Merge branch 'refspace' into 'master'

Refspace

See merge request !12

README.md

@@ -56,10 +56,15 @@ NeuroImage, 76(1), 400-411. DOI: 10.1016/j.neuroimage.2013.03.015
         -p <folder>                            Protocols folder (all masks in same standard space) (Default=$FSLDIR/etc/xtract_data/<SPECIES>)
         -stdwarp <std2diff> <diff2std>         Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
         -gpu                                   Use GPU version
-        -native                           Run tractography in native (diffusion) space
         -res <mm>                              Output resolution (Default=same as in protocol folders unless '-native' used)
         -ptx_options <options.txt>	           Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10)
 
+        And EITHER:
+        -native                                Run tractography in native (diffusion) space
+
+        OR:
+        -ref <refimage> <diff2ref> <ref2diff>  Reference image for running tractography in reference space, Diff2Reference and Reference2Diff transforms
+
 ```
 ---------------------------------------------------------------------
 

xtract

@@ -4,7 +4,7 @@
 #
 #   SHCOPYRIGHT
 
-# Written by Saad Jbabdi & Stam Sotiropoulos (based on Marius de Groot autoPtx code)
+# Written by Saad Jbabdi, Stam Sotiropoulos & Shaun Warrington (based on Marius de Groot autoPtx code)
 # Protocols created by Rogier Mars et al.
 
 # Location of probtrackx2_gpu binary
@@ -32,10 +32,15 @@ Usage:
        -p <folder>                            Protocols folder (all masks in same standard space) (Default=$FSLDIR/etc/xtract_data/<SPECIES>)
        -stdwarp <std2diff> <diff2std>         Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
        -gpu                                   Use GPU version
-       -native                           Run tractography in native (diffusion) space
        -res <mm>                              Output resolution (Default=same as in protocol folders unless '-native' used)
        -ptx_options <options.txt>	            Pass extra probtrackx2 options as a text file to override defaults, e.g. --steplength=0.2 --distthresh=10)
 
+       And EITHER:
+       -native                                Run tractography in native (diffusion) space
+
+       OR:
+       -ref <refimage> <diff2ref> <ref2diff>  Reference image for running tractography in reference space, Diff2Reference and Reference2Diff transforms
+
 EOF
     exit 1
 }
@@ -70,6 +75,9 @@ ptx_opts=""
 stdref=""
 gpu=0
 nat=0
+ref=""
+diff2ref=""
+ref2diff=""
 spec=""
 res=-1
 list=0
@@ -86,6 +94,7 @@ while [ ! -z "$1" ];do
 	-stdwarp) std2diff=$2;diff2std=$3;shift;shift;;
 	-gpu) gpu=1;;
 	-native) nat=1;;
+  -ref) ref=$2;diff2ref=$3;ref2diff=$4;shift;shift;shift;;
 	-res) res=$2;shift;;
   -list) list=1;shift;;
 	-ptx_options) ptx_opts=`cat $2`;shift;;
@@ -126,6 +135,19 @@ if [ "$std2diff" == "" ];then
 	echo "Image $diff2std not found."
 	exit 1
     fi
+elif [ ! "$ref" == "" ];then
+    if [ "$diff2ref" == "" ] || [ "$ref2diff" == "" ];then
+  echo "If running in ref space, you must specify '-ref <refimage> <diff2ref> <ref2diff>'"
+  exit 1
+    fi
+    if [ `$FSLDIR/bin/imtest $diff2ref` -eq 0 ];then
+  echo "Image $diff2ref not found."
+  exit 1
+    fi
+    if [ `$FSLDIR/bin/imtest $ref2diff` -eq 0 ];then
+  echo "Image $ref2diff not found."
+  exit 1
+    fi
 fi
 
 echo SPECIES $spec
@@ -226,11 +248,18 @@ if [ ! "$str" == "$strdef" ];then
     echo "samples=1, 1 means 1000. Use '#' to skip lines"
     errflag=1
   elif [ ${tchk[0]} -eq 1 ];then
-    echo "Using subset of XTRACT protocols and getting 'nsamples' from default structure file."
+    echo " -- getting 'nsamples' from default structure file"
     seedget=1
   fi
 fi
 
+# Check space option
+if [ $nat -eq 1 ] && [ ! "$ref" == "" ];then
+    echo "You have selected the native space and ref space options"
+    echo "Must select EITHER '-native', '-ref <refimage> <diff2ref> <ref2diff>', OR use the default standard space"
+    errflag=1
+fi
+
 if [ "$errflag" -eq 1 ];then
     echo ""
     echo "Exit without doing anything.."
@@ -249,8 +278,17 @@ opts=" $opts --loopcheck --forcedir --opd --ompl --seedref=$stdref --sampvox=1 -
 # Add any user-defined ptx options
 opts=" $opts $ptx_opts"
 
-if [ "$nat" -eq 0 ];then
-    opts="$opts --xfm=$std2diff --invxfm=$diff2std "
+if [ "$nat" -eq 0 ] && [ "$ref" == "" ];then
+    opts="$opts --seedref=$stdref --xfm=$std2diff --invxfm=$diff2std "
+elif [ ! "$ref" == "" ]; then
+    opts="$opts --seedref=$ref --xfm=$ref2diff --invxfm=$diff2ref "
+fi
+
+# If running in reference space, combine std2diff and diff2ref for std2ref
+if [ ! "$ref" == "" ];then
+    echo " -- combining standard-to-diffusion and diffusion-to-reference transforms"
+    std2ref=$out/standard2ref
+    $FSLDIR/bin/convertwarp -o $std2ref -r $ref --warp1=$std2diff --warp2=$diff2ref
 fi
 
 # Loop over structures
@@ -290,7 +328,7 @@ while read structstring; do
 	#  DEALING WITH RESAMPLING --
 	# Pick space to run tractography in (diffusion or standard)
 	if [ "$nat" -eq 1 ];then
-	    echo " -- transforming masks into native space"
+	    echo "${struct} -- transforming masks into native space"
 	    mkdir -p $out/masks/$struct
 	    for m in seed stop exclude;do
 		if [ `$FSLDIR/bin/imtest $maskdir/$m` -eq 1 ];then
@@ -299,6 +337,16 @@ while read structstring; do
 		fi
 		eval "${m}=$out/masks/$struct/$m"
 	    done
+  elif [ ! "$ref" == "" ];then
+      echo "${struct} -- transforming masks into ref space"
+      mkdir -p $out/masks/$struct
+      for m in seed stop exclude;do
+    if [ `$FSLDIR/bin/imtest $maskdir/$m` -eq 1 ];then
+        $FSLDIR/bin/applywarp -i $maskdir/$m -o $out/masks/$struct/$m -w $std2ref -r $ref -d float
+        $FSLDIR/bin/fslmaths $out/masks/$struct/$m -thr 0.1 -bin $out/masks/$struct/$m -odt char
+    fi
+    eval "${m}=$out/masks/$struct/$m"
+      done
 	else
 	    for m in seed stop exclude;do
 		if [ $res -gt 0 ];then
@@ -325,6 +373,13 @@ while read structstring; do
 		$FSLDIR/bin/fslmaths $out/masks/$struct/$t -thr 0.1 -bin $out/masks/$struct/$t -odt char
 	    done
 	    echo $out/masks/$struct/target* > $targetfile
+  elif [ ! "$ref" == "" ];then
+      for tfile in $targets;do
+    t=`basename $tfile`
+    $FSLDIR/bin/applywarp -i $tfile -o $out/masks/$struct/$t -w $std2ref -r $ref -d float
+    $FSLDIR/bin/fslmaths $out/masks/$struct/$t -thr 0.1 -bin $out/masks/$struct/$t -odt char
+      done
+      echo $out/masks/$struct/target* > $targetfile
 	else
 	    if [ $res -gt 0 ];then
 		# Resample at a different resolution