error: mean: DIM must be an integer and a valid dimension / selxavg3-sess with octave - Freesurfer

11 Jan 2017


      Dear FreeSurfers,
I just wanted to share a solution for an issue that can arise when running
selxavg3-sess with octave instead of Matlab.
In fast_selxavg3.m (which is called by selxavg3) there is a line (579 in
my version) that computes the mean of an array by calling the mean
function with the DIM argument, which specifies the dimension over which
the average should be computed (4th dimension in this case):
rho1mn.vol = mean(rho1.vol,4);
This line will throw an error under octave if the number of dimensions of
the array rho1.vol is smaller than 4. In Matlab it will simply return the
array.
To solve this issue for octave users one can use a simple if-else
statement to check for the number of dimensions and return the unchanged
volume if the number of dimensions is smaller than four or if the fourth
dimension is a singleton, like this:
if 4 > ndims(rho1.vol) || size(rho1.vol,4) == 1
   rho1mn.vol = rho1.vol;
else
   rho1mn.vol = mean(rho1.vol,4);
end
Best,
Michael