#!/bin/bash
export SUBJECTS_DIR="/home/ZhangJianfeng_04/DouMin_respiration/recon_all"

datadir="/home/ZhangJianfeng_04/DouMin_respiration/T1_nii"

for subj_dir in ${datadir}/*/; do
    if [ -d "${subj_dir}" ]; then
        subj_id=$(basename "${subj_dir}")
        echo "subj_id = $subj_id"
        echo "subj_dir = $subj_dir"
        T1Img="${subj_dir}/${subj_id}_t1.nii"
        recon-all -i "${T1Img}" -s "${subj_id}" -all
    fi
done