From f8d1ee706d78bdb7d5755ad9996949c5bc657891 Mon Sep 17 00:00:00 2001
From: Mark Jenkinson <mark@fmrib.ox.ac.uk>
Date: Tue, 22 Aug 2006 17:54:43 +0000
Subject: [PATCH] Made all siena scripts call fast1 rather than fast (which is
about to become fast2)
---
lesions_0.1 | 4 ++--
lesions_0.2 | 4 ++--
lesions_0.3 | 4 ++--
siena_diff.cc | 2 +-
sienax | 4 ++--
5 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/lesions_0.1 b/lesions_0.1
index fd0e70b..9fcf470 100755
--- a/lesions_0.1
+++ b/lesions_0.1
@@ -34,7 +34,7 @@ fi
# brain-extract t1 and run segmentation; pve_0 should be CSF only
${FSLDIR}/bin/bet $1 $1_brain -m
-${FSLDIR}/bin/fast -e -ov $1_brain
+${FSLDIR}/bin/fast1 -e -ov $1_brain
# register t1 to standard space and invert transform
${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in $1_brain -omat $1_brain_2_std.mat
@@ -65,7 +65,7 @@ ${FSLDIR}/bin/avwmaths $2_brain_mask $2_brain_mask
${FSLDIR}/bin/avwmaths $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/fast $t2segopts -c $nclasses -e -ov $2_brain
+${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
diff --git a/lesions_0.2 b/lesions_0.2
index a2c204c..c7e4de8 100755
--- a/lesions_0.2
+++ b/lesions_0.2
@@ -50,7 +50,7 @@ done
# brain-extract t1 and run segmentation; pve_0 should be CSF only
${FSLDIR}/bin/bet $A ${A}_brain -m
-${FSLDIR}/bin/fast -e -ov ${A}_brain
+${FSLDIR}/bin/fast1 -e -ov ${A}_brain
# register t1 to standard space and invert transform
${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_brain_2_std.mat
@@ -79,7 +79,7 @@ ${FSLDIR}/bin/flirt -in ${A}_brain_mask -out ${B}_brain_mask -ref $B -applyxfm -
${FSLDIR}/bin/avwmaths $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/fast $t2segopts -c $nclasses -e -ov ${B}_brain
+${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
diff --git a/lesions_0.3 b/lesions_0.3
index 6273f26..425a6d2 100644
--- a/lesions_0.3
+++ b/lesions_0.3
@@ -51,7 +51,7 @@ echo "working" > ${A}_lesions.txt
# brain-extract t1 and run segmentation; pve_0 should be CSF only
${FSLDIR}/bin/bet $A ${A}_brain -m
-${FSLDIR}/bin/fast -e -ov ${A}_brain
+${FSLDIR}/bin/fast1 -e -ov ${A}_brain
# register t1 to standard space and invert transform
${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_brain_2_std.mat
@@ -80,7 +80,7 @@ ${FSLDIR}/bin/flirt -in ${A}_brain_mask -out ${B}_brain_mask -ref $B -applyxfm -
${FSLDIR}/bin/avwmaths $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/fast $t2segopts -c $nclasses -e -ov ${B}_brain
+${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
diff --git a/siena_diff.cc b/siena_diff.cc
index 3ff2bf8..f57e388 100644
--- a/siena_diff.cc
+++ b/siena_diff.cc
@@ -227,7 +227,7 @@ if(1) // always done unless the above uncommented and used instead of this test
cout << "saving image 1 to disk prior to segmentation" << endl;
save_volume(in1,argv1+"_halfwayto_"+argv2+"_brain");
in1.destroy();
- sprintf(thestring,"%s/bin/fast %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
+ sprintf(thestring,"%s/bin/fast1 %s %s %s_halfwayto_%s_brain > %s_halfwayto_%s_brain.vol 2>&1",
fsldir,segtype,segoptions,argv[1],argv[2],argv[1],argv[2]);
cout << thestring << endl;
system(thestring);
diff --git a/sienax b/sienax
index f5a05f4..c9116b7 100755
--- a/sienax
+++ b/sienax
@@ -138,7 +138,7 @@ fi
echo "" >> ${I}.sienax
echo "---------- segment tissue into types --------------------------------" >> ${I}.sienax
if [ $nseg = 2 ] ; then
- ${FSLDIR}/bin/fast -c 2 $imtype -e -ov $segopts ${I}_stdmaskbrain >> ${I}.sienax 2>&1
+ ${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`
@@ -150,7 +150,7 @@ else
${FSLDIR}/bin/avwmaths_32R $lm -bin -mul -1 -add 1 -mul ${I}_stdmaskbrain ${I}_stdmaskbrain
fi
- ${FSLDIR}/bin/fast $imtype -e -ov $segopts ${I}_stdmaskbrain >> ${I}.sienax 2>&1
+ ${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
--
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