diff --git a/bedpostx_postproc.sh b/bedpostx_postproc.sh index 0372862d4a67998b56bbfe96d1500ce03459800d..6cee95b4c742a99507ff63428ac00377e64c95d2 100755 --- a/bedpostx_postproc.sh +++ b/bedpostx_postproc.sh @@ -2,14 +2,14 @@ subjdir=$1 -numfib=`${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples | wc -w | awk '{print $1}'` +numfib=`${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples* | wc -w | awk '{print $1}'` fib=1 while [ $fib -le $numfib ] do - ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples` - ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples` - ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples` + ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples*` + ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples*` + ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples*` ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples diff --git a/post_xfibres b/post_xfibres index 1aedb8e355ded635cd2ce08151b2dc571ded5802..af845ed0b2a027f30d28093a7719c51f1369cb60 100755 --- a/post_xfibres +++ b/post_xfibres @@ -16,18 +16,18 @@ else fi cd $dirname -numfib=`${FSLDIR}/bin/imglob *f*samples |wc -w` +numfib=`${FSLDIR}/bin/imglob *f*samples* |wc -w` echo "$numfib fibres" fib=1; -${FSLDIR}/bin/fslroi `${FSLDIR}/bin/imglob *f1samples` numfibs 0 1 +${FSLDIR}/bin/fslroi `${FSLDIR}/bin/imglob *f1samples*` numfibs 0 1 ${FSLDIR}/bin/fslmaths numfibs -mul 0 numfibs while [ $fib -le $numfib ];do echo $fib - ${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/imglob *f${fib}samples` -Tmean mean_f${fib}samples + ${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/imglob *f${fib}samples*` -Tmean mean_f${fib}samples ${FSLDIR}/bin/fslmaths mean_f${fib}samples -thr $thresh -bin ${$}bin${fib} ${FSLDIR}/bin/fslmaths numfibs -add ${$}bin${fib} numfibs - ${FSLDIR}/bin/make_dyadic_vectors `${FSLDIR}/bin/imglob *th${fib}samples` `${FSLDIR}/bin/imglob *ph${fib}samples` dyads${fib} + ${FSLDIR}/bin/make_dyadic_vectors `${FSLDIR}/bin/imglob *th${fib}samples*` `${FSLDIR}/bin/imglob *ph${fib}samples*` dyads${fib} fib=`echo "$fib +1"|bc`; done rm ${$}bin*