diff --git a/rubix_postproc.sh b/rubix_postproc.sh index e7785705a786de6d2855d2f420e2b4eeedd0bf42..5f2b995d6b3ead85f5b167ac1e44b5b2858a69d4 100644 --- a/rubix_postproc.sh +++ b/rubix_postproc.sh @@ -17,9 +17,21 @@ do ${FSLDIR}/bin/fslmerge -z ${out_dir}/merged_f${fib}samples `${FSLDIR}/bin/imglob ${out_dir}/diff_slices/data_slice_*/f${fib}samples*` ${FSLDIR}/bin/fslmaths ${out_dir}/merged_f${fib}samples -Tmean ${out_dir}/mean_f${fib}samples ${FSLDIR}/bin/make_dyadic_vectors ${out_dir}/merged_th${fib}samples ${out_dir}/merged_ph${fib}samples ${out_dir}/mean_f${fib}samples ${out_dir}/dyads${fib} 95 + if [ $fib -ge 2 ];then + ${FSLDIR}/bin/maskdyads ${out_dir}/dyads${fib} ${out_dir}/mean_f${fib}samples + fi fib=$(($fib + 1)) done +if [ `${FSLDIR}/bin/imtest ${out_dir}/mean_f1samples` -eq 1 ];then + ${FSLDIR}/bin/fslmaths ${out_dir}/mean_f1samples -mul 0 ${out_dir}/mean_fsumsamples + fib=1 + while [ $fib -le $numfib ] + do + ${FSLDIR}/bin/fslmaths ${out_dir}/mean_fsumsamples -add ${out_dir}/mean_f${fib}samples ${out_dir}/mean_fsumsamples + fib=$(($fib + 1)) + done +fi if [ `${FSLDIR}/bin/imtest ${out_dir}/diff_slices/data_slice_0000/mean_dsamples` -eq 1 ];then ${FSLDIR}/bin/fslmerge -z ${out_dir}/mean_dsamples `${FSLDIR}/bin/imglob ${out_dir}/diff_slices/data_slice_*/mean_dsamples*` @@ -81,21 +93,21 @@ done echo Removing intermediate files -if [ `imtest ${out_dir}/merged_th1samples` -eq 1 ];then - if [ `imtest ${out_dir}/merged_ph1samples` -eq 1 ];then - if [ `imtest ${out_dir}/merged_f1samples` -eq 1 ];then +if [ `${FSLDIR}/bin/imtest ${out_dir}/merged_th1samples` -eq 1 ];then + if [ `${FSLDIR}/bin/imtest ${out_dir}/merged_ph1samples` -eq 1 ];then + if [ `${FSLDIR}/bin/imtest ${out_dir}/merged_f1samples` -eq 1 ];then rm -rf ${out_dir}/diff_slices rm -f ${out_dir}/dataLR_slice_* rm -f ${out_dir}/dataHR_newslice_* - rm -f ${out_dir}/maskLR_slice_* - if [ `imtest ${out_dir}/grad_devLR_slice_0000` -eq 1 ];then + rm -f ${out_dir}/nodif_brain_maskLR_slice_* + if [ `${FSLDIR}/bin/imtest ${out_dir}/grad_devLR_slice_0000` -eq 1 ];then rm -f ${out_dir}/grad_devLR_slice_* fi - if [ `imtest ${out_dir}/grad_devHR_newslice_0000` -eq 1 ];then + if [ `${FSLDIR}/bin/imtest ${out_dir}/grad_devHR_newslice_0000` -eq 1 ];then rm -f ${out_dir}/grad_devHR_newslice_* fi fi fi fi -echo Done \ No newline at end of file +echo Done