How to go to each directory and execute a name-dependent command?-CodePudding

I have a folder that contains several sub-folders, and each sub-folder contains a *.nii file. The directory structure is:

parent_directory
 - JACK (folders are titled as first-names)
    - *.nii (each .nii file is named a random unique combination of letters&numbers)
 - JILL
    - *.nii
 - JOE
    - *.nii
 - JANE
    - *.nii

I want to execute this command:

fslreorient2std input output

The "input" must be the name of the .nii file, and ideally I want the output to be named or_*.nii.

How can I cd to each subfolder in my directory, and execute this command where I place "input" as the unique name of the *.nii file in each subfolder? Thank you!

CodePudding user response：

Use nested loops. The outer loop iterates over the subdirectories. It performs cd in a subshell so that it automatically returns to the original shell when done.

The inner loop iterates over the *.nii files, adding the or_ prefix to produce the output filename.

for dir in */
do (
    cd "$dir"
    for file in *.nii
    do
        fslreorient2std "$file" "or_$file"
    done
)
done

CodePudding user response：

Untested, using just one loop and bash parameter expansion:

cd parent_directory
for file in J*/*.nii; do
    ( cd $(dirname "$file") && fslreorient2std "${file##*/}" "or_${file##*/}" )
done

The ( ) create a subshell, that way, each call to cd start from parent_directory