Changed convert_xfm usage to non-medx style

lesions_0.1

@@ -38,7 +38,7 @@ ${FSLDIR}/bin/fast -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 $1_brain_2_tal.mat
-${FSLDIR}/bin/convert_xfm -inverse -matonly -omat tal_2_$1_brain.mat $1_brain_2_tal.mat
+${FSLDIR}/bin/convert_xfm -inverse -omat tal_2_$1_brain.mat $1_brain_2_tal.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
@@ -56,7 +56,7 @@ ${FSLDIR}/bin/avwmaths $1_csf -dil2 -mul strucseg_2_$1_brain -add $1_grot -bin $
 
 # register t2 to t1 and invert transform
 ${FSLDIR}/bin/flirt -in $2 -ref $1 -omat $2_to_$1.mat
-${FSLDIR}/bin/convert_xfm -inverse -matonly -omat $1_to_$2.mat $2_to_$1.mat
+${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

lesions_0.2

@@ -54,7 +54,7 @@ ${FSLDIR}/bin/fast -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 ${A}_brain_2_tal.mat
-${FSLDIR}/bin/convert_xfm -inverse -matonly -omat tal_2_${A}_brain.mat ${A}_brain_2_tal.mat
+${FSLDIR}/bin/convert_xfm -inverse -omat tal_2_${A}_brain.mat ${A}_brain_2_tal.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
@@ -72,7 +72,7 @@ ${FSLDIR}/bin/avwmaths ${A}_csf -dil2 -mul strucseg_2_${A}_brain -add ${A}_grot
 
 # register t2 to t1 and invert transform
 ${FSLDIR}/bin/flirt -in $B -ref $A -omat ${B}_to_${A}.mat
-${FSLDIR}/bin/convert_xfm -inverse -matonly -omat ${A}_to_${B}.mat ${B}_to_${A}.mat
+${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

lesions_0.3

@@ -55,7 +55,7 @@ ${FSLDIR}/bin/fast -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 ${A}_brain_2_tal.mat
-${FSLDIR}/bin/convert_xfm -inverse -matonly -omat tal_2_${A}_brain.mat ${A}_brain_2_tal.mat
+${FSLDIR}/bin/convert_xfm -inverse -omat tal_2_${A}_brain.mat ${A}_brain_2_tal.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
@@ -73,7 +73,7 @@ ${FSLDIR}/bin/avwmaths ${A}_csf -dil2 -mul strucseg_2_${A}_brain -add ${A}_grot
 
 # register t2 to t1 and invert transform
 ${FSLDIR}/bin/flirt -in $B -ref $A -omat ${B}_to_${A}.mat
-${FSLDIR}/bin/convert_xfm -inverse -matonly -omat ${A}_to_${B}.mat ${B}_to_${A}.mat
+${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

siena

@@ -127,10 +127,10 @@ if [ $dotal = 1 ] ; then
     echo "----------  standard space masking  ----------------------------------" >> ${A}_to_${B}.siena
     ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${A}_brain -omat ${A}_to_tal.mat >> ${A}_to_${B}.siena
     ${FSLDIR}/bin/flirt -ref ${FSLDIR}/etc/standard/avg152T1_brain -in ${B}_brain -omat ${B}_to_tal.mat >> ${A}_to_${B}.siena
-    ${FSLDIR}/bin/convert_xfm -matonly -inverse -omat ${A}_to_tal_inv.mat ${A}_to_tal.mat
-    ${FSLDIR}/bin/convert_xfm -matonly -inverse -omat ${B}_to_tal_inv.mat ${B}_to_tal.mat
+    ${FSLDIR}/bin/convert_xfm -inverse -omat ${A}_to_tal_inv.mat ${A}_to_tal.mat
+    ${FSLDIR}/bin/convert_xfm -inverse -omat ${B}_to_tal_inv.mat ${B}_to_tal.mat
 
-    ${FSLDIR}/bin/convert_xfm -matonly -concat ${B}_to_tal_inv.mat -omat ${A}_to_${B}_tmp.mat ${A}_to_tal.mat
+    ${FSLDIR}/bin/convert_xfm -concat ${B}_to_tal_inv.mat -omat ${A}_to_${B}_tmp.mat ${A}_to_tal.mat
     RMSDIFF=`${FSLDIR}/bin/rmsdiff ${A}_to_${B}.mat ${A}_to_${B}_tmp.mat $A | sed 's/\..*$/ /g'` # last part makes it integer
     echo "rmsdiff for standard space transform is $RMSDIFF mm" >> ${A}_to_${B}.siena
     if [ $RMSDIFF -ge 10 ] ; then

siena_flirt

@@ -32,11 +32,11 @@ ${FSLDIR}/bin/pairreg ${A2}_brain ${A1}_brain ${A2}_brain_skull ${A1}_brain_skul
 # replace both transforms with "average" (reduces error level AND makes system symmetric)
 F=${A1}_to_${A2}.mat
 B=${A2}_to_${A1}.mat
-${FSLDIR}/bin/convert_xfm -matonly -concat $B -omat tmp_${F}_then_${B} $F
+${FSLDIR}/bin/convert_xfm -concat $B -omat tmp_${F}_then_${B} $F
 ${FSLDIR}/bin/avscale tmp_${F}_then_${B} ${A1} > tmp_${F}_then_${B}.avscale
 ${FSLDIR}/bin/extracttxt Backward tmp_${F}_then_${B}.avscale 4 1 > tmp_${F}_then_${B}_halfback
-${FSLDIR}/bin/convert_xfm -matonly -concat tmp_${F}_then_${B}_halfback -omat $F $F
-${FSLDIR}/bin/convert_xfm -inverse -matonly -omat $B $F
+${FSLDIR}/bin/convert_xfm -concat tmp_${F}_then_${B}_halfback -omat $F $F
+${FSLDIR}/bin/convert_xfm -inverse -omat $B $F
 /bin/rm tmp_${F}_then_${B} tmp_${F}_then_${B}.avscale tmp_${F}_then_${B}_halfback
 
 # replace the .mat matrix that takes 2->1 with one that takes 2->halfway and one that takes 1->halfway

sienax

@@ -116,7 +116,7 @@ echo "VSCALING $vscale" >> ${I}.sienax
 
 echo ""                                                                        >> ${I}.sienax
 echo "----------  mask with talairach mask  ---------------------------------" >> ${I}.sienax
-${FSLDIR}/bin/convert_xfm -matonly -inverse -omat ${I}2tal_inv.mat ${I}2tal.mat
+${FSLDIR}/bin/convert_xfm -inverse -omat ${I}2tal_inv.mat ${I}2tal.mat
 MASK=${FSLDIR}/etc/standard/avg152T1_brain_mask_dil
 if [ "$talroi" != "" ] ; then
     ${FSLDIR}/bin/avwmaths $MASK $talroi ${I}_talmaskroi