Shell Programming and Scripting

/root/001/folder2/image4.nii.gz
/root/002/folder2/image4.nii.gz

/root/001/folder2/image5.nii.gz
/root/002/folder2/image5.nii.gz

for file in `cat 1.txt`; do
	ln -si $file ./root/00*/folder2/*5*_done.nii.gz
done

#!/bin/ksh
COUNT=1
while read LNKFILE1
do
    LNKFILE2=$(awk 'NR == "'${COUNT}'"' 2.txt)
    ln -si ${LNKFILE1} ${LNKFILE2}_done
    COUNT=$(($COUNT + 1))
done < 1.txt

complain() {
  printf "%s\n" "$*"
  continue
}

while read file && read link<&3
do
  # determine directories
  dir_file=${file%/*}
  dir_link=${link%/*}

  # determine name of new link
  new_link=${link%.*.*}_done.${link#*.}

  # determine name the local link should point to
  local_file=${file##*/}
  
  # complain if there are things wrong
  [ -e "$file" ]                || complain "file $file does not exist"
  [ "$dir_file" = "$dir_link" ] || complain "The directories of $file and $link are not the same, so a local symlink cannot be made"
  [ ! -e "$new_link" ]          || complain "An entry for $new_link already exists"

  # create the link
  ln -s "$local_file" "$new_link"
done < 1.txt 3<2.txt