From 00f93defac95b8fdc31dc02321aad3ee4df8df87 Mon Sep 17 00:00:00 2001
From: Stamatios Sotiropoulos <stam@fmrib.ox.ac.uk>
Date: Fri, 21 Jun 2013 12:10:19 +0000
Subject: [PATCH] Added gradient nonlinearity correction and filtering modes
options
---
rubix_postproc.sh | 21 +++++++++-----
rubix_preproc.sh | 71 +++++++++++++++++++++++++++++++++++++----------
2 files changed, 70 insertions(+), 22 deletions(-)
diff --git a/rubix_postproc.sh b/rubix_postproc.sh
index 75ea19a..e778570 100644
--- a/rubix_postproc.sh
+++ b/rubix_postproc.sh
@@ -1,9 +1,10 @@
#!/bin/sh
-out_dir=$1
-dataLR=$2
-maskLR=$3
-dataHR=$4
+subjdir=$1
+filterflag=$2
+
+out_dir=${subjdir}.rubiX
+maskLR=nodif_brain_maskLR
numfib=`${FSLDIR}/bin/imglob ${out_dir}/diff_slices/data_slice_0000/f*samples* | wc -w | awk '{print $1}'`
@@ -84,9 +85,15 @@ 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
rm -rf ${out_dir}/diff_slices
- rm -f ${out_dir}/${dataLR}_slice_*
- rm -f ${out_dir}/${dataHR}_newslice_*
- rm -f ${out_dir}/${maskLR}_slice_*
+ 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}/grad_devLR_slice_*
+ fi
+ if [ `imtest ${out_dir}/grad_devHR_newslice_0000` -eq 1 ];then
+ rm -f ${out_dir}/grad_devHR_newslice_*
+ fi
fi
fi
fi
diff --git a/rubix_preproc.sh b/rubix_preproc.sh
index fe23981..85c55b6 100644
--- a/rubix_preproc.sh
+++ b/rubix_preproc.sh
@@ -1,18 +1,51 @@
#!/bin/sh
-dataLR=$1
-maskLR=$2
-dataHR=$3
-out_dir=$4
+subjdir=$1
+filterflag=$2
+gflag=$3
-${FSLDIR}/bin/fslslice $dataLR $out_dir/$dataLR
-${FSLDIR}/bin/fslslice $maskLR $out_dir/$maskLR
-${FSLDIR}/bin/fslslice $dataHR $out_dir/$dataHR
+out_dir=${subjdir}.rubiX
+maskLR=nodif_brain_maskLR
-pixdim3LR=`$FSLDIR/bin/fslval $dataLR pixdim3`
-pixdim3HR=`$FSLDIR/bin/fslval $dataHR pixdim3`
-nslicesLR=`$FSLDIR/bin/fslval $dataLR dim3`
-nslicesHR=`$FSLDIR/bin/fslval $dataHR dim3`
+if [ ${filterflag} -eq 1 ]; then
+ cp ${subjdir}/bvals $out_dir/bvalsLR
+ cp ${subjdir}/bvecs $out_dir/bvecsLR
+ cp ${subjdir}/bvecs $out_dir/bvecsHR
+ cp ${subjdir}/bvals $out_dir/bvalsHR
+ ${FSLDIR}/bin/fslslice $subjdir/data $out_dir/$dataHR
+ HighRes=`fslval ${subjdir}/data pixdim1`
+ LowRes=`echo "${HighRes} * 2" | bc -l`
+ echo "Create Downsampled version of data at ${LowRes} mm isotropic"
+ flirt -in ${subjdir}/nodif_brain_mask -ref ${subjdir}/nodif_brain_mask -applyisoxfm ${LowRes} -interp nearestneighbour -out ${out_dir}/nodif_brain_maskLR
+ flirt -in ${subjdir}/data -ref ${subjdir}/data -applyisoxfm ${LowRes} -interp sinc -out ${out_dir}/dataLR
+ if [ ${gflag} -eq 1 ]; then
+ echo "Create Downsampled version of grad_dev at ${LowRes} mm isotropic"
+ flirt -in ${subjdir}/grad_dev -ref ${subjdir}/grad_dev -applyisoxfm ${LowRes} -interp nearestneighbour -out ${out_dir}/grad_devLR
+ ${FSLDIR}/bin/fslslice $subjdir/grad_dev $out_dir/grad_devHR
+ ${FSLDIR}/bin/fslslice ${out_dir}/grad_devLR $out_dir/grad_devLR
+ fi
+ dataHRname=${subjdir}/data
+ dataLRname=${out_dir}/dataLR
+else
+ cp ${subjdir}/bvalsLR $out_dir/bvalsLR
+ cp ${subjdir}/bvecsLR $out_dir/bvecsLR
+ cp ${subjdir}/bvecsHR $out_dir/bvecsHR
+ cp ${subjdir}/bvalsHR $out_dir/bvalsHR
+ ${FSLDIR}/bin/fslslice $subjdir/dataLR $out_dir/$dataLR
+ ${FSLDIR}/bin/fslslice $subjdir/$maskLR $out_dir/$maskLR
+ ${FSLDIR}/bin/fslslice $subjdir/dataHR $out_dir/$dataHR
+ if [ ${gflag} -eq 1 ]; then
+ ${FSLDIR}/bin/fslslice $subjdir/grad_devLR $out_dir/grad_devLR
+ ${FSLDIR}/bin/fslslice $subjdir/grad_devHR $out_dir/grad_devHR
+ fi
+ dataLRname=${subjdir}/dataLR
+ dataHRname=${subjdir}/dataHR
+fi
+
+pixdim3LR=`$FSLDIR/bin/fslval ${dataLRname} pixdim3`
+pixdim3HR=`$FSLDIR/bin/fslval ${dataHRname} pixdim3`
+nslicesLR=`$FSLDIR/bin/fslval ${dataLRname} dim3`
+nslicesHR=`$FSLDIR/bin/fslval ${dataHRname} dim3`
zratio=`echo "scale=0; $pixdim3LR / $pixdim3HR" | bc -l`
slice=0
@@ -25,14 +58,22 @@ do
do
HRslice=`echo "( ( $slice + 1 ) * $zratio ) - $count" | bc -l`
HRslicezp=`$FSLDIR/bin/zeropad $HRslice 4`
- filenames[arr_cnt]=${out_dir}/${dataHR}_slice_${HRslicezp}
+ filenames[arr_cnt]=${out_dir}/dataHR_slice_${HRslicezp}
+ gfilenames[arr_cnt]=${out_dir}/grad_devHR_slice_${HRslicezp}
count=$(($count - 1))
arr_cnt=$(($arr_cnt + 1))
done
- fslmerge -z ${out_dir}/${dataHR}_newslice_${slicezp} `echo ${filenames[*]}`
+ fslmerge -z ${out_dir}/dataHR_newslice_${slicezp} `echo ${filenames[*]}`
+ if [ ${gflag} -eq 1 ]; then
+ fslmerge -z ${out_dir}/grad_devHR_newslice_${slicezp} `echo ${gfilenames[*]}`
+ fi
slice=$(($slice + 1))
done
-rm -f ${out_dir}/${dataHR}_slice_*
-
+rm -f ${out_dir}/dataHR_slice_*
+#rm -f ${out_dir}/dataLR
+if [ ${gflag} -eq 1 ]; then
+ rm -f ${out_dir}/grad_devHR_slice_*
+# rm -f ${out_dir}/grad_devLR
+fi
echo Done
--
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