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Commit a783afc8 authored by Matthew Webster's avatar Matthew Webster
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new imglob

parent 5167c0b8
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bedpostx_postproc.sh
+ 4
− 4
View file @ a783afc8
......@@ -2,14 +2,14 @@
subjdir=$1
numfib=`${FSLDIR}/bin/imglob -oneperimage ${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 -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/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
......
correct_and_average
+ 1
− 1
View file @ a783afc8
......@@ -57,7 +57,7 @@ while [ ${avg} -le ${numavgs} ]; do
fslroi ${$}${1}_b0_correct ${$}avg_${avg}_scan_${scan} $tmp;
scan=`expr $scan + 1`;
done
fslmerge -t ${$}avg_${avg}_all `imglob -oneperimage ${$}avg_${avg}_scan_*`
fslmerge -t ${$}avg_${avg}_all `imglob ${$}avg_${avg}_scan_*`
fslmaths data -add ${$}avg_${avg}_all data;
avg=`expr $avg + 1`;
......
eddy_correct
+ 1
− 1
View file @ a783afc8
......@@ -26,7 +26,7 @@ fi
fslroi $input $output $ref 1
fslsplit $input
full_list=`${FSLDIR}/bin/imglob -oneperimage vol????.*`
full_list=`${FSLDIR}/bin/imglob vol????.*`
for i in $full_list ; do
echo processing $i
......
ocmr_preproc
+ 4
− 4
View file @ a783afc8
......@@ -17,12 +17,12 @@ nep=`echo *ep2d_* |wc -w`
nlp=`echo *lp2d_* |wc -w`
if [ $nep -gt 1 ];then
a1=`imglob -oneperimage images_?_*ep2d_*`
a2=`imglob -oneperimage images_??_*ep2d_*`
a1=`imglob images_?_*ep2d_*`
a2=`imglob images_??_*ep2d_*`
fslmerge -t big4D $a1 $a2
elif [ $nlp -gt 1 ];then
a1=`imglob -oneperimage images_?_*lp2d_*`
a2=`imglob -oneperimage images_??_*lp2d_*`
a1=`imglob images_?_*lp2d_*`
a2=`imglob images_??_*lp2d_*`
fslmerge -t big4D $a1 $a2
fi
......
old_bedpost
+ 3
− 3
View file @ a783afc8
......@@ -198,9 +198,9 @@ done
##this will have to change..
echo "Merging outputs into 4D files"
${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/fslmerge -z ${subjdir}.bedpost/merged_thsamples `${FSLDIR}/bin/imglob ${subjdir}.bedpost/diff_slices/data_slice_*/th_samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpost/merged_phsamples `${FSLDIR}/bin/imglob ${subjdir}.bedpost/diff_slices/data_slice_*/ph_samples`
${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpost/merged_fsamples `${FSLDIR}/bin/imglob ${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
......
old_bedpostX
+ 4
− 4
View file @ a783afc8
......@@ -216,14 +216,14 @@ done
#postprocess $subjdir
numfib=`${FSLDIR}/bin/imglob -oneperimage ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples |wc -w`
numfib=`${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples |wc -w`
echo number of fibres $numfib
fib=1;
while [ $fib -le $numfib ];do
${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/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
......
post_xfibres
+ 4
− 4
View file @ a783afc8
......@@ -16,18 +16,18 @@ else
fi
cd $dirname
numfib=`${FSLDIR}/bin/imglob -oneperimage *f*samples |wc -w`
numfib=`${FSLDIR}/bin/imglob *f*samples |wc -w`
echo "$numfib fibres"
fib=1;
${FSLDIR}/bin/fslroi `${FSLDIR}/bin/imglob -oneperimage *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 -oneperimage *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 -oneperimage *th${fib}samples` `${FSLDIR}/bin/imglob -oneperimage *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*
......
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