Content Comparison

#PBS -P 
#PBS -N BASE_processing
#PBS -l select=1:ncpus=2:ngpus=1:mem=32GB
#PBS -q=main
#PBS -l walltime=10:00:00

#PBS -q defaultQ

module load python/3.6.5
module load openmpi-gcc/3.1.3
module load cuda/10.0.130
module load mrtrix3tissue/5.2.7
module load singularity/3.5.3
module load fsl/6.0.3
module load ants/2.3.2
module load mrtrix3/3.0.1
module load freesurfer/6.0.0
source $FREESURFER_HOME/SetUpFreeSurfer.sh
export SUBJECTS_DIR=/scratch/ProjectPreprocessing

# CODE FOR TERMINAL												                                                							                            
# list='XXX_XXX
# XXX_XXX
# XXX_XXX'							                                        
# for i in $list ; do qsub -v base=$i FS_BASE_Processing.pbs; done 

echo ${base}
cd $SUBJECTS_DIR

time_points=$(find ${SUBJECTS_DIR} -iname "${base}_MR*")
NumTPs=( $time_points )

if [[ ${#NumTPs[@]} = 2 ]]
	then
	recon-all -base $base -tp ${base}_MR1 -tp ${base}_MR2 -all -openmp 4
elif [[ ${#NumTPs[@]} = 3 ]]
	then
	recon-all -base $base -tp ${base}_MR1 -tp ${base}_MR2 -tp ${base}_MR3 -all -openmp 4
elif [[ ${#NumTPs[@]} = 4 ]]
	then
	recon-all -base $base -tp ${base}_MR1 -tp ${base}_MR2 -tp ${base}_MR3 -tp ${base}_MR4 -all -openmp 4
elif [[ ${#NumTPs[@]} = 5 ]]
	then
	recon-all -base $base -tp ${base}_MR1 -tp ${base}_MR2 -tp ${base}_MR3 -tp ${base}_MR4 -tp ${base}_MR5 -all -openmp 4
elif [[ ${#NumTPs[@]} = 6 ]]
	then
	recon-all -base $base -tp ${base}_MR1 -tp ${base}_MR2 -tp ${base}_MR3 -tp ${base}_MR4 -tp ${base}_MR5 -tp ${base}_MR6 -all -openmp 4
elif [[ ${#NumTPs[@]} = 7 ]]
	then
	recon-all -base $base -tp ${base}_MR1 -tp ${base}_MR2 -tp ${base}_MR3 -tp ${base}_MR4 -tp ${base}_MR5 -tp ${base}_MR6 -tp ${base}_MR7 -all -openmp 4
else
	# if there is only one timepoint
	echo 'there is either only one timepoint (no longitudinal data) or there are more than 8, please edit the script."
fi