#!/bin/bash

#PBS    -l  nodes=1:ppn=12
#PBS    -l  walltime=00:10:00
#PBS    -e  0.error1
#PBS    -o  0.output1
#PBS    -N  FreeSurfer_crosssectional_Track2010

cd $PBS_O_WORKDIR

module load bc/1.06
module load gcc/4.3.3


export FREESURFER_HOME=/local/software/rh53/freesurfer/5.3.0/freesurfer
source $FREESURFER_HOME/SetUpFreeSurfer.sh

export SUBJECTS_DIR=/home/mb4/test/free/track2010FS


#export FSFAST_HOME=$FREESURFER_HOME/fsfast
#export FSF_OUTPUT_FORMAT=nii.gz
#export MNI_DIR=$FREESURFER_HOME/mni
#export FSL_DIR=$FREESURFER_HOME/fsl
#export MINC_BIN_DIR=$FREESURFER_HOME/mni/bin
#export PATH=$FREESURFER_HOME/bin:$FSFAST_HOME/bin:$MNI_DIR/bin:$FSL_DIR/bin:$FREESURFER_HOME:$PATH


for i in `cat /home/mb4/test/free/track2010FS/list3.txt`
do
recon-all  -i /home/mb4/test/free/track2010FS/${i}.nii -sd $SUBJECTS_DIR   -subjid ${i} -autorecon1 -cw256
recon-all  -subjid /home/mb4/test/free/track2010FS/${i} -autorecon2 -autorecon3 -localGI
done