UNIX for Beginners Questions & Answers

sub-001
--ses-T1
---- anat
--------File.nii
--ses-T2
----anat
 -------File.nii
sub-002

set data_root = /Users/whatever/ever/Scans
# --------------------------------------------------
# get a list of subjects
  cd $data_root
  set subjects = ( sub-* )
  echo $subjects

# --------------------------------------------------
# process all subjects
  foreach subj_id ( $subjects )
     
     echo $subj_id
     # foreach subj_id get list of sessions
     cd $data_root/$subj_id
     set session = ( ses-T* )
     echo $session
  
     # for all sessions 
     foreach session_num ( $session )
		  
		  #move to anat directory
		  cd $data_root/$subj_id/$session_num/anat
		  #for all items
		  foreach item ( * )
		  #create variable filename with part of file before the "." 
		  set filename = (`echo $item | awk -F '[.]' '{print $1}'`)
		  #convert nii to AFNI file and run 3dcopy 
		  3dcopy $item $filename 
                 #make a new directory called nii
                  mkdir  $data_root/$subj_id/$session_num/anat/nii
                 #move all nii.gz files to new directory
                 mv *.nii.gz $data_root/$subj_id/$session_num/anat/nii    
     end
     
  end