Move files into sub-subfolders based on their file name, for multiple subfolders

Question

I have 100+ subfolders (P_XXX), each containing three sets of files (run1, run2 and run3):

/Analysis   
  /P_076
      /run1
      /run2
      /run3
      swu_run1_P_076_vol_001.nii
      swu_run1_P_076_vol_002.nii
      swu_run2_P_076_vol_001.nii
      swu_run2_P_076_vol_002.nii
      swu_run3_P_076_vol_001.nii
      swu_run3_P_076_vol_002.nii   
   /P_102
      /run1
      /run2
      /run3
      swu_run1_P_102_vol_001.nii
      swu_run1_P_102_vol_002.nii
      swu_run2_P_102_vol_001.nii
      swu_run2_P_102_vol_002.nii
      swu_run3_P_102_vol_001.nii
      swu_run3_P_102_vol_002.nii

I would like to move the three sets of files to its own subfolders (run1, run2 and run3) within the existing subfolder:

/Analysis
  /P_076
     /run1 
        swu_run1_P_076_vol_001.nii
        swu_run1_P_076_vol_002.nii
     /run2
        swu_run2_P_076_vol_001.nii
        swu_run2_P_076_vol_002.nii
     /run3
        swu_run3_P_076_vol_001.nii
        swu_run3_P_076_vol_002.nii
  /P_102
     /run1
        swu_run1_P_102_vol_001.nii
        swu_run1_P_102_vol_002.nii
      /run2 
        swu_run2_P_102_vol_001.nii
        swu_run2_P_102_vol_002.nii
      /run3
        swu_run3_P_102_vol_001.nii
        swu_run3_P_102_vol_002.nii

The below code does the trick when I run the script within the subfolder (P_XXX):

for f in swu_run?_*.nii; do
       num=${f:7:1}
       mv "$f" run"$num"/
    
done'

But I am struggling to find the appropriate for loop to make it work from the parent directory (Analysis), rather than manually running it within each subfolder. I tried the following:

find . -type f -name '*.nii' -exec bash -c '
for f in swu_run?_*.nii; do
     num=${f:7:1}
     mv "$f" run"$num"/
 
done' bash {} +

This returns the error message cannot stat 'swu_run?_*.nii': No such file or directory.

How do I run the code at the level of the Analysis folder, so that each P_XXX subfolder is reorganised in three further subfolders (run1, run2 and run3) with their matching files in one go?

Answer 1

You could use two loops with bash:

cd /path/to/Analysis
shopt -s nullglob
for i in {1..3}; do
  for f in */swu_run${i}_*.nii; do
     mv "$f" "${f%/*}/run${i}/"
  done
done

The enabled nullglob shell option makes sure that the inner loop is not entered if */swu_run${i}_*.nii doesn't match any files (already moved or missing).

The parameter expansion ${f%/*} removes the shortest suffix pattern /* leaving the path of the parent directory.