Bash - Move files that contain certain string

Question

I have two folders: Controls and Patients . Inside each one of these there are several folders for different individuals ( CO1 , CO2 ), with this organization:

   Controls

   └───C01
   │   └───ROIS 
   │       └───rs_rois (imgs inside)
   │   └───Cortical_masks
   │       └─── accumbens
   │       └─── putamen
   │       └─── caudatus
   │   
   └───C02
   │   └───ROIS 
   │       └───rs_rois (imgs inside)
   │   └───Cortical_masks
   │       └─── accumbens
   │       └─── putamen
   │       └─── caudatus

And the same for Patients

I want to move the imgs from rs_rois to Cortical_masks folder based on a substring of their names. So for example L_accumbens_rsfmri file should go to accumbens folder and R_caudate_rsfmri should go to caudate folder.

This is what I have:

#!/bin/bash
DIR="/media/roy"; cd "$DIR/Analysis" || exit
for group in Controls Patients; do
    for case in "$group"/*; do
        for file in $DIR/Analysis/$case/ROIS2/rs_roi/*; do
            if grep -q accumbens "$file"; then
                mv $file $DIR/Analysis/$case/Cortical_masks/accumbens
            elif grep -q putamen "$file"; then
                mv $file $DIR/Analysis/$case/Cortical_masks/putamen
            elif grep -q caudate "$file"; then
                mv $file $DIR/Analysis/$case/Cortical_masks/caudate
            fi
        done;
    done;
done;

This script doesn´t do anything, why is that? If I add some echo statements, I can see that the for file loop goes through all my files, but the code never gets to the mv statements.

Answer 1

The problem is that the grep expression you use looks for the string ( accumbens , etc) in the contents of the file instead of in the name of the file.

Replace each grep by a pattern match like if [[ $file =~ accumbens ]] ...

The script then becomes:

#!/bin/bash
DIR="/media/roy"; cd "$DIR/Analysis" || exit
for group in Controls Patients; do
    for case in "$group"/*; do
        for file in $DIR/Analysis/$case/ROIS2/rs_roi/*; do
            if [[ $file =~ accumbens ]]; then
                mv $file $DIR/Analysis/$case/Cortical_masks/accumbens
            elif [[ $file =~ putamen ]]; then
                mv $file $DIR/Analysis/$case/Cortical_masks/putamen
            elif [[ $file =~ caudate ]]; then
                mv $file $DIR/Analysis/$case/Cortical_masks/caudate
            fi
        done;
    done;
done;

Answer 2

Use find .

#!/bin/bash
cd /path/to/Analysis/
for group in Control Patients; do
  for case in "$group"/*; do
    orig="$group/$case/ROIS/rs_rois"
    dest="$group/$case/Cortica_masks"
    find "$orig" -type f -name '*accumbens*' -exec mv {} "$dest" \;
    find "$orig" -type f -name '*putamen*' -exec mv {} "$dest" \;
    find "$orig" -type f -name '*caudate*' -exec mv {} "$dest" \;
  done
done

This is a clear way that doesn't need string comparations.

Answer 3

Would something like this work?

make a file.txt containing the strings you want

cat file.txt

caudate

putamen

Then

while read p; do mv $p $DIR/Analysis/$case/Cortical_masks/${p} done < file.txt