Made all siena scripts call fast1 rather than fast (which is about to become fast2)

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
 

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
 

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
 

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);

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