From e787e5410b9890f3d7a69076d8c69247f1e51ba2 Mon Sep 17 00:00:00 2001
From: Matthew Webster <mwebster@fmrib.ox.ac.uk>
Date: Wed, 25 Jul 2007 10:54:18 +0000
Subject: [PATCH] avw2fsl
---
lesions_0.1 | 24 ++++++++++++------------
lesions_0.2 | 20 ++++++++++----------
lesions_0.3 | 20 ++++++++++----------
siena | 48 ++++++++++++++++++++++++------------------------
siena_cal | 12 ++++++------
siena_flow2std | 10 +++++-----
sienax | 38 +++++++++++++++++++-------------------
7 files changed, 86 insertions(+), 86 deletions(-)
diff --git a/lesions_0.1 b/lesions_0.1
index af7f40c..a974565 100755
--- a/lesions_0.1
+++ b/lesions_0.1
@@ -41,14 +41,14 @@ ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${1}_brain -o
${FSLDIR}/bin/convert_xfm -inverse -omat std_2_${1}_brain.mat ${1}_brain_2_std.mat
# dilate (6mm) standard space structural segmentation, bring into t1 space and re-binarise
-${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dil -dil -dil strucseg_2_${1}_brain
+${FSLDIR}/bin/fslmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dilM -dilM -dilM strucseg_2_${1}_brain
${FSLDIR}/bin/flirt -in strucseg_2_${1}_brain -ref ${1}_brain -out strucseg_2_${1}_brain -applyxfm -init std_2_${1}_brain.mat
-${FSLDIR}/bin/avwmaths strucseg_2_${1}_brain -bin strucseg_2_${1}_brain
+${FSLDIR}/bin/fslmaths strucseg_2_${1}_brain -bin strucseg_2_${1}_brain
# produce t1-derived CSF mask and also dilate in-plane: 5 voxels outside central mask, 1 voxel inside mask
-${FSLDIR}/bin/avwmaths ${1}_brain_pve_0 -thr 0.3 -bin ${1}_csf
-${FSLDIR}/bin/avwmaths ${1}_csf -dil2 -dil2 -dil2 -dil2 -dil2 -sub strucseg_2_${1}_brain -thr 0.5 -bin ${1}_grot
-${FSLDIR}/bin/avwmaths ${1}_csf -dil2 -mul strucseg_2_${1}_brain -add ${1}_grot -bin ${1}_csf_dil
+${FSLDIR}/bin/fslmaths ${1}_brain_pve_0 -thr 0.3 -bin ${1}_csf
+${FSLDIR}/bin/fslmaths ${1}_csf -kernel 2D -dilM -dilM -dilM -dilM -dilM -sub strucseg_2_${1}_brain -thr 0.5 -bin ${1}_grot
+${FSLDIR}/bin/fslmaths ${1}_csf -kernel 2D -dilM -mul strucseg_2_${1}_brain -add ${1}_grot -bin ${1}_csf_dil
@@ -60,23 +60,23 @@ ${FSLDIR}/bin/convert_xfm -inverse -omat ${1}_to_${2}.mat ${2}_to_${1}.mat
# transform t1 brain mask into t2 space, dilate slightly and apply to t2 to get t2 brain
${FSLDIR}/bin/flirt -in ${1}_brain_mask -out ${2}_brain_mask -ref ${2} -applyxfm -init ${1}_to_${2}.mat
-#${FSLDIR}/bin/avwmaths ${2}_brain_mask -dil ${2}_brain_mask
-${FSLDIR}/bin/avwmaths ${2}_brain_mask ${2}_brain_mask
-${FSLDIR}/bin/avwmaths ${2} -mas ${2}_brain_mask ${2}_brain
+#${FSLDIR}/bin/fslmaths ${2}_brain_mask -dilM ${2}_brain_mask
+${FSLDIR}/bin/fslmaths ${2}_brain_mask ${2}_brain_mask
+${FSLDIR}/bin/fslmaths ${2} -mas ${2}_brain_mask ${2}_brain
# run segmentation on t2; pve_0 should be CSF+lesions; transform into t1 space, remask with t1 brain mask
${FSLDIR}/bin/fast1 $t2segopts -c $nclasses -e -ov ${2}_brain
${FSLDIR}/bin/flirt -in $t2lesions -ref ${1} -out ${1}_lesion+CSF -applyxfm -init ${2}_to_${1}.mat
-${FSLDIR}/bin/avwmaths ${1}_lesion+CSF -mas ${1}_brain_mask ${1}_lesion+CSF
+${FSLDIR}/bin/fslmaths ${1}_lesion+CSF -mas ${1}_brain_mask ${1}_lesion+CSF
#### combine to remove CSF from CSF+lesions ############################################
# combine masks and use to mask out CSF from t2-derived lesion+CSF probability; output lesion volume
-${FSLDIR}/bin/avwmaths_32R ${1}_csf -mul -1 -add 1 -mul ${1}_lesion+CSF -thr 0.3 -bin ${1}_lesions+ucsf
-${FSLDIR}/bin/avwmaths_32R ${1}_csf_dil -mul -1 -add 1 -mul ${1}_lesion+CSF ${1}_lesions
-echo `${FSLDIR}/bin/avwstats ${1}_lesions -m -v | awk '{print "2 k " ${1} " " $3 " * 1000 / p" }' | dc -` > ${1}_lesions.txt
+${FSLDIR}/bin/fslmaths ${1}_csf -mul -1 -add 1 -mul ${1}_lesion+CSF -thr 0.3 -bin ${1}_lesions+ucsf -odt float
+${FSLDIR}/bin/fslmaths ${1}_csf_dil -mul -1 -add 1 -mul ${1}_lesion+CSF ${1}_lesions -odt float
+echo `${FSLDIR}/bin/fslstats ${1}_lesions -m -v | awk '{print "2 k " ${1} " " $3 " * 1000 / p" }' | dc -` > ${1}_lesions.txt
echo "${1} `cat ${1}_lesions.txt`"
# create display output
diff --git a/lesions_0.2 b/lesions_0.2
index 88aa1aa..3680778 100755
--- a/lesions_0.2
+++ b/lesions_0.2
@@ -57,14 +57,14 @@ ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -o
${FSLDIR}/bin/convert_xfm -inverse -omat std_2_${A}_brain.mat ${A}_brain_2_std.mat
# dilate (6mm) standard space ventricles+deep-grey, bring into t1 space and re-binarise to make "CENTRAL MASK"
-${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dil -dil -dil strucseg_2_${A}_brain
+${FSLDIR}/bin/fslmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dilM -dilM -dilM strucseg_2_${A}_brain
${FSLDIR}/bin/flirt -in strucseg_2_${A}_brain -ref ${A}_brain -out strucseg_2_${A}_brain -applyxfm -init std_2_${A}_brain.mat
-${FSLDIR}/bin/avwmaths strucseg_2_${A}_brain -bin strucseg_2_${A}_brain
+${FSLDIR}/bin/fslmaths strucseg_2_${A}_brain -bin strucseg_2_${A}_brain
# produce t1-derived CSF mask and also dilate in-plane: 5 voxels outside CENTRAL MASK, 1 voxel inside mask
-${FSLDIR}/bin/avwmaths ${A}_brain_pve_0 -thr 0.3 -bin ${A}_csf
-${FSLDIR}/bin/avwmaths ${A}_csf -dil2 -dil2 -dil2 -dil2 -dil2 -sub strucseg_2_${A}_brain -thr 0.5 -bin ${A}_grot
-${FSLDIR}/bin/avwmaths ${A}_csf -dil2 -mul strucseg_2_${A}_brain -add ${A}_grot -bin ${A}_csf_dil
+${FSLDIR}/bin/fslmaths ${A}_brain_pve_0 -thr 0.3 -bin ${A}_csf
+${FSLDIR}/bin/fslmaths ${A}_csf -kernel 2D -dilM -dilM -dilM -dilM -dilM -sub strucseg_2_${A}_brain -thr 0.5 -bin ${A}_grot
+${FSLDIR}/bin/fslmaths ${A}_csf -kernel 2D -dilM -mul strucseg_2_${A}_brain -add ${A}_grot -bin ${A}_csf_dil
@@ -76,21 +76,21 @@ ${FSLDIR}/bin/convert_xfm -inverse -omat ${A}_to_${B}.mat ${B}_to_${A}.mat
# transform t1 brain mask into t2 space and apply to t2 to get t2_brain
${FSLDIR}/bin/flirt -in ${A}_brain_mask -out ${B}_brain_mask -ref $B -applyxfm -init ${A}_to_${B}.mat
-${FSLDIR}/bin/avwmaths $B -mas ${B}_brain_mask ${B}_brain
+${FSLDIR}/bin/fslmaths $B -mas ${B}_brain_mask ${B}_brain
# run segmentation on t2; $t2lesions should be CSF+lesions; transform into t1 space, remask with t1 brain mask
${FSLDIR}/bin/fast1 $t2segopts -c $nclasses -e -ov ${B}_brain
${FSLDIR}/bin/flirt -in $t2lesions -ref $A -out ${A}_lesion+CSF -applyxfm -init ${B}_to_${A}.mat
-${FSLDIR}/bin/avwmaths ${A}_lesion+CSF -mas ${A}_brain_mask ${A}_lesion+CSF
+${FSLDIR}/bin/fslmaths ${A}_lesion+CSF -mas ${A}_brain_mask ${A}_lesion+CSF
#### combine to remove CSF from CSF+lesions ############################################
# combine masks and use to mask out CSF from t2-derived lesion+CSF probability; output lesion volume
-${FSLDIR}/bin/avwmaths_32R ${A}_csf_dil -mul -1 -add 1 -mul ${A}_lesion+CSF ${A}_lesions
-${FSLDIR}/bin/avwmaths_32R ${A}_lesions -thr $lesion_thr ${A}_lesions_thr
-echo `${FSLDIR}/bin/avwstats ${A}_lesions_thr -m -v | awk '{print "2 k " $1 " " $3 " * 1000 / p" }' | dc -` > ${A}_lesions.txt
+${FSLDIR}/bin/fslmaths ${A}_csf_dil -mul -1 -add 1 -mul ${A}_lesion+CSF ${A}_lesions -odt float
+${FSLDIR}/bin/fslmaths ${A}_lesions -thr $lesion_thr ${A}_lesions_thr -odt float
+echo `${FSLDIR}/bin/fslstats ${A}_lesions_thr -m -v | awk '{print "2 k " $1 " " $3 " * 1000 / p" }' | dc -` > ${A}_lesions.txt
echo "$A `cat ${A}_lesions.txt`"
# create display output
diff --git a/lesions_0.3 b/lesions_0.3
index 09abe2b..0469850 100644
--- a/lesions_0.3
+++ b/lesions_0.3
@@ -58,14 +58,14 @@ ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -o
${FSLDIR}/bin/convert_xfm -inverse -omat std_2_${A}_brain.mat ${A}_brain_2_std.mat
# dilate (6mm) standard space ventricles+deep-grey, bring into t1 space and re-binarise to make "CENTRAL MASK"
-${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dil -dil -dil strucseg_2_${A}_brain
+${FSLDIR}/bin/fslmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 3.5 -bin -dilM -dilM -dilM strucseg_2_${A}_brain
${FSLDIR}/bin/flirt -in strucseg_2_${A}_brain -ref ${A}_brain -out strucseg_2_${A}_brain -applyxfm -init std_2_${A}_brain.mat
-${FSLDIR}/bin/avwmaths strucseg_2_${A}_brain -bin strucseg_2_${A}_brain
+${FSLDIR}/bin/fslmaths strucseg_2_${A}_brain -bin strucseg_2_${A}_brain
# produce t1-derived CSF mask and also dilate in-plane: 5 voxels outside CENTRAL MASK, 1 voxel inside mask
-${FSLDIR}/bin/avwmaths ${A}_brain_pve_0 -thr 0.3 -bin ${A}_csf
-${FSLDIR}/bin/avwmaths ${A}_csf -dil2 -dil2 -dil2 -dil2 -dil2 -sub strucseg_2_${A}_brain -thr 0.5 -bin ${A}_grot
-${FSLDIR}/bin/avwmaths ${A}_csf -dil2 -mul strucseg_2_${A}_brain -add ${A}_grot -bin ${A}_csf_dil
+${FSLDIR}/bin/fslmaths ${A}_brain_pve_0 -thr 0.3 -bin ${A}_csf
+${FSLDIR}/bin/fslmaths ${A}_csf -kernel 2D -dilM -dilM -dilM -dilM -dilM -sub strucseg_2_${A}_brain -thr 0.5 -bin ${A}_grot
+${FSLDIR}/bin/fslmaths ${A}_csf -kernel 2D -dilM -mul strucseg_2_${A}_brain -add ${A}_grot -bin ${A}_csf_dil
@@ -77,21 +77,21 @@ ${FSLDIR}/bin/convert_xfm -inverse -omat ${A}_to_${B}.mat ${B}_to_${A}.mat
# transform t1 brain mask into t2 space and apply to t2 to get t2_brain
${FSLDIR}/bin/flirt -in ${A}_brain_mask -out ${B}_brain_mask -ref $B -applyxfm -init ${A}_to_${B}.mat
-${FSLDIR}/bin/avwmaths $B -mas ${B}_brain_mask ${B}_brain
+${FSLDIR}/bin/fslmaths $B -mas ${B}_brain_mask ${B}_brain
# run segmentation on t2; $t2lesions should be CSF+lesions; transform into t1 space, remask with t1 brain mask
${FSLDIR}/bin/fast1 $t2segopts -c $nclasses -e -ov ${B}_brain
${FSLDIR}/bin/flirt -in $t2lesions -ref $A -out ${A}_lesion+CSF -applyxfm -init ${B}_to_${A}.mat
-${FSLDIR}/bin/avwmaths ${A}_lesion+CSF -mas ${A}_brain_mask ${A}_lesion+CSF
+${FSLDIR}/bin/fslmaths ${A}_lesion+CSF -mas ${A}_brain_mask ${A}_lesion+CSF
#### combine to remove CSF from CSF+lesions ############################################
# combine masks and use to mask out CSF from t2-derived lesion+CSF probability; output lesion volume
-${FSLDIR}/bin/avwmaths_32R ${A}_csf_dil -mul -1 -add 1 -mul ${A}_lesion+CSF ${A}_lesions
-${FSLDIR}/bin/avwmaths_32R ${A}_lesions -thr $lesion_thr ${A}_lesions_thr
-echo `${FSLDIR}/bin/avwstats ${A}_lesions_thr -m -v | awk '{print "2 k " $1 " " $3 " * 1000 / p" }' | dc -` > ${A}_lesions.txt
+${FSLDIR}/bin/fslmaths ${A}_csf_dil -mul -1 -add 1 -mul ${A}_lesion+CSF ${A}_lesions -odt float
+${FSLDIR}/bin/fslmaths ${A}_lesions -thr $lesion_thr ${A}_lesions_thr -odt float
+echo `${FSLDIR}/bin/fslstats ${A}_lesions_thr -m -v | awk '{print "2 k " $1 " " $3 " * 1000 / p" }' | dc -` > ${A}_lesions.txt
echo "$A `cat ${A}_lesions.txt`"
# create display output
diff --git a/siena b/siena
index 2bd80c6..08ed59d 100755
--- a/siena
+++ b/siena
@@ -53,8 +53,8 @@ sdo="-m"
dostd=0
stdmask=0
stdroi=""
-origin3=37 # `avwval ${FSLDIR}/etc/standard/avg152T1 origin3`
-pixdim3=2 # `avwval ${FSLDIR}/etc/standard/avg152T1 pixdim3`
+origin3=37 # `fslval ${FSLDIR}/etc/standard/avg152T1 origin3`
+pixdim3=2 # `fslval ${FSLDIR}/etc/standard/avg152T1 pixdim3`
while [ _$1 != _ ] ; do
@@ -101,8 +101,8 @@ sdo="${sdo}${is_t2}"
echo "---------- extract brain --------------------------------------------" >> ${A}_to_${B}.siena
${FSLDIR}/bin/bet $A ${A}_brain -s -m $betopts >> ${A}_to_${B}.siena
${FSLDIR}/bin/bet $B ${B}_brain -s -m $betopts >> ${A}_to_${B}.siena
-${FSLDIR}/bin/avwmaths++ ${A}_brain -sub `$FSLDIR/bin/avwstats++ ${A}_brain -p 0` -mas ${A}_brain_mask ${A}_brain -odt float
-${FSLDIR}/bin/avwmaths++ ${B}_brain -sub `$FSLDIR/bin/avwstats++ ${B}_brain -p 0` -mas ${B}_brain_mask ${B}_brain -odt float
+${FSLDIR}/bin/fslmaths ${A}_brain -sub `$FSLDIR/bin/fslstats ${A}_brain -p 0` -mas ${A}_brain_mask ${A}_brain -odt float
+${FSLDIR}/bin/fslmaths ${B}_brain -sub `$FSLDIR/bin/fslstats ${B}_brain -p 0` -mas ${B}_brain_mask ${B}_brain -odt float
echo "" >> ${A}_to_${B}.siena
echo "---------- register brains and skulls -------------------------------" >> ${A}_to_${B}.siena
@@ -111,18 +111,18 @@ ${FSLDIR}/bin/siena_flirt $A $B >> ${A}_to_${B}.siena 2>&1
echo "" >> ${A}_to_${B}.siena
echo "---------- produce valid masks --------------------------------------" >> ${A}_to_${B}.siena
-XDIM=`${FSLDIR}/bin/avwval $A dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
-YDIM=`${FSLDIR}/bin/avwval $A dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
-ZDIM=`${FSLDIR}/bin/avwval $A dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
-${FSLDIR}/bin/avwmaths ${A}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${A}_valid_mask
-XDIM=`${FSLDIR}/bin/avwval $B dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
-YDIM=`${FSLDIR}/bin/avwval $B dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
-ZDIM=`${FSLDIR}/bin/avwval $B dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
-${FSLDIR}/bin/avwmaths ${B}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${B}_valid_mask
+XDIM=`${FSLDIR}/bin/fslval $A dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
+YDIM=`${FSLDIR}/bin/fslval $A dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
+ZDIM=`${FSLDIR}/bin/fslval $A dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
+${FSLDIR}/bin/fslmaths ${A}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${A}_valid_mask
+XDIM=`${FSLDIR}/bin/fslval $B dim1` ; XDIM=`echo "$XDIM 2 - p" | dc -`
+YDIM=`${FSLDIR}/bin/fslval $B dim2` ; YDIM=`echo "$YDIM 2 - p" | dc -`
+ZDIM=`${FSLDIR}/bin/fslval $B dim3` ; ZDIM=`echo "$ZDIM 2 - p" | dc -`
+${FSLDIR}/bin/fslmaths ${B}_brain_mask -mul 0 -add 1 -roi 1 $XDIM 1 $YDIM 1 $ZDIM 0 1 ${B}_valid_mask
${FSLDIR}/bin/flirt -in ${B}_valid_mask -ref $A -out ${B}_valid_mask_to_${A} -applyxfm -init ${B}_to_${A}.mat -paddingsize 0
${FSLDIR}/bin/flirt -in ${A}_valid_mask -ref $B -out ${A}_valid_mask_to_${B} -applyxfm -init ${A}_to_${B}.mat -paddingsize 0
-${FSLDIR}/bin/avwmaths ${A}_valid_mask -mul ${B}_valid_mask_to_${A} ${A}_valid_mask_with_$B
-${FSLDIR}/bin/avwmaths ${B}_valid_mask -mul ${A}_valid_mask_to_${B} ${B}_valid_mask_with_$A
+${FSLDIR}/bin/fslmaths ${A}_valid_mask -mul ${B}_valid_mask_to_${A} ${A}_valid_mask_with_$B
+${FSLDIR}/bin/fslmaths ${B}_valid_mask -mul ${A}_valid_mask_to_${B} ${B}_valid_mask_with_$A
if [ $dostd = 1 ] ; then
echo "" >> ${A}_to_${B}.siena
@@ -143,20 +143,20 @@ if [ $dostd = 1 ] ; then
if [ $stdmask = 1 ] ; then
${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_brain_mask_dil2 -ref $A -out ${A}_stdmask -applyxfm -init ${A}_to_std_inv.mat
${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_brain_mask_dil2 -ref $B -out ${B}_stdmask -applyxfm -init ${B}_to_std_inv.mat
- ${FSLDIR}/bin/avwmaths ${A}_stdmask -thr 0.5 -bin ${A}_stdmask
- ${FSLDIR}/bin/avwmaths ${B}_stdmask -thr 0.5 -bin ${B}_stdmask
- ${FSLDIR}/bin/avwmaths ${A}_brain_mask -mas ${A}_stdmask ${A}_brain_mask
- ${FSLDIR}/bin/avwmaths ${B}_brain_mask -mas ${B}_stdmask ${B}_brain_mask
+ ${FSLDIR}/bin/fslmaths ${A}_stdmask -thr 0.5 -bin ${A}_stdmask
+ ${FSLDIR}/bin/fslmaths ${B}_stdmask -thr 0.5 -bin ${B}_stdmask
+ ${FSLDIR}/bin/fslmaths ${A}_brain_mask -mas ${A}_stdmask ${A}_brain_mask
+ ${FSLDIR}/bin/fslmaths ${B}_brain_mask -mas ${B}_stdmask ${B}_brain_mask
fi
if [ "$stdroi" != "" ] ; then
- ${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_brain_mask -mul 0 -add 1 $stdroi ${A}_and_${B}_stdmask
+ ${FSLDIR}/bin/fslmaths ${FSLDIR}/etc/standard/avg152T1_brain_mask -mul 0 -add 1 $stdroi ${A}_and_${B}_stdmask
${FSLDIR}/bin/flirt -in ${A}_and_${B}_stdmask -ref $A -out ${A}_stdmask -applyxfm -init ${A}_to_std_inv.mat
${FSLDIR}/bin/flirt -in ${A}_and_${B}_stdmask -ref $B -out ${B}_stdmask -applyxfm -init ${B}_to_std_inv.mat
- ${FSLDIR}/bin/avwmaths ${A}_stdmask -thr 0.5 -bin ${A}_stdmask
- ${FSLDIR}/bin/avwmaths ${B}_stdmask -thr 0.5 -bin ${B}_stdmask
- ${FSLDIR}/bin/avwmaths ${A}_valid_mask_with_$B -mul ${A}_stdmask ${A}_valid_mask_with_$B
- ${FSLDIR}/bin/avwmaths ${B}_valid_mask_with_$A -mul ${B}_stdmask ${B}_valid_mask_with_$A
+ ${FSLDIR}/bin/fslmaths ${A}_stdmask -thr 0.5 -bin ${A}_stdmask
+ ${FSLDIR}/bin/fslmaths ${B}_stdmask -thr 0.5 -bin ${B}_stdmask
+ ${FSLDIR}/bin/fslmaths ${A}_valid_mask_with_$B -mul ${A}_stdmask ${A}_valid_mask_with_$B
+ ${FSLDIR}/bin/fslmaths ${B}_valid_mask_with_$A -mul ${B}_stdmask ${B}_valid_mask_with_$A
fi
fi
@@ -179,7 +179,7 @@ echo "" >> ${A}_to_${B}.siena
pbvc_average=`echo "10 k $pbvc_forward $pbvc_backward - 2.0 / p" | dc -`
echo "finalPBVC $pbvc_average %" >> ${A}_to_${B}.siena
-${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow -mul -1 ${A}_to_${B}_flowneg
+${FSLDIR}/bin/fslmaths ${A}_to_${B}_flow -mul -1 ${A}_to_${B}_flowneg
${FSLDIR}/bin/overlay 0 0 ${A}_halfwayto_${B} -a ${A}_to_${B}_flow 0.01 1 ${A}_to_${B}_flowneg 0.01 1 ${A}_halfwayto_${B}_render
if [ $debug = 0 ] ; then
diff --git a/siena_cal b/siena_cal
index 2b62cf9..2e10a62 100755
--- a/siena_cal
+++ b/siena_cal
@@ -27,13 +27,13 @@ m=$3
M=`echo "5 k 1.0 $m / p" | dc -`
shift 3
-o1=`${FSLDIR}/bin/avwval ${input} dim1`
-o2=`${FSLDIR}/bin/avwval ${input} dim2`
-o3=`${FSLDIR}/bin/avwval ${input} dim3`
+o1=`${FSLDIR}/bin/fslval ${input} dim1`
+o2=`${FSLDIR}/bin/fslval ${input} dim2`
+o3=`${FSLDIR}/bin/fslval ${input} dim3`
-v1=`${FSLDIR}/bin/avwval ${input} pixdim1 | sed "s/-//g"`
-v2=`${FSLDIR}/bin/avwval ${input} pixdim2 | sed "s/-//g"`
-v3=`${FSLDIR}/bin/avwval ${input} pixdim3 | sed "s/-//g"`
+v1=`${FSLDIR}/bin/fslval ${input} pixdim1 | sed "s/-//g"`
+v2=`${FSLDIR}/bin/fslval ${input} pixdim2 | sed "s/-//g"`
+v3=`${FSLDIR}/bin/fslval ${input} pixdim3 | sed "s/-//g"`
t1=`echo "5 k $m 1.0 - $o1 * $v1 * _0.5 * p" | dc -`
t2=`echo "5 k $m 1.0 - $o2 * $v2 * _0.5 * p" | dc -`
diff --git a/siena_flow2std b/siena_flow2std
index abc9a15..134ed1b 100755
--- a/siena_flow2std
+++ b/siena_flow2std
@@ -48,14 +48,14 @@ ${FSLDIR}/bin/convert_xfm -omat ${A}_halfwayto_${B}_inv.mat -inverse ${A}_halfwa
${FSLDIR}/bin/convert_xfm -omat ${A}_halfwayto_${B}_to_std.mat -concat ${A}_to_std.mat ${A}_halfwayto_${B}_inv.mat
# dilate flow image, -> standard space -> mask with ss edge image -> blur -> remask
-${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil ${A}_to_${B}_flow_dil
-${FSLDIR}/bin/avwmaths ${B}_to_${A}_flow -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil -dil ${A}_to_${B}_flow_dilback
-${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_dil -sub ${A}_to_${B}_flow_dilback -div 2 ${A}_to_${B}_flow_dil
+${FSLDIR}/bin/fslmaths ${A}_to_${B}_flow -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM ${A}_to_${B}_flow_dil
+${FSLDIR}/bin/fslmaths ${B}_to_${A}_flow -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM -dilM ${A}_to_${B}_flow_dilback
+${FSLDIR}/bin/fslmaths ${A}_to_${B}_flow_dil -sub ${A}_to_${B}_flow_dilback -div 2 ${A}_to_${B}_flow_dil
/bin/rm ${A}_to_${B}_flow_dilback*
${FSLDIR}/bin/flirt -in ${A}_to_${B}_flow_dil -ref ${FSLDIR}/etc/standard/avg152T1_brain -out ${A}_to_${B}_flow_to_std -applyxfm -init ${A}_halfwayto_${B}_to_std.mat
-${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_to_std -mas ${FSLDIR}/etc/standard/avg152T1_edges ${A}_to_${B}_flow_to_std
+${FSLDIR}/bin/fslmaths ${A}_to_${B}_flow_to_std -mas ${FSLDIR}/etc/standard/avg152T1_edges ${A}_to_${B}_flow_to_std
${FSLDIR}/bin/ip ${A}_to_${B}_flow_to_std ${A}_to_${B}_flow_to_std 0 -s 10
-${FSLDIR}/bin/avwmaths ${A}_to_${B}_flow_to_std -mas ${FSLDIR}/etc/standard/avg152T1_edges ${A}_to_${B}_flow_to_std
+${FSLDIR}/bin/fslmaths ${A}_to_${B}_flow_to_std -mas ${FSLDIR}/etc/standard/avg152T1_edges ${A}_to_${B}_flow_to_std
# cleanup
if [ $debug = 0 ] ; then
diff --git a/sienax b/sienax
index 07b91df..67a0062 100755
--- a/sienax
+++ b/sienax
@@ -50,8 +50,8 @@ betopts=""
segopts=""
nseg=3
stdroi=""
-origin3=37 # `avwval ${FSLDIR}/etc/standard/avg152T1 origin3`
-pixdim3=2 # `avwval ${FSLDIR}/etc/standard/avg152T1 pixdim3`
+origin3=37 # `fslval ${FSLDIR}/etc/standard/avg152T1 origin3`
+pixdim3=2 # `fslval ${FSLDIR}/etc/standard/avg152T1 pixdim3`
imtype=-t1
while [ _$1 != _ ] ; do
@@ -102,7 +102,7 @@ fi
echo "---------- extract brain --------------------------------------------" >> ${I}.sienax
${FSLDIR}/bin/bet $I ${I}_brain -s -m $betopts >> ${I}.sienax
-${FSLDIR}/bin/avwmaths++ ${I}_brain -sub `$FSLDIR/bin/avwstats++ ${I}_brain -p 0` -mas ${I}_brain_mask ${I}_brain -odt float
+${FSLDIR}/bin/fslmaths ${I}_brain -sub `$FSLDIR/bin/fslstats ${I}_brain -p 0` -mas ${I}_brain_mask ${I}_brain -odt float
echo "" >> ${I}.sienax
echo "---------- register to stdairach space using brain and skull --------" >> ${I}.sienax
@@ -120,19 +120,19 @@ echo "---------- mask with std mask ---------------------------------------" >
${FSLDIR}/bin/convert_xfm -inverse -omat ${I}2std_inv.mat ${I}2std.mat
MASK=${FSLDIR}/etc/standard/avg152T1_brain_mask_dil
if [ "$stdroi" != "" ] ; then
- ${FSLDIR}/bin/avwmaths $MASK $stdroi ${I}_stdmaskroi
+ ${FSLDIR}/bin/fslmaths $MASK $stdroi ${I}_stdmaskroi
MASK=${I}_stdmaskroi
fi
${FSLDIR}/bin/flirt -in $MASK -ref ${I}_brain -out ${I}_stdmask -applyxfm -init ${I}2std_inv.mat
-${FSLDIR}/bin/avwmaths ${I}_stdmask -thr 0.5 -bin ${I}_stdmask
-${FSLDIR}/bin/avwmaths ${I}_brain -mask ${I}_stdmask ${I}_stdmaskbrain
+${FSLDIR}/bin/fslmaths ${I}_stdmask -thr 0.5 -bin ${I}_stdmask
+${FSLDIR}/bin/fslmaths ${I}_brain -mas ${I}_stdmask ${I}_stdmaskbrain
if [ $regional = 1 ] ; then
${FSLDIR}/bin/flirt -in ${FSLDIR}/etc/standard/avg152T1_strucseg_periph -ref ${I}_brain -out ${I}_stdmask_segperiph -applyxfm -init ${I}2std_inv.mat
- ${FSLDIR}/bin/avwmaths ${I}_stdmask_segperiph -thr 0.5 -bin ${I}_stdmask_segperiph
- ${FSLDIR}/bin/avwmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 4.5 -bin ${I}_tmpmask
+ ${FSLDIR}/bin/fslmaths ${I}_stdmask_segperiph -thr 0.5 -bin ${I}_stdmask_segperiph
+ ${FSLDIR}/bin/fslmaths ${FSLDIR}/etc/standard/avg152T1_strucseg -thr 4.5 -bin ${I}_tmpmask
${FSLDIR}/bin/flirt -in ${I}_tmpmask -ref ${I}_brain -out ${I}_stdmask_segvent -applyxfm -init ${I}2std_inv.mat
- ${FSLDIR}/bin/avwmaths ${I}_stdmask_segvent -thr 0.5 -bin ${I}_stdmask_segvent
+ ${FSLDIR}/bin/fslmaths ${I}_stdmask_segvent -thr 0.5 -bin ${I}_stdmask_segvent
/bin/rm ${I}_tmpmask*
fi
@@ -142,21 +142,21 @@ if [ $nseg = 2 ] ; then
${FSLDIR}/bin/fast1 -c 2 $imtype -e -ov $segopts ${I}_stdmaskbrain >> ${I}.sienax 2>&1
echo "" >> ${I}.sienax
echo "---------- convert brain volume into normalised volume --------------" >> ${I}.sienax
- S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_pve_1 -m -v`
+ S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1 -m -v`
xa=`echo $S | awk '{print $1}'`
xb=`echo $S | awk '{print $3}'`
ubrain=`echo "2 k $xa $xb * 1 / p" | dc -`
nbrain=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
else
if [ _$lm != _ ] ; then
- ${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_stdmaskbrain ${I}_stdmaskbrain
+ ${FSLDIR}/bin/fslmaths $lm -bin -mul -1 -add 1 -mul ${I}_stdmaskbrain ${I}_stdmaskbrain -odt float
fi
${FSLDIR}/bin/fast1 $imtype -e -ov $segopts ${I}_stdmaskbrain >> ${I}.sienax 2>&1
if [ _$lm != _ ] ; then
- ${FSLDIR}/bin/avwmaths_32R $lm -bin -max ${I}_stdmaskbrain_pve_2 ${I}_stdmaskbrain_pve_2
- ${FSLDIR}/bin/avwmaths_32SI $lm -bin -mul 3 -max ${I}_stdmaskbrain_seg ${I}_stdmaskbrain_seg
+ ${FSLDIR}/bin/fslmaths $lm -bin -max ${I}_stdmaskbrain_pve_2 ${I}_stdmaskbrain_pve_2 -odt float
+ ${FSLDIR}/bin/fslmaths $lm -bin -mul 3 -max ${I}_stdmaskbrain_seg ${I}_stdmaskbrain_seg -odt int
fi
echo "" >> ${I}.sienax
@@ -164,29 +164,29 @@ else
echo "" >> ${I}.sienax
echo "tissue volume unnormalised-volume" >> ${I}.sienax
if [ $regional = 1 ] ; then
- ${FSLDIR}/bin/avwmaths_32R ${I}_stdmaskbrain_pve_1 -mas ${I}_stdmask_segperiph ${I}_stdmaskbrain_pve_1_segperiph
- S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_pve_1_segperiph -m -v`
+ ${FSLDIR}/bin/fslmaths ${I}_stdmaskbrain_pve_1 -mas ${I}_stdmask_segperiph ${I}_stdmaskbrain_pve_1_segperiph -odt float
+ S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1_segperiph -m -v`
xa=`echo $S | awk '{print $1}'`
xb=`echo $S | awk '{print $3}'`
uxg=`echo "2 k $xa $xb * 1 / p" | dc -`
xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
echo "pgrey $xg $uxg (peripheral grey)" >> ${I}.sienax
- ${FSLDIR}/bin/avwmaths_32R ${I}_stdmaskbrain_pve_0 -mas ${I}_stdmask_segvent ${I}_stdmaskbrain_pve_0_segvent
- S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_pve_0_segvent -m -v`
+ ${FSLDIR}/bin/fslmaths ${I}_stdmaskbrain_pve_0 -mas ${I}_stdmask_segvent ${I}_stdmaskbrain_pve_0_segvent -odt float
+ S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_0_segvent -m -v`
xa=`echo $S | awk '{print $1}'`
xb=`echo $S | awk '{print $3}'`
uxg=`echo "2 k $xa $xb * 1 / p" | dc -`
xg=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
echo "vcsf $xg $uxg (ventricular CSF)" >> ${I}.sienax
fi
- S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_pve_1 -m -v`
+ S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_1 -m -v`
xa=`echo $S | awk '{print $1}'`
xb=`echo $S | awk '{print $3}'`
ugrey=`echo "2 k $xa $xb * 1 / p" | dc -`
ngrey=`echo "2 k $xa $xb * $vscale * 1 / p" | dc -`
echo "GREY $ngrey $ugrey" >> ${I}.sienax
- S=`${FSLDIR}/bin/avwstats ${I}_stdmaskbrain_pve_2 -m -v`
+ S=`${FSLDIR}/bin/fslstats ${I}_stdmaskbrain_pve_2 -m -v`
xa=`echo $S | awk '{print $1}'`
xb=`echo $S | awk '{print $3}'`
uwhite=`echo "2 k $xa $xb * 1 / p" | dc -`
--
GitLab