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In the following script, the for loop only outputs till unph4. I tried to write the value of $coils directly but doesn't work as well. I tried other iteration values to see the maximum I am getting is 9 (does the iteration number have to be a single digit?)

coil=34;

bash_command = sprintf(['for ph in all/ph[1-$coil].nii\n' ...
'do\n' ...
'   base=`basename $ph`;\n' ...
'   dir=`dirname $ph`;\n' ...
'   mag=$dir/"mag"${base:2};\n' ...
'   unph="unph"${base:2};\n' ...
'   prelude -a $mag -p $ph -u $unph -n 12&\n' ...
'done\n' ...
'wait\n' ...
'gunzip -f unph*.gz\n']);

unix(bash_command);
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Because all/ph[1-34].nii matches at most 4 files: all/ph1.nii, all/ph2.nii, all/ph3.nii, and all/ph4.nii.

In shell patterns, a construction of the form [char1-char2] matches the characters which sort between char1 and char2; so [1-34] matchs 1, 2, 3 and 4.

You may want to change the for loop to

for i in $(seq 1 $coil)
do
    ph=all/ph${i}.nii
    ...
done
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  • Thank you. However, it is still not working. I have files from all/ph1.nii to all/ph34.nii. I am getting the error 'Dimensions of matrices being concatenated are not consistent.' Not sure what that means. Can you please suggest anything else? Commented Nov 22, 2018 at 19:57
  • It is working -- that's an error message from your application prelude. It has nothing to do with the shell, or with Linux. I cannot possibly know what your application does, and what parameters and data it expects; you may want to ask on a specialized forum dedicated to the specific application. Commented Nov 22, 2018 at 21:30

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