#!/bin/sh
study=$1
shift

id=$1
shift

dir=$1
shift

debug=0

#First get the freesurfer processed MRIs
${FREESURFER_HOME}/bin/mri_vol2vol --mov ${SUBJECTS_DIR}/${study}_${id}/mri/nu.mgz --targ ${SUBJECTS_DIR}/${study}_${id}/mri/rawavg.mgz --regheader --o ${dir}/${id}_tmp_nu_in_rawavg.mgz
${FREESURFER_HOME}/bin/mri_convert --in_type mgz --out_type nii ${dir}/${id}_tmp_nu_in_rawavg.mgz ${dir}/${id}_tmp.nii.gz
${FSLDIR}/bin/fslreorient2std ${dir}/${id}_tmp ${dir}/${id}_struc
${FREESURFER_HOME}/bin/mri_vol2vol --mov ${SUBJECTS_DIR}/${study}_${id}/mri/brain.mgz --targ ${SUBJECTS_DIR}/${study}_${id}/mri/rawavg.mgz --regheader --o ${dir}/${id}_tmp_brain_in_rawavg.mgz
${FREESURFER_HOME}/bin/mri_convert --in_type mgz --out_type nii ${dir}/${id}_tmp_brain_in_rawavg.mgz ${dir}/${id}_tmp_brain.nii.gz
${FSLDIR}/bin/fslreorient2std ${dir}/${id}_tmp_brain ${dir}/${id}_brain 

if [ $debug = 0 ] ; then
    rm ${dir}/${id}_tmp* 
fi