+1,5);
data(1,2:6) = {'Lesion_Mask_mm3', 'Contralateral_Mask_mm2', 'Mean_Lesion_DWI', 'Mean_Lesion_FLAIR', 'Mean_Contralateral_FLAIR'};

for i = 1 : Nd
    disp(sprintf('Working on case %d of %d: %s',i,Nd,d(i).name))
    f = find(d(i).name=='_');
    prefix = d(i).name(1:f(1));  
    ipsimaskfile = fullfile(datadir,[prefix 'LF_Lesion_Mask.nii.gz']);
    contramaskfile = fullfile(datadir,[prefix 'LF_Contralateral_Mask.nii.gz']);
    dwifile = fullfile(datadir,[prefix 'LF_DWI_Nonlinear_lncc5sx30vel_Coregistration.nii.gz']);
    flairfile = fullfile(datadir,[prefix 'LF_FLAIR.nii.gz']);

    IMmri = MRIread(ipsimaskfile);
    CMmri = MRIread(contramaskfile);
    Dmri = MRIread(dwifile);
    Fmri = MRIread(flairfile);
    
    I = IMmri.vol > (max(IMmri.vol(:))/2);
    C = CMmri.vol > (max(CMmri.vol(:))/2);
    D = double(Dmri.vol);
    F = double(Fmri.vol);

    data(i+1,:) = { ...
        prefix(1:end-1); ...               
        sum(I(:)) * prod(IMmri.volres); ...
        sum(C(:)) * prod(CMmri.volres); ...              
        mean(D(I)); ...                   
        mean(F(I)); ...                   
        mean(F(C)); ...
        };

    disp(data)

output_file = fullfile(resultspath,'FLAIR_SIR_NEW_2.csv');
writecell(data, output_file);
disp('All done!');
end

Answer 1

[Cris LaPierre]

This error occurs when your logical index has more elements than the array you are indexing with it.

ind1 = logical([0 1 1 0]);
A = rand(1,4);

% works
A(ind1)

ans = 1×2

0.3485 0.9401

% your error
ind2 = logical([0 1 1 0 1]);
A(ind2)

The logical indices contain a true value outside of the array bounds.