For loops for functions that create structure arrays.

I've got two questions regarding the automation of the functions. I'm trying to create a for loop for each function.

For spm_vol: I would like to loop through a number of nifti files (P in the following syntax). V is a structure array.

V = spm_vol(P)

The following code works (i.e. produces a cell array containing one structure for each nifti file):

for i = 1:size(beta_list)
V = spm_vol(beta_list(:,i));
end

But it also gives the following error:

"Index in position 2 exceeds array bounds (must not exceed 1)."

Can you suggest any changes I need to make to avoid this error?

For clarity - beta_list is a 61x1 cell array containing file names.

I then want to use spm_read_vols for each structure, but this code doesn't work:

for j = 1:size(V)
[a, XYZ] = spm_read_vols(V(:,j));
end

The following error is produced:

Dot indexing is not supported for variables of this type.

Error in spm_check_orientations (line 24)

dims = cat(1,V.dim);

Error in spm_read_vols (line 25)

spm_check_orientations(V);

Answer 1

[Stephen23]

Your indexing throws an error because beta_list has only one column but you are trying to access columns 2 to 61, which don't exist. As soon as your code tries to access the second (non-existent) column it will throw that error. A simpler and more robust approach is to use linear indexing rather than subscript indexing:

for k = 1:numel(beta_list)
    V = spm_vol(beta_list{k});
    ... do whatever with V
end

https://www.mathworks.com/help/matlab/matlab_prog/access-data-in-a-cell-array.html

[Katrina Portelli]

Thank you! your answer makes a lot of sense but for some reason when I try this, it only gives me the result for the last row of the beta_list variable. Any thoughts?

[Stephen23]

"Any thoughts?"

I guess that you didn't use any indexing into the output variable, in which case each iteration will simply overwrite the entire output variable (so after the last iteration only the output from the last iteration will remain). If the output of each iteration is a scalar structure with exactly the same fields and the output variable is not defined before the loop then you could just use indexing to implicitly create and allocate the output structure array:

for k = 1:numel(beta_list)
    S(k) = spm_vol(beta_list{k});
end

Personally I prefer a slightly more robust approach of allocating to a preallocated cell array:

N = numel(beta_list);
C = cell(1,N); % preallocate cell array
for k = 1:N
    C{k} = spm_vol(beta_list{k});
end
S = [C{:}]; % concatenate scalar structures into structure array

Read more:

https://www.mathworks.com/help/matlab/matlab_prog/access-multiple-elements-of-a-nonscalar-struct-array.html

https://www.mathworks.com/help/matlab/matlab_prog/comma-separated-lists.html

https://www.mathworks.com/matlabcentral/answers/320713-how-to-operate-on-comma-separated-lists

Answer 2

[Jan]

Remember, that size() replies a vector, e.g. [1 x 10]. Then

for j = 1:size(V)    

means 1:[1, 10], but the colon operator uses the first element of the vector only.

Specify the wanted dimension instead:

for j = 1:size(V, 2)   % or size(V, 1) on demand    

[Katrina Portelli]

Thank you! That produced the cell array without throwing an error.