In my path, I have totally 120 cases, each case has two files, the path looks like this:
00001_FA.nii.gz
00001_FA_grot.nii.gz
00002_FA.nii.gz
00002_FA_grot.nii.gz
.. ..
00120_FA.nii.gz
00120_FA_grot.nii.gz
I want to do fslstats 00001_FA_nii.gz -k 00001_FA_grot.nii.gz -m then repeat the process till the 00120 case.
How to write the command? Thanks
You need to use a loop function (for, for instance, is pretty helpful). Also, you need to convert 1, 2, 3 .. 119, 120 to a 5-digits format. You can do that thanks to printf.
And there is your script :
for i in {1..120} ; do
j=$(printf %05d $i)
fslstats ${j}_FA_nii.gz -k ${j}_FA_grot.nii.gz -m
done
As @steeldriver noted in the comments, bash can now understand leading 0 in braces, so you can substitute
for i in {1..120} ; do
j=$(printf %05d $i)
with
for j in {00001..00120} ; do
for j in {00001..00120}; do– steeldriver May 26 '20 at 17:55