ANTSnormalizeAnat.sh

#!/bin/bash

#Define environment parameters
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

#specify where ANTS is installed
export PATH=/software/ANTS:$PATH
export ANTSPATH=/software/ANTS/


#Define experiment specific parameters
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

#specify list of subjects
subjectList='subject1 subject2 subject3'

#specify folder names
experimentDir=~SOMEPATH/experiment               #parent folder
inputDir=$experimentDir/AnatomicalImages         #folder containing anatomical images
templateName=$experimentDir/data/normtemp.nii.gz #path to and name of normtemplate
normAnatOutDir=$experimentDir/normAnat           #outputdir of the normalized T1 files

#specify parameters for antsIntroduction.sh
#compulsory arguments
ImageDimension=3
OutPrefix=''
ReferenceImage=$templateName

#optional arguments
IgnoreHDRWarning=1
MaxIteration=30x90x20
N3Correct=0
QualityCheck=0
MetricType='PR'
TransformationType='GR'

#Do you want to overwrite existing output files? (1 = yes, 0 = no)
overwrite=0


#Write the main script
#~~~~~~~~~~~~~~~~~~~~~

#If not created yet, let's create a new output folder
if [ ! -d $normAnatOutDir ]
then
   mkdir -p $normAnatOutDir
fi

#go into the folder where the script should be run
cd $normAnatOutDir

#go through all subjects
for subj in $subjectList
do

   #if anatomy of the subject wasn't normalized yet or if overwrite was set to 1=yes
   # the antsIntroduction script gets executed
   if [ ! -e $normAnatOutDir/$OutPrefix$subj"deformed.nii.gz" ] || [ $overwrite == 1 ]
   then
      #assemble the command for the script from the input parameters defined above
      cmd="bash $ANTSPATH/antsIntroduction.sh -d $ImageDimension -r $ReferenceImage \
                -i $inputDir/$subj.nii -o $normAnatOutDir/$OutPrefix$subj \
                -f $IgnoreHDRWarning -m $MaxIteration -n $N3Correct -q $QualityCheck \
                -s $MetricType -t $TransformationType"
      echo $cmd #state the command
      eval $cmd #execute the command
   else
      echo -e "NOTICE: ${OutPrefix}${subj}deformed.nii.gz does already exist! \
               Skipping to next subject."
   fi
done #subj done