3rd.sh

#!/bin/bash
#$ -S /bin/bash

set -x -e

#prepross code path
export preroot=/home/lixinwei/daiyu/prepross
# Original data path
cd /home/lixinwei/daiyu/initial_data/image

labelpath=/home/lixinwei/daiyu/initial_data/labels


# registration template
template=$preroot/MNI152_T1_1mm.nii.gz

for im in *_d_n4_trun_hism.nii.gz;do
  bn=$(basename $im _d_n4_trun_hism.nii.gz)

  # hippocampus 
  seg=$labelpath/${bn}_mask.nii.gz
  seg_template=$labelpath/${bn}_mask_template.nii.gz

  #t1-->template
  $preroot/greedy -d 3 -a -dof 6 -m NCC 2x2x2 -i $template $im -o ${bn}_3t_greedy_t1_to_template_init_rigid.mat -n 400x0x0x0 -ia-image-centers -search 400 5 5
  $preroot/greedy -d 3 -a -m NCC 2x2x2 -i $template $im -o ${bn}_3t_greedy_t1_to_template.mat -n 400x80x40x0 -ia ${bn}_3t_greedy_t1_to_template_init_rigid.mat 
  #reslice to template (get whole brain image)
  $preroot/greedy -d 3 -rm $im ${bn}_3t_reslice_t1_to_template.nii.gz -rf $template -ri LABEL 0.2vox -rm $seg $seg_template -r ${bn}_3t_greedy_t1_to_template.mat
 
done