Alexsavio scripts

FSL Tools

create_mean_template.sh

  #!/bin/bash

  #This script reads all images from the $subjs_root directory and creates a new smoothed image with the mean intensity value of all the images.

  subjs_root=../Female/original
  target_dir=$PWD
  cd $subjs_root
  
  cont=0
  subj_num=`ls *t88_gfc*hdr | wc -l`
  
  template=template.nii.gz
  temp=temp.nii.gz
  
  
  if [ -f $template ]
  then
     rm -f $template
  fi
  
  if [ -f $temp ]
  then
     rm -f $temp
  fi
  
  ls *hdr | while read vol;
  do
     cont=$(($cont + 1))
  
     echo $cont - $vol
  
     if [ -f $template ]
     then
        tmp=`fslstats $vol -r` 
        max_intensity=${tmp:`expr index "$tmp" ' '`:${#tmp}}
        fslmaths -dt double $vol  -div $subj_num $temp
        fslmaths -dt double $temp -add $template $template -odt double
     else
        tmp=`fslstats $vol -r` 
        max_intensity=${tmp:`expr index "$tmp" ' '`:${#tmp}}
        fslmaths -dt double $vol -div $subj_num $template
     fi
  done
  
  cont=`ls *hdr | wc -l`
  
  #smooth
  fslmaths $template -kernel gauss 2 -fmean $template
  
  mv $template $target_dir
  
  rm -f $temp
  
  echo $cont files processed.