xtract

#!/bin/bash

#   Copyright (C) 2019 University of Oxford
#
#   SHCOPYRIGHT

# 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
ptxbin_gpu=$FSLDIR/bin/probtrackx2_gpu

# Location of xtract data
datadir=$FSLDIR/data/xtract_data

Usage() {
    cat << EOF

Usage:
    xtract -bpx <bedpostX_dir> -out <outputDir> -species <SPECIES> [options]
    xtract -bpx <bedpostX_dir> -out <outputDir> -species CUSTOM -str <file> -p <folder> -stdref <reference> [options]
    xtract -list

    Compulsory arguments:

       -bpx <folder>                          Path to bedpostx folder
       -out <folder>                          Path to output folder
       -species <SPECIES>                     One of HUMAN or MACAQUE or CUSTOM

    If -species CUSTOM:
      -str <file>                            Structures file (format: format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
      -p <folder>                            Protocols folder (all masks in same standard space)
      -stdref <reference>                    Standard space reference image

    Optional arguments:
       -list                                  List the tract names used in XTRACT
       -str <file>                            Structures file (format: <tractName> per line OR format: <tractName> [samples=1], 1 means 1000, '#' to skip lines)
       -p <folder>                            Protocols folder (all masks in same standard space) (Default=$FSLDIR/data/xtract_data/<SPECIES>)
       -stdwarp <std2diff> <diff2std>         Standard2diff and Diff2standard transforms (Default=bedpostx_dir/xfms/{standard2diff,diff2standard})
       -stdref <reference>                    Standard space reference image (Default = $FSLDIR/data/standard/MNI152_T1_1mm [HUMAN], $datadir/standard/F99/mri/struct_brain [MACAQUE])
       -gpu                                   Use GPU version
       -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
}

Splash (){

cat <<EOF

 __  _______ ____      _    ____ _____
 \ \/ /_   _|  _ \    / \  / ___|_   _|
  \  /  | | | |_) |  / _ \| |     | |
  /  \  | | |  _ <  / ___ \ |___  | |
 /_/\_\ |_| |_| \_\/_/   \_\____| |_|

EOF

}

Splash

[ "$1" = "" ] && Usage


# Set default options
bpx=""
out=""
str=""
p=""
std2diff=""
ptx_opts=""
stdref=""
gpu=0
nat=0
ref=""
diff2ref=""
ref2diff=""
spec=""
res=-1
list=0
seedget=0 # if user specifies -str and format is <tractName>, try to get nseeds from default structureList (i.e. if using a subset of XTRACT tracts)

# Parse command-line arguments
while [ ! -z "$1" ];do
    case "$1" in
	-bpx) bpx=$2;shift;;
	-out) out=$2;shift;;
	-str) str=$2;shift;;
	-p)   p=$2;shift;;
	-species) spec=$2;shift;;  # converts to uppercase
	-stdwarp) std2diff=$2;diff2std=$3;shift;shift;;
  -stdref) stdref=$2;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;;

	*) echo "Unknown option '$1'";exit 1;;
    esac
    shift
done

# list argument
if [ "$list" -eq 1 ];then
    tractNames=""
    echo ""
    echo "Tract names:"
    while read structstring; do
      struct=`echo $structstring | awk '{print $1}'`
      if [ "${struct:0:1}" == "#" ];then
    	foo=0
      elif [ "$struct" == "" ];then
    	foo=0
      else
      tractNames="${tractNames} ${struct},"
      fi
    done < $datadir/Human/structureList
    echo ${tractNames%,}
    exit 1
fi

# Default warps
if [ "$std2diff" == "" ];then
    std2diff=$bpx/xfms/standard2diff
    diff2std=$bpx/xfms/diff2standard
    if [ `$FSLDIR/bin/imtest $std2diff` -eq 0 ];then
	echo "Image $std2diff not found."
	exit 1
    fi
    if [ `$FSLDIR/bin/imtest $diff2std` -eq 0 ];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

# GPU stuff
if [ $gpu -eq 0 ];then
    ptxbin=$FSLDIR/bin/probtrackx2
else
    # Temp location of CUDA code
    ptxbin=${ptxbin_gpu}
fi

# Check compulsory arguments
errflag=0
if [ "$bpx" == "" ];then
    echo "Must set compulsory argument '-bpx'"
    errflag=1
elif [ ! -d $bpx ];then
    echo "Bedpostx folder $bpx not found"
    errflag=1
fi
if [ "$out" == "" ];then
    echo "Must set compulsory argument '-out'"
    errflag=1
fi

# Check which species and protocols to run
if [ "$spec" == "" ];then
  echo "Must set compulsory argument '-species'"
  errflag=1
elif [ "$spec" == "HUMAN" ];then
    if [ "$stdref" == "" ];then
        stdref=$FSLDIR/data/standard/MNI152_T1_1mm
    fi
    strdef=$datadir/Human/structureList
    if [ "$p" == "" ];then
      p=$datadir/Human
      if [ "$str" == "" ];then
        str=$p/structureList
      fi
    elif [ ! "$p" == "" ];then
      if [ "$str" == "" ];then
        echo "If selecting a protocol folder, must set argument '-str'"
        errflag=1
      fi
    fi
elif [ "$spec" == "MACAQUE" ];then
    if [ "$stdref" == "" ];then
        stdref=$datadir/standard/F99/mri/struct_brain
    fi
    strdef=$datadir/Macaque/structureList
    if [ "$p" == "" ];then
      p=$datadir/Macaque
      if [ "$str" == "" ];then
        str=$p/structureList
      fi
    elif [ ! "$p" == "" ];then
      if [ "$str" == "" ];then
        echo "If selecting a protocol folder, must set argument '-str'"
        errflag=1
      fi
    fi
elif [ "$spec" == "CUSTOM" ];then
    if [ "$stdref" == "" ];then
        echo "If -species CUSTOM, must set argument '-stdref'"
        errflag=1
    fi
    if [ "$p" == "" ];then
        echo "If -species CUSTOM, must set argument '-p'"
        errflag=1
    fi
    if [ "$str" == "" ];then
        echo "If -species CUSTOM, must set argument '-str'"
        errflag=1
    fi
else
    echo "Species must be one of HUMAN or MACAQUE or CUSTOM"
    errflag=1
fi

# Check that -stdref, -str and -p exist
if [ ! `$FSLDIR/bin/imtest $stdref` -eq 1 ];then
  echo "Standard space reference image '-stdref' $stdref not found"
  errflag=1
fi
if [ ! -d $p ];then
  echo "Protocol folder $p not found"
  errflag=1
fi
if [ ! -f $str ];then
  echo "Structures files $str not found"
  errflag=1
fi

if [ "$errflag" -eq 1 ];then
    echo ""
    echo "Exit without doing anything.."
    exit 1
fi

# Check -str file format
if [ "$spec" == "HUMAN" ] || [ "$spec" == "MACAQUE" ];then
tchk=()
if [ ! "$str" == "$strdef" ];then
  while read structstring; do
    struct=`echo $structstring | awk '{print $1}'`
    if [ "${struct:0:1}" == "#" ];then
  	foo=0
    elif [ "$struct" == "" ];then
  	foo=0
    else
      if [ "`echo $structstring | awk '{print $2}'`" == "" ];then
      tchk+=("1") # if empty, then 1 - get nseeds from default -str file
      else
      tchk+=("0")
      fi
    fi
  done < $str
  IFS=$'\n'; tchk=($(sort <<<"${tchk[*]}")); unset IFS
  if [ ! "${tchk[0]}" -eq "${tchk[${#tchk[@]}-1]}" ];then
    echo ""
    echo "-str file format is inconsistent. Format should be either:"
    echo "<tractName> per line"
    echo "OR"
    echo "<tractName> [samples=1] per line"
    echo "samples=1, 1 means 1000. Use '#' to skip lines"
    errflag=1
  elif [ ${tchk[0]} -eq 1 ];then
    echo " -- getting 'nsamples' from default structure file"
    seedget=1
  fi
fi
elif [ "$spec" == "CUSTOM" ];then
# add in check for str file format, user must provide number of seeds
  while read structstring; do
    struct=`echo $structstring | awk '{print $1}'`
    if [ "${struct:0:1}" == "#" ];then
    foo=0
    elif [ "$struct" == "" ];then
    foo=0
    else
      if [ "`echo $structstring | awk '{print $2}'`" == "" ];then
      echo "If using -species CUSTOM -str file format must follow:"
      echo "<tractName> [samples=1] per line"
      echo "samples=1, 1 means 1000. Use '#' to skip lines"
      errflag=1
      fi
    fi
  done < $str
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.."
    exit 1
fi

# Create output folders
mkdir -p $out
mkdir -p $out/logs
mkdir -p $out/tracts

# Set common ptx options
opts=" -s $bpx/merged -m $bpx/nodif_brain_mask -V 1"
opts=" $opts --loopcheck --forcedir --opd --ompl --seedref=$stdref --sampvox=1 --randfib=1 "

# Add any user-defined ptx options
opts=" $opts $ptx_opts"

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
commands=$out/commands.txt
rm -rf $commands
echo "Preparing submission script..."
while read structstring; do
  struct=`echo $structstring | awk '{print $1}'`
  # skip empty lines and lines that start with '#'
  if [ "${struct:0:1}" == "#" ];then
	# do nothing
	foo=0
	#echo "----- Skip line $structstring -----"
  elif [ "$struct" == "" ];then
	# do nothing
	foo=0
	#echo "----- Skip empty line -----"
  else
	#echo "autoTrack $struct"
	mkdir -p $out/tracts/$struct

  # if running a subset of tracts and -str format is <tractName>, check for nseed in str file
  if [ "$seedget" -eq 1 ]; then
      nseed=`grep -w ${struct} $strdef | awk '{print $2}'`
      if [ "$nseed" == "" ];then
        echo "Couldn't find number of samples for '$struct'. Exiting now."
        exit 1
      fi
  else
	    nseed=`echo $structstring | awk '{print $2}'`
	    if [ "$nseed" == "" ];then nseed=1; fi
  fi
	nseed=$(echo "scale=0; 1000 * ${nseed} / 1"|bc)

	maskdir=$p/$struct

	#  DEALING WITH RESAMPLING --
	# Pick space to run tractography in (diffusion or standard)
	if [ "$nat" -eq 1 ];then
	    echo "${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
		    $FSLDIR/bin/applywarp -i $maskdir/$m -o $out/masks/$struct/$m -w $std2diff -r $bpx/nodif_brain_mask -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/$m"
	    done
  elif [ ! "$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
		    # Resample at a different resolution
		    mkdir -p $out/masks/$struct
		    if [ `$FSLDIR/bin/imtest $maskdir/$m` -eq 1 ];then
			$FSLDIR/bin/flirt -in $maskdir/$m -out $out/masks/$struct/$m -applyisoxfm $res -ref $maskdir/$m
			$FSLDIR/bin/fslmaths $out/masks/$struct/$m -thr 0.1 -bin $out/masks/$struct/$m -odt char
		    fi
		    eval "${m}=$out/masks/$struct/$m"
		else
		    eval "${m}=$maskdir/$m"
		fi
	    done
	fi

	# Deal with targets (in cases where there may be more than one)
	targets=`imglob $maskdir/target*`
	targetfile=$out/tracts/$struct/targets.txt
	if [ "$nat" -eq 1 ];then
	    for tfile in $targets;do
		t=`basename $tfile`
		$FSLDIR/bin/applywarp -i $tfile -o $out/masks/$struct/$t -w $std2diff -r $bpx/nodif_brain_mask -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* > $targetfile
  elif [ ! "$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
		for tfile in $targets;do
		    t=`basename $tfile`
		    $FSLDIR/bin/flirt -in $tfile -out $out/masks/$struct/$t -applyisoxfm $res -ref $tfile
		    $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
		echo $targets > $targetfile
	    fi
	fi

	# Get generic options
	o=$opts

        # Add inclusion/exclusion masks
	if [ `$FSLDIR/bin/imtest $stop` -eq 1 ];then
	    o="$o --stop=$stop"
	fi
	if [ `$FSLDIR/bin/imtest $exclude` -eq 1 ];then
	    o="$o --avoid=$exclude"
	fi

	# Add seed/target
	o1="$o --nsamples=$nseed -x $seed "

	if [ "x${targets}" != "x" ];then #Add waypoints if there are any
       	    o1=" $o1 --waypoints=$targetfile "
	fi

        # Outputs
	o1=" $o1 -o density --dir=$out/tracts/$struct"


	# Does the protocol define a second run with inverted seed / target masks?
	if [ -e $maskdir/invert ]; then  #Invert-mode
	    if 	[ `$FSLDIR/bin/imtest $maskdir/target.nii.gz` -eq 1 ];then 	# Check if a target.nii.gz image exists when invert option has been selected.
		mkdir -p $out/tracts/$struct/tractsInv
		if [ `$FSLDIR/bin/imtest $out/masks/$struct/target.nii.gz` -eq 1 ]; then
		    target=$out/masks/$struct/target
		else
		    target=$maskdir/target
		fi
		o2="$o --nsamples=$nseed -x ${target} --waypoints=$seed -o density --dir=$out/tracts/$struct/tractsInv"

		# merge runs for forward and inverted tractography runs and then normalise (create commands but don't execute)
		mergecmd="$FSLDIR/bin/fslmaths $out/tracts/$struct/density -add $out/tracts/$struct/tractsInv/density $out/tracts/$struct/sum_density"

		#Add waypoints (create command but don't execute)
		addcmd="echo \"scale=5; \`cat $out/tracts/$struct/waytotal\` + \`cat $out/tracts/$struct/tractsInv/waytotal\` \"|bc > $out/tracts/$struct/sum_waytotal"

		# Waypoint normalisation (create command but don't execute)
		normcmd="$FSLDIR/bin/fslmaths $out/tracts/$struct/sum_density -div \`cat $out/tracts/$struct/sum_waytotal\` $out/tracts/$struct/densityNorm"

		# Append to command list
		echo "$ptxbin $o1; $ptxbin $o2; $mergecmd; $addcmd; $normcmd" >> $commands
	    else
		echo "Invert Option selected, but more than one target defined! A 'target.nii.gz' is expected. Exiting now"
		exit 1
	    fi
	else  	#No invert-mode
	    # Waypoint normalisation (create command but don't execute)
	    normcmd="$FSLDIR/bin/fslmaths $out/tracts/$struct/density -div \`cat $out/tracts/$struct/waytotal\` $out/tracts/$struct/densityNorm"

	    # Append to command list
	    echo "$ptxbin $o1; $normcmd" >> $commands
	fi
    fi

done < $str

chmod +x $commands

if [ "x$SGE_ROOT" != "x" ]; then  # Submit all commands to run in parallel on the cluster
    # One job per tract for a CPU cluster, one job for all tracts for a GPU cluster.
    if [ $gpu -eq 0 ];then
	fsl_sub -T 2160 -q long.q -l $out/logs -N xtract -t $commands
    else
	fsl_sub -T 300 -q $FSLGECUDAQ -l $out/logs -N xtract $commands
    fi
else   # If no SGE, run locally
    sh $commands
fi

#EOF