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Commit 298534c2 authored by Matthew Webster's avatar Matthew Webster
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avw2fsl

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with 75 additions and 75 deletions
bedpost_datacheck
+ 8
− 8
View file @ 298534c2
......@@ -9,7 +9,7 @@ DIR=$1;
for img in ${DIR}/data ${DIR}/nodif ${DIR}/nodif_brain_mask ;do
if [ `${FSLDIR}/bin/imtest $img` -eq 1 ] ; then
echo $img
${FSLDIR}/bin/avwinfo $img;
${FSLDIR}/bin/fslinfo $img;
echo ""
else
echo $img does not exist;
......@@ -25,14 +25,14 @@ done
if [ `${FSLDIR}/bin/imtest ${DIR}/data` -eq 1 -a `${FSLDIR}/bin/imtest ${DIR}/nodif_brain_mask` -eq 1 ];then
dx=`${FSLDIR}/bin/avwval ${DIR}/data dim1`
dy=`${FSLDIR}/bin/avwval ${DIR}/data dim2`
dz=`${FSLDIR}/bin/avwval ${DIR}/data dim3`
dt=`${FSLDIR}/bin/avwval ${DIR}/data dim4`
dx=`${FSLDIR}/bin/fslval ${DIR}/data dim1`
dy=`${FSLDIR}/bin/fslval ${DIR}/data dim2`
dz=`${FSLDIR}/bin/fslval ${DIR}/data dim3`
dt=`${FSLDIR}/bin/fslval ${DIR}/data dim4`
nbmx=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim1`
nbmy=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim2`
nbmz=`${FSLDIR}/bin/avwval ${DIR}/nodif_brain_mask dim3`
nbmx=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim1`
nbmy=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim2`
nbmz=`${FSLDIR}/bin/fslval ${DIR}/nodif_brain_mask dim3`
if [ $dx -ne $nbmx -o $dy -ne $nbmy -o $dz -ne $nbmz ];then
......
bedpostx
+ 1
− 1
View file @ 298534c2
......@@ -106,7 +106,7 @@ echo Queuing preprocessing stages
preprocid=`${FSLDIR}/bin/fsl_sub -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostX_preproc.sh ${subjdir}`
echo Queuing parallel processing stage
nslices=`${FSLDIR}/bin/avwval ${subjdir}/data dim3`
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
[ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
for ((slice=0; slice < $nslices; slice++)) ; do
echo "${FSLDIR}/bin/bedpostX_single_slice.sh $subjdir $nfibres $fudge $burnin $slice" \
......
bedpostx_postproc.sh
+ 6
− 6
View file @ 298534c2
......@@ -12,12 +12,12 @@ subjdir=$1
numfib=`${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples | wc -w | awk '{print $1}'`
for ((fib=1; fib<=$numfib; fib++));do
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${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
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpostX/merged_th${fib}samples ${subjdir}.bedpostX/merged_ph${fib}samples ${subjdir}.bedpostX/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}
done
......
bedpostx_preproc.sh
+ 3
− 3
View file @ 298534c2
......@@ -12,11 +12,11 @@ subjdir=$1
echo Copying files to bedpost directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
${FSLDIR}/bin/avwmaths\
${FSLDIR}/bin/fslmaths\
${subjdir}/nodif\
-mas ${subjdir}/nodif_brain_mask\
${subjdir}.bedpostX/nodif_brain
${FSLDIR}/bin/avwslice ${subjdir}/data
${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
${FSLDIR}/bin/fslslice ${subjdir}/data
${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask
echo Done
correct_and_average
+ 7
− 7
View file @ 298534c2
......@@ -38,10 +38,10 @@ b0_numbers=`cat $avgfile |grep -v '^ *$' |sed -n "${numlines}p"`;
ab0=`echo $b0_numbers |awk '{print \$1}'`
eddy_correct ${1} ${$}${1}_b0_correct $ab0
total_vols=`avwval $1 dim4`;
total_vols=`fslval $1 dim4`;
vols_per_avg=`echo "10k $total_vols $numavgs / p"|dc -`;
avwroi ${1} data 0 ${vols_per_avg};
avwmaths data -mul 0 data;
fslroi ${1} data 0 ${vols_per_avg};
fslmaths data -mul 0 data;
avg=1;scan=1;
......@@ -54,15 +54,15 @@ while [ ${avg} -le ${numavgs} ]; do
echo $avg $scan $tmp $vols_per_avg
avwroi ${$}${1}_b0_correct ${$}avg_${avg}_scan_${scan} $tmp;
fslroi ${$}${1}_b0_correct ${$}avg_${avg}_scan_${scan} $tmp;
scan=`expr $scan + 1`;
done
avwmerge -t ${$}avg_${avg}_all `imglob -oneperimage ${$}avg_${avg}_scan_*`
avwmaths data -add ${$}avg_${avg}_all data;
fslmerge -t ${$}avg_${avg}_all `imglob -oneperimage ${$}avg_${avg}_scan_*`
fslmaths data -add ${$}avg_${avg}_all data;
avg=`expr $avg + 1`;
done
avwmaths data -div ${numavgs} data;
fslmaths data -div ${numavgs} data;
rm ${$}*
......
doc/fdt_probtrackx.htm
+ 1
− 1
View file @ 298534c2
Source diff could not be displayed: it is too large. Options to address this: view the blob.
eddy_correct
+ 3
− 3
View file @ 298534c2
......@@ -22,9 +22,9 @@ if [ `${FSLDIR}/bin/imtest $input` -eq 0 ];then
exit
fi
avwroi $input $output $ref 1
fslroi $input $output $ref 1
avwsplit $input
fslsplit $input
full_list=`${FSLDIR}/bin/imglob -oneperimage vol*`
for i in $full_list ; do
......@@ -33,7 +33,7 @@ for i in $full_list ; do
${FSLDIR}/bin/flirt -in $i -ref $output -nosearch -o $i -paddingsize 1 >> ${output}.ecclog
done
avwmerge -t $output $full_list
fslmerge -t $output $full_list
/bin/rm vol*
facalc
+ 10
− 10
View file @ 298534c2
......@@ -25,15 +25,15 @@ exit
fi
${FSLDIR}/bin/avwmaths ${bn}_L1 -add ${bn}_L2 -add ${bn}_L3 -div 3 tmpMD
${FSLDIR}/bin/avwmaths ${bn}_L1 -sqr tmpL1sq
${FSLDIR}/bin/avwmaths ${bn}_L2 -sqr tmpL2sq
${FSLDIR}/bin/avwmaths ${bn}_L3 -sqr tmpL3sq
${FSLDIR}/bin/avwmaths ${bn}_L1 -sub tmpMD -sqr tmpl1subsq
${FSLDIR}/bin/avwmaths ${bn}_L2 -sub tmpMD -sqr tmpl2subsq
${FSLDIR}/bin/avwmaths ${bn}_L3 -sub tmpMD -sqr tmpl3subsq
${FSLDIR}/bin/avwmaths tmpL1sq -add tmpL2sq -add tmpL3sq denom
${FSLDIR}/bin/avwmaths tmpl1subsq -add tmpl2subsq -add tmpl3subsq -mul 1.5 numer
${FSLDIR}/bin/avwmaths numer -div denom -sqrt ${ob}_FA
${FSLDIR}/bin/fslmaths ${bn}_L1 -add ${bn}_L2 -add ${bn}_L3 -div 3 tmpMD
${FSLDIR}/bin/fslmaths ${bn}_L1 -sqr tmpL1sq
${FSLDIR}/bin/fslmaths ${bn}_L2 -sqr tmpL2sq
${FSLDIR}/bin/fslmaths ${bn}_L3 -sqr tmpL3sq
${FSLDIR}/bin/fslmaths ${bn}_L1 -sub tmpMD -sqr tmpl1subsq
${FSLDIR}/bin/fslmaths ${bn}_L2 -sub tmpMD -sqr tmpl2subsq
${FSLDIR}/bin/fslmaths ${bn}_L3 -sub tmpMD -sqr tmpl3subsq
${FSLDIR}/bin/fslmaths tmpL1sq -add tmpL2sq -add tmpL3sq denom
${FSLDIR}/bin/fslmaths tmpl1subsq -add tmpl2subsq -add tmpl3subsq -mul 1.5 numer
${FSLDIR}/bin/fslmaths numer -div denom -sqrt ${ob}_FA
${FSLDIR}/bin/imrm tmpMD tmpL1sq tmpL2sq tmpL3sq tmpl1subsq tmpl2subsq tmpl3subsq numer denom
ocmr_preproc
+ 11
− 11
View file @ 298534c2
......@@ -19,16 +19,16 @@ nlp=`echo *lp2d_* |wc -w`
if [ $nep -gt 1 ];then
a1=`imglob -oneperimage images_?_*ep2d_*`
a2=`imglob -oneperimage images_??_*ep2d_*`
avwmerge -t big4D $a1 $a2
fslmerge -t big4D $a1 $a2
elif [ $nlp -gt 1 ];then
a1=`imglob -oneperimage images_?_*lp2d_*`
a2=`imglob -oneperimage images_??_*lp2d_*`
avwmerge -t big4D $a1 $a2
fslmerge -t big4D $a1 $a2
fi
#nslices=${1}
#zsize=`avwval big4D dim3`
#tsize=`avwval big4D dim4`
#zsize=`fslval big4D dim3`
#tsize=`fslval big4D dim4`
#tpts=`echo "10k $zsize $nslices /p "|dc -`
#afterdot=`echo $tpts | awk -F . '{print \$2}'`
#foo=`echo $afterdot|grep [123456798]`
......@@ -37,15 +37,15 @@ fi
# exit 1
#fi
#tpts=`echo "$tpts \* $tsize" |bc"'
#xsize=`avwval big4D dim1`
#ysize=`avwval big4D dim2`
#xvoxsize=`avwval big4D pixdim1`
#yvoxsize=`avwval big4D pixdim2`
#zvoxsize=`avwval big4D pixdim3`
#datatype=`avwval big4D datatype`
#xsize=`fslval big4D dim1`
#ysize=`fslval big4D dim2`
#xvoxsize=`fslval big4D pixdim1`
#yvoxsize=`fslval big4D pixdim2`
#zvoxsize=`fslval big4D pixdim3`
#datatype=`fslval big4D datatype`
#avwcreatehd $xsize $ysize $nslices $tpts $xvoxsize $yvoxsize $zvoxsize 0 0 0 0# $datatype big4D
#fslcreatehd $xsize $ysize $nslices $tpts $xvoxsize $yvoxsize $zvoxsize 0 0 0 0# $datatype big4D
......
old_bedpost
+ 10
− 10
View file @ 298534c2
......@@ -151,16 +151,16 @@ mkdir -p ${subjdir}.bedpost/diff_slices
echo copying files to bedpost directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpost
${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpost
${FSLDIR}/bin/avwmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpost/nodif_brain
${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpost/nodif_brain
mkdir -p ${subjdir}.bedpost/logs
mkdir -p ${subjdir}.bedpost/logs/pid_${$}
nslices=`${FSLDIR}/bin/avwval ${subjdir}/data dim3`
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
${FSLDIR}/bin/avwslice ${subjdir}/data
${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
${FSLDIR}/bin/fslslice ${subjdir}/data
${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask
#for parallel processing, the following need to be setup elsewhere
#FSLMACHINELIST="list of machines (can be duplicated for two processors etc.)"
......@@ -198,12 +198,12 @@ done
##this will have to change..
echo "Merging outputs into 4D files"
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples`
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bedpost/mean_thsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpost/diff_slices/data_slice_*/f_samples`
${FSLDIR}/bin/fslmaths ${subjdir}.bedpost/merged_thsamples -Tmean ${subjdir}.bedpost/mean_thsamples
${FSLDIR}/bin/fslmaths ${subjdir}.bedpost/merged_phsamples -Tmean ${subjdir}.bedpost/mean_phsamples
${FSLDIR}/bin/fslmaths ${subjdir}.bedpost/merged_fsamples -Tmean ${subjdir}.bedpost/mean_fsamples
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpost/merged_thsamples ${subjdir}.bedpost/merged_phsamples ${subjdir}.bedpost/nodif_brain_mask ${subjdir}.bedpost/dyadic_vectors
......
old_bedpostX
+ 10
− 10
View file @ 298534c2
......@@ -171,16 +171,16 @@ mkdir -p ${subjdir}.bedpostX/diff_slices
echo copying files to bedpostX directory
cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
${FSLDIR}/bin/avwmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
mkdir -p ${subjdir}.bedpostX/logs
mkdir -p ${subjdir}.bedpostX/logs/pid_${$}
nslices=`${FSLDIR}/bin/avwval ${subjdir}/data dim3`
nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
${FSLDIR}/bin/avwslice ${subjdir}/data
${FSLDIR}/bin/avwslice ${subjdir}/nodif_brain_mask
${FSLDIR}/bin/fslslice ${subjdir}/data
${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask
#for parallel processing, the following need to be setup elsewhere
#FSLMACHINELIST="list of machines (can be duplicated for two processors etc.)"
......@@ -221,12 +221,12 @@ echo number of fibres $numfib
fib=1;
while [ $fib -le $numfib ];do
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
${FSLDIR}/bin/avwmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
${FSLDIR}/bin/avwmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_*/f${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
${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpostX/merged_th${fib}samples ${subjdir}.bedpostX/merged_ph${fib}samples ${subjdir}.bedpostX/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}
......
post_xfibres
+ 5
− 5
View file @ 298534c2
......@@ -20,13 +20,13 @@ numfib=`${FSLDIR}/bin/imglob -oneperimage *f*samples |wc -w`
echo "$numfib fibres"
fib=1;
${FSLDIR}/bin/avwroi `${FSLDIR}/bin/imglob -oneperimage *f1samples` numfibs 0 1
${FSLDIR}/bin/avwmaths numfibs -mul 0 numfibs
${FSLDIR}/bin/fslroi `${FSLDIR}/bin/imglob -oneperimage *f1samples` numfibs 0 1
${FSLDIR}/bin/fslmaths numfibs -mul 0 numfibs
while [ $fib -le $numfib ];do
echo $fib
${FSLDIR}/bin/avwmaths `${FSLDIR}/bin/imglob -oneperimage *f${fib}samples` -Tmean mean_f${fib}samples
${FSLDIR}/bin/avwmaths mean_f${fib}samples -thr $thresh -bin ${$}bin${fib}
${FSLDIR}/bin/avwmaths numfibs -add ${$}bin${fib} numfibs
${FSLDIR}/bin/fslmaths `${FSLDIR}/bin/imglob -oneperimage *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 -oneperimage *th${fib}samples` `${FSLDIR}/bin/imglob -oneperimage *ph${fib}samples` dyads${fib}
fib=`echo "$fib +1"|bc`;
done
......
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