#!/bin/bash # =========================================================================== # Name: do_13_ssw.bash # Author: LB # Date: 7/12/22 # Syntax: bash do_13_ssw.bash SUBJ # Arguments: SUBJ: subject ID # Desc: This script will run all chosen scans through the # @SSwarper program for skullstripping (SS) and nonlinear # alignment (warping) of T1w anatomical to a template # Req: 1) AFNI # Notes: Run this before afni_proc.py, and provide its outputs there. # =========================================================================== # Biowulf loading module load afni # ------------------------------ get inputs --------------------------------- if [ "$#" -eq 1 ]; then subj=$1 else echo "Specify participant ID Please" exit 1 fi # ------------------------------ define paths --------------------------------- pwd_dir=`pwd` proj_dir=${pwd_dir%/*} anatdir=${proj_dir}/Anat/${subj} # dir with T1w anatomical funcdir=${proj_dir}/Func/${subj} # dir with FMRI/EPI stimdir=${proj_dir}/Behav/${subj} # dir with stim timing files analysisdir=${proj_dir}/Analysis/${subj} # dir with SSW results; output here MNItemplate=${pwd_dir}/MNI152_2009_template_SSW.nii.gz echo "++ Template: ${MNItemplate}" # --------------------------- check input dsets ------------------------------ # anat if [ -f "${anatdir}/${subj}_T1.nii" ] ; then cat <