Use local version of helper progs where installed in same directory. …

…Helps with bundling and running multiple version
physimals · Apr 3, 2017 · 87ee95e · 87ee95e
1 parent 42217ec
commit 87ee95e
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Showing 5 changed files with 153 additions and 136 deletions.
diff --git a/asl_calib.in b/asl_calib.in
@@ -8,6 +8,11 @@
 #
 # SHCOPYRIGHT
 
+# Make script use local copies of helper scripts/programs in the same
+# directory, if present. This allows for multiple versions of the scripts
+# to be used, possibly with bundled dependencies
+PATH=`dirname $0`:${FSLDIR}/bin:${PATH}
+
 #deal with options
 
 Usage() {
@@ -182,15 +187,7 @@ done
 echo "ASL_CALIB"
 
 # set the version of fabber to use
-fabber=fabber
-#fabber=$FSLDIR/bin/fabber
-if [ ! -z $devel ]; then
-    fabber=~chappell/cproject/fabber/fabber
-    if [ $FSLMACHTYPE = linux_64-gcc4.1 ]; then #assumption that the architecuture tell me that we are on a jalapeno node
-	echo "We are on jalapeno"
-	fabber=~chappell/cproject/jalapeno/fabber/fabber
-    fi
-fi
+fabber=fabber_asl
 
 #check for mandatory inputs
 if [ -z $calib ]; then
@@ -227,7 +224,7 @@ if [ ! -d $outdir ]; then
 fi
 
 # make a temporary directory to work in - delete at end
-tmpbase=`$FSLDIR/bin/tmpnam`
+tmpbase=`tmpnam`
 temp_calib=${tmpbase}_asl_calib
 mkdir $temp_calib
 
@@ -311,7 +308,7 @@ echo "Tissue reference : $tissref" >> $log
 
 # command line override of default T1 and T2
 if [ ! -z $T1rin ]; then
-    if [ `${FSLDIR}/bin/imtest $T1rin` ]; then
+    if [ `imtest $T1rin` ]; then
 	# we have been supplied with a T1 image - record that here to process later
 	T1rim=$T1rin
 	echo "Loading T1 image for reference region: T1im" >> $log
@@ -321,7 +318,7 @@ if [ ! -z $T1rin ]; then
     fi
 fi
 if [ ! -z $T2rin ]; then
-    if [ `${FSLDIR}/bin/imtest $T2rin` ]; then
+    if [ `imtest $T2rin` ]; then
 	# we have been supplied with a T2 image - record that here to process later
 	T2rim=$T2rin
 	echo "Loading T2 image for reference region: T2im" >> $log
@@ -395,7 +392,7 @@ fi
 if [ $tissref = "none" ]; then
 # whole brain M0
 # in this case use the brain mask
-    ${FSLDIR}/bin/imcp $bmask $temp_calib/refmask
+    imcp $bmask $temp_calib/refmask
     maskflag=1
     echo "Brain mask is being used as the reference tissue (beware!)" >> $log
 fi
@@ -502,8 +499,8 @@ if [ -z $maskflag ]; then
 
     if [ ! -z $fasthasrun ] && [ -z $senson ]; then
         # also extract the bias field and convert to sensitivity image (as long as we have already been supplied by a sensivity iamge or reference)
-	${FSLDIR}/bin/applywarp --ref=$calib --in=$temp_calib/seg_bias --out=$temp_calib/biasfield --premat=$temp_calib/high2low.mat --super --interp=spline --superlevel=4
-	${FSLDIR}/bin/fslmaths $temp_calib/biasfield -recip $temp_calib/sens
+	applywarp --ref=$calib --in=$temp_calib/seg_bias --out=$temp_calib/biasfield --premat=$temp_calib/high2low.mat --super --interp=spline --superlevel=4
+	fslmaths $temp_calib/biasfield -recip $temp_calib/sens
 	senson=1
 	echo "Using bias field from structural image for sensitivity correction" >> $log
     fi
@@ -521,7 +518,7 @@ if [ -z $maskflag ]; then
 
 else
     #use supplied tissue reference mask
-    ${FSLDIR}/bin/imcp $mask $temp_calib/refmask
+    imcp $mask $temp_calib/refmask
     echo "Using supplied reference tissue mask: $mask" >> $log
 fi
 
@@ -636,10 +633,10 @@ elif [ $mode = satrecov ]; then
     if [ ! -z $senson ]; then
 	echo "Apply sensitivity image to data for reference tisse M0 estimation" >> $log
         # apply sensitivity map to calibration image - ONLY for the reference tissue calculations
-	${FSLDIR}/bin/fslmaths $calib -div $temp_calib/sens $temp_calib/calib_senscorr
+	fslmaths $calib -div $temp_calib/sens $temp_calib/calib_senscorr
     else
 	# no sensitivity correction required, but copy image over ready for next command
-	${FSLDIR}/bin/imcp $calib $temp_calib/calib_senscorr
+	imcp $calib $temp_calib/calib_senscorr
     fi
     echo "FABBER within reference tissue mask" >> $log
     $fabber --data=$temp_calib/calib_senscorr --mask=$mask --output=$temp_calib/satrecov --data-order=singlefile --model=satrecov --noise=white --method=vb $tislist $llopts $sropts --t1=$T1r

diff --git a/asl_preproc.in b/asl_preproc.in
@@ -8,6 +8,11 @@
 #
 # SHCOPYRIGHT
 
+# Make script use local copies of helper scripts/programs in the same
+# directory, if present. This allows for multiple versions of the scripts
+# to be used, possibly with bundled dependencies
+PATH=`dirname $0`:${FSLDIR}/bin:${PATH}
+
 Usage() {
     echo "ASL_PREPROC"
     echo "Version: ${GIT_SHA1} ${GIT_DATE}"
@@ -47,7 +52,7 @@ if [ -z $1 ]; then
     exit 1
 fi
 
-perfusion_subtract=${FSLDIR}/bin/perfusion_subtract
+perfusion_subtract=perfusion_subtract
 
 until [ -z $1 ]; do
     case $1 in
@@ -92,7 +97,7 @@ echo "ASL_PREPROC"
 oldpwd=`pwd`
 
 
-tmpbase=`$FSLDIR/bin/tmpnam`
+tmpbase=`tmpnam`
 if [ -z $debug ]; then
     tempdir=${tmpbase}_asl_pre
 else

diff --git a/asl_reg.in b/asl_reg.in
@@ -8,6 +8,11 @@
 #
 # SHCOPYRIGHT
 
+# Make script use local copies of helper scripts/programs in the same
+# directory, if present. This allows for multiple versions of the scripts
+# to be used, possibly with bundled dependencies
+PATH=`dirname $0`:${FSLDIR}/bin:${PATH}
+
 Usage() {
     echo "ASL_REG"
     echo "Version: ${GIT_SHA1} ${GIT_DATE}"
@@ -182,7 +187,7 @@ if [ ! -d $outdir ]; then
 fi
 
 # make a temporary directory to work in - delete at end
-tmpbase=`$FSLDIR/bin/tmpnam`
+tmpbase=`tmpnam`
 if [ -z $debug ]; then
     tempdir=${tmpbase}_asl_reg
 else
@@ -219,7 +224,7 @@ fi
 # BET the structural image if required
 if [ -z $sbet ]; then
     echo "Running BET on structural image"
-    $FSLDIR/bin/bet $struc $tempdir/struc_brain
+    bet $struc $tempdir/struc_brain
     sbet=$tempdir/struc_brain
 fi
 
@@ -228,20 +233,20 @@ if [ -z $finalonly ]; then
     echo "Registration MAIN stage (FLIRT)"
     if [ -z $lowstrucflag ]; then
 	#Step1: 3DOF translation only transformation
-	$FSLDIR/bin/flirt -in $cfile -ref $sbet -schedule $FSLDIR/etc/flirtsch/xyztrans.sch -omat $tempdir/low2high1.mat -out $tempdir/low2hig1 $inittext $weigthinstr
+	flirt -in $cfile -ref $sbet -schedule $FSLDIR/etc/flirtsch/xyztrans.sch -omat $tempdir/low2high1.mat -out $tempdir/low2hig1 $inittext $weigthinstr
 	#step2: 6DOF transformation with small search region
-	$FSLDIR/bin/flirt -in $cfile -ref $sbet -dof $DOF -omat $tempdir/low2high.mat -init $tempdir/low2high1.mat -schedule $flirtsch -out $tempdir/low2high $weigthinstr
+	flirt -in $cfile -ref $sbet -dof $DOF -omat $tempdir/low2high.mat -init $tempdir/low2high1.mat -schedule $flirtsch -out $tempdir/low2high $weigthinstr
     else
 	#as we have a structural image in perfusion space use it to improve registration
 	echo "Using structral image in perfusion space ($lowstruc)"
 	#Step1: 3DOF translation only transformation perfusion->lowstruc
-	$FSLDIR/bin/flirt -in $cfile -ref $lowstruc -schedule $FSLDIR/etc/flirtsch/xyztrans.sch -omat $tempdir/low2low1.mat $inittext $weigthinstr
+	flirt -in $cfile -ref $lowstruc -schedule $FSLDIR/etc/flirtsch/xyztrans.sch -omat $tempdir/low2low1.mat $inittext $weigthinstr
 	#Step2: 6DOF limited transformation in perfusion space
-	$FSLDIR/bin/flirt -in $cfile -ref $lowstruc -dof $DOF -schedule $flirtsch -init $tempdir/low2low1.mat -omat $tempdir/low2low.mat $weigthinstr
+	flirt -in $cfile -ref $lowstruc -dof $DOF -schedule $flirtsch -init $tempdir/low2low1.mat -omat $tempdir/low2low.mat $weigthinstr
 	#step3: 6DOF transformation of lowstruc to struc
-	$FSLDIR/bin/flirt -in $lowstruc -ref $sbet -omat $tempdir/str2str.mat
+	flirt -in $lowstruc -ref $sbet -omat $tempdir/str2str.mat
 	#step4: combine the two transformations
-	$FSLDIR/bin/convert_xfm -omat $tempdir/low2high.mat -concat $tempdir/str2str.mat $tempdir/low2low.mat
+	convert_xfm -omat $tempdir/low2high.mat -concat $tempdir/str2str.mat $tempdir/low2low.mat
     fi
     # update the init text ready for the 'final' step to start with the result of the MAIN registration
     epi_inittext="--init=$tempdir/low2high.mat"
@@ -255,9 +260,9 @@ if [ -z $mainonly ]; then
 echo "Registration FINAL stage (BBR)"
     if [ -z $tissseg ]; then
 	# Running FAST segmentation
-	$FSLDIR/bin/fast -o $tempdir/struct_fast $sbet
+	fast -o $tempdir/struct_fast $sbet
 	# WM segmentation
-	$FSLDIR/bin/fslmaths $tempdir/struct_fast_pve_2 -thr 0.5 -bin ${tempdir}/fast_tissseg
+	fslmaths $tempdir/struct_fast_pve_2 -thr 0.5 -bin ${tempdir}/fast_tissseg
 	tissseg=${tempdir}/fast_tissseg
     fi
 
@@ -266,47 +271,47 @@ echo "Registration FINAL stage (BBR)"
 	convert_xfm -omat $tempdir/high2low.mat -inverse $tempdir/low2high.mat
 
 	fslmaths $sbet -thr 0 -bin $tempdir/struct_brain_mask
-	${FSLDIR}/bin/flirt -in $tempdir/struct_brain_mask -ref $infile -applyxfm -init $tempdir/high2low.mat -out $tempdir/mask -interp trilinear
-	${FSLDIR}/bin/fslmaths $tempdir/mask -thr 0.25 -bin -fillh $tempdir/mask
-	${FSLDIR}/bin/fslcpgeom $infile $tempdir/mask
+	flirt -in $tempdir/struct_brain_mask -ref $infile -applyxfm -init $tempdir/high2low.mat -out $tempdir/mask -interp trilinear
+	fslmaths $tempdir/mask -thr 0.25 -bin -fillh $tempdir/mask
+	fslcpgeom $infile $tempdir/mask
 	mask=$tempdir/mask
     fi
     #  apply mask to asldata
-    $FSLDIR/bin/fslmaths $infile -mas $mask $tempdir/asldata_brain
+    fslmaths $infile -mas $mask $tempdir/asldata_brain
     # copy mask to output for future reference
-    ${FSLDIR}/bin/imcp $mask $outdir/mask
+    imcp $mask $outdir/mask
 
     # do a final refinement of the registration using the perfusion and the white matter segmentation - using epi_reg to get BBR (and allow for fielmap correction in future)
 
     if [ -z $fmap ]; then
     # Without fieldmap
-    $FSLDIR/bin/epi_reg --epi=$tempdir/asldata_brain --t1=$struc --t1brain=$sbet $epi_inittext --out=$tempdir/low2high_final --wmseg=$tissseg $weigthinstr
+    epi_reg --epi=$tempdir/asldata_brain --t1=$struc --t1brain=$sbet $epi_inittext --out=$tempdir/low2high_final --wmseg=$tissseg $weigthinstr
     else
 	# With fieldmap
 	fmapregstr=""
 	if [ ! -z $nofmapreg ]; then
 	   fmapregstr="--nofmapreg"
 	fi
-    $FSLDIR/bin/epi_reg --epi=$tempdir/asldata_brain --t1=$struc --t1brain=$sbet $epi_inittext --out=$tempdir/low2high_final --wmseg=$tissseg $weigthinstr --fmap=$fmap --fmapmag=$fmapmag --fmapmagbrain=$fmapmagbrain --pedir=$pedir --echospacing=$echospacing $fmapregstr
+    epi_reg --epi=$tempdir/asldata_brain --t1=$struc --t1brain=$sbet $epi_inittext --out=$tempdir/low2high_final --wmseg=$tissseg $weigthinstr --fmap=$fmap --fmapmag=$fmapmag --fmapmagbrain=$fmapmagbrain --pedir=$pedir --echospacing=$echospacing $fmapregstr
     fi
 
-    #	$FSLDIR/bin/flirt -ref $sbet -in $infile -dof 6 -cost bbr -wmseg $wmseg -init $tempdir/low2high.mat -omat $tempdir/low2high.mat -out $tempdir/low2high_final -schedule ${FSLDIR}/etc/flirtsch/bbr.sch
+    #	flirt -ref $sbet -in $infile -dof 6 -cost bbr -wmseg $wmseg -init $tempdir/low2high.mat -omat $tempdir/low2high.mat -out $tempdir/low2high_final -schedule ${FSLDIR}/etc/flirtsch/bbr.sch
 
     echo "BBR end"
 
     #OUTPUT
     echo "Saving FINAL output"
     cp $outdir/asl2struct.mat $outdir/asl2struct_init.mat # save the initial transformation matrix to allow chekcing if this part failed
     cp $tempdir/low2high_final.mat $outdir/asl2struct.mat #the transformation matrix from epi_reg - this overwrites the version from MAIN registration
-    ${FSLDIR}/bin/convert_xfm -omat $outdir/struct2asl.mat -inverse $outdir/asl2struct.mat #often useful to have the inverse transform, so calcuate it
+    convert_xfm -omat $outdir/struct2asl.mat -inverse $outdir/asl2struct.mat #often useful to have the inverse transform, so calcuate it
     if [ ! -z $fmap ]; then
-	${FSLDIR}/bin/imcp $tempdir/low2high_final_warp $outdir/asl2struct_warp #the warp from epi_reg
+	imcp $tempdir/low2high_final_warp $outdir/asl2struct_warp #the warp from epi_reg
     fi
-    ${FSLDIR}/bin/imcp $tempdir/low2high_final $outdir/asl2struct # save the transformed image to check on the registration
+    imcp $tempdir/low2high_final $outdir/asl2struct # save the transformed image to check on the registration
 
     # copy the edge image from epi_reg output as that is good for visualisation
-    ${FSLDIR}/bin/imcp $tissseg $outdir/tissseg
-    ${FSLDIR}/bin/imcp $tempdir/low2high_final_fast_wmedge $outdir/tissedge
+    imcp $tissseg $outdir/tissseg
+    imcp $tempdir/low2high_final_fast_wmedge $outdir/tissedge
 fi
 
 ## ASL-->standard transformation (if specified)