bet_nw

#!/bin/sh

#   -IN2 <image> option added by...
#   Nathan Wetter (nwetter2@illinois.edu)
#   Brad Sutton (bsutton@illinois.edu)
#   Magnetic Resonance Functional Imaging Lab
#   University of Illinois at Urbana-Champaign
#   November 2013

#   bet - wrapper script for lots of different bet functionality
#
#   Stephen Smith, FMRIB Image Analysis Group
#   SIENA eye cleanup option by Marco Battaglini and Nicola De Stefano, Siena
#
#   Copyright (C) 2005-2012 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
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#   Imaging of the Brain), Department of Clinical Neurology, Oxford
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#   
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# {{{ Usage()

Usage() {
    cat <<EOF
bet_nw - A modified version of FSL's bet, updated to make use of multispectral images

For research purposes only! Please see LICENSE.txt

Nate Wetter <nwetter2@illinois.edu>
Brad Sutton <bsutton@illinois.edu>
Magnetic Resonance Functional Imaging Lab <mrfil.bioen.illinois.edu>
University of Illinois at Urbana-Champaign <illinois.edu>

Usage:    bet_nw <input> <output> [options]

Main bet2 options:
  -o            generate brain surface outline overlaid onto original image
  -m            generate binary brain mask
  -s            generate approximate skull image
  -n            don't generate segmented brain image output
  -f <f>        fractional intensity threshold (0->1); default=0.5; smaller values give larger brain outline estimates
  -g <g>        vertical gradient in fractional intensity threshold (-1->1); default=0; positive values give larger brain outline at bottom, smaller at top
  -r <r>        head radius (mm not voxels); initial surface sphere is set to half of this
  -c <x y z>    centre-of-gravity (voxels not mm) of initial mesh surface.
  -t            apply thresholding to segmented brain image and mask
  -e            generates brain surface as mesh in .vtk format
  -dil <d>      when used with -IN2, dilates brain mask d times
  -fast         when used with -IN2, use FAST to complete extraction (experimental)
  -png          generates png images

Variations on default bet2 functionality (mutually exclusive options):
  (default)     just run bet2
  -R            robust brain centre estimation (iterates BET several times)
  -S            eye & optic nerve cleanup (can be useful in SIENA)
  -B            bias field & neck cleanup (can be useful in SIENA)
  -Z            improve BET if FOV is very small in Z (by temporarily padding end slices)
  -F            apply to 4D FMRI data (uses -f 0.3 and dilates brain mask slightly)
  -A            run bet2 and then betsurf to get additional skull and scalp surfaces (includes registrations)
  -A2 <T2>      as with -A, when also feeding in non-brain-extracted T2 (includes registrations)
  -IN2 <image>  use this image from same subject to extract brain from <input> - useful for SIENA, where T2 may yield the best brain/nonbrain contrast while T1 has the best gray/white matter contrast

Miscellaneous options:
  -v          verbose (switch on diagnostic messages)
  -h          display this help, then exits
  -d          debug (don't delete temporary intermediate images)

Last updated: September 24, 2014

EOF
    exit 1
}

# }}}
# {{{ get_dims()

get_dims() {
    xdim=`${FSLDIR}/bin/fslval $1 dim1 | sed 's/-//g'`
    ydim=`${FSLDIR}/bin/fslval $1 dim2 | sed 's/-//g'`
    zdim=`${FSLDIR}/bin/fslval $1 dim3 | sed 's/-//g'`
    xpixdim=`${FSLDIR}/bin/fslval $1 pixdim1 | sed 's/-//g'`
    ypixdim=`${FSLDIR}/bin/fslval $1 pixdim2 | sed 's/-//g'`
    zpixdim=`${FSLDIR}/bin/fslval $1 pixdim3 | sed 's/-//g'`
    #echo $xdim $ydim $zdim $xpixdim $ypixdim $zpixdim
}

# }}}
# {{{ find_centre_in_mm()

# find_centre_in_mm() {
#     centre=`${FSLDIR}/bin/fslstats $1 -l 0.001 -C`
#     x=`echo $centre $xpixdim | awk '{print "10 k " $1 " " $4 " * p"}' | dc -`
#     y=`echo $centre $ypixdim | awk '{print "10 k " $2 " " $4 " * p"}' | dc -`
#     z=`echo $centre $zpixdim | awk '{print "10 k " $3 " " $4 " * p"}' | dc -`
#     #echo $x $y $z
# }

# }}}
# {{{ find_centre_in_voxels()

find_centre_in_voxels() {
    centre=`${FSLDIR}/bin/fslstats $1 -l 0.001 -C`
    x=`echo $centre | awk '{print $1}'`
    y=`echo $centre | awk '{print $2}'`
    z=`echo $centre | awk '{print $3}'`
    #echo $x $y $z
}

# }}}

# {{{ parse IN and OUT options

[ "$2" = "" ] && Usage
IN=`${FSLDIR}/bin/remove_ext $1`
OUT=`${FSLDIR}/bin/remove_ext $2`
shift 2
if [ `${FSLDIR}/bin/imtest $IN` = 0 ] ; then
    echo ""
    echo "Error: input image $IN not valid"
    echo ""
    exit 1
fi

# }}}
# {{{ setup variable defaults

debug=0
verbose=0
variation=0
skull=0
bet2opts=""
fast=0
dil=0
png=0

# }}}
# {{{ parse options

while [ _$1 != _ ] ; do
    if [ $1 = -o ] || [ $1 = -m ] || [ $1 = -s ] || [ $1 = -n ] || [ $1 = -t ] || [ $1 = -e ] ; then
        bet2opts="$bet2opts $1"
        if [ $1 = -s ] ; then
          skull=1
        fi
        shift
    elif [ $1 = -f ] || [ $1 = -g ] || [ $1 = -r ]; then
	[ "$2" = "" ] && Usage
        bet2opts="$bet2opts $1 $2"
        shift 2
    elif [ $1 = -c ] ; then
	[ "$4" = "" ] && Usage
        bet2opts="$bet2opts $1 $2 $3 $4"
        shift 4
    elif [ $1 = -R ] ; then
	variation=1
        shift
    elif [ $1 = -S ] ; then
	variation=2
        shift
    elif [ $1 = -Z ] ; then
	variation=3
        shift
    elif [ $1 = -F ] ; then
	variation=4
        shift
    elif [ $1 = -A ] ; then
	variation=5
        shift
    elif [ $1 = -A2 ] ; then
	[ "$2" = "" ] && Usage
	variation=6
	IN2=$2
        shift 2
    elif [ $1 = -B ] ; then
	variation=7
        shift
    elif [ $1 = -IN2 ] ; then
        [ "$2" = "" ] && Usage
        variation=8
	    IN2=$2
	    shift 2
    elif [ $1 = -v ] ; then
	verbose=1
	bet2opts="$bet2opts -v"
        shift
    elif [ $1 = -d ] ; then
	debug=1
        shift
    elif [ $1 = -fast ] ; then
        fast=1
        shift
    elif [ $1 = -dil ] ; then
        dil=$2
        shift 2
    elif [ $1 = -png ] ; then
        png=1
        shift
    else
	Usage
    fi
done

if [ $verbose = 1 ] ; then
    echo IN=$IN
    echo OUT=$OUT
    echo bet2opts="${bet2opts}"
    echo verbose=$verbose
    echo debug=$debug
    echo variation=$variation
    echo IN2=$IN2
fi

# }}}
# {{{ process variations

if [ $variation = 0 ] ; then
    ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
elif [ $variation = 1 ] ; then
    # {{{ BET robust

bet2opts=`echo $bet2opts | sed 's/-n//g'`
get_dims $IN

i=1
while [ $i -gt 0 ] ; do
    #echo $i
    if [ $i = 1 ] ; then
	${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
	find_centre_in_voxels $OUT
    else
	${FSLDIR}/bin/bet2 $IN $OUT $bet2opts -c $x $y $z
	ox=$x; oy=$y; oz=$z;
	find_centre_in_voxels $OUT
	diffsq=`echo "0 k $ox $x - 2 ^ $oy $y - 2 ^ + $oz $z - 2 ^ + 1 / p" | dc -`
	#echo $diffsq
	if [ $diffsq -lt 1 ] || [ $i -gt 10 ] ; then
	    i=_10
	fi
    fi
    i=`echo "$i 1 + p" | dc -`
done

# }}}
elif [ $variation = 2 ] ; then
    # {{{ SIENA eye cleanup

#### get the raw brain and skull images
${FSLDIR}/bin/bet2 $IN ${OUT}_tmp_betraw -s $bet2opts

#### run betpremask (keep intermediate files around using -d) and feed it into bet
${FSLDIR}/bin/standard_space_roi $IN ${OUT}_tmp_premask -b -d
${FSLDIR}/bin/bet2 ${OUT}_tmp_premask ${OUT}_tmp_premask_bet -n -m -f 0.4 $bet2opts

#### bring eye mask from standard space into native and dilate, mostly in 2D and then invert
${FSLDIR}/bin/flirt -ref $IN -in ${FSLDIR}/data/standard/MNI152_T1_2mm_eye_mask -applyxfm -init ${OUT}_tmp_premask_tmp_to_std_inv.mat -datatype float -out ${OUT}_tmp_eye_mask
${FSLDIR}/bin/fslmaths ${OUT}_tmp_eye_mask -thr 0.5 -bin -dilF -kernel 2D -dilF -dilF -dilF -dilF -dilF -dilF -dilF ${OUT}_tmp_eyes7dil -odt short
${FSLDIR}/bin/fslmaths ${OUT}_tmp_eyes7dil -mul -1 -add 1 ${OUT}_tmp_eyes7dil_inv

#### mask original brain mask with inverted-eye-mask, ADD betpremask_bet_mask and X by original brain
${FSLDIR}/bin/fslmaths ${OUT}_tmp_betraw -bin -mas ${OUT}_tmp_eyes7dil_inv -add ${OUT}_tmp_premask_bet_mask -bin -mul ${OUT}_tmp_betraw ${OUT}_tmp_prebrain

#### find upper threshold used to delete eyes
Mean=`${FSLDIR}/bin/fslstats ${OUT}_tmp_prebrain -M`
SD=`${FSLDIR}/bin/fslstats ${OUT}_tmp_prebrain -S`
thr=`echo "10 k 3.5 $SD * $Mean + p" | dc -`

#### apply threshold and a little morphology (twice) to cleanup further and produce final brain image
${FSLDIR}/bin/fslmaths ${OUT}_tmp_prebrain -uthr $thr -bin -ero -dilF -dilF -ero -mul ${OUT}_tmp_prebrain -uthr $thr -bin -kernel 2D -ero -dilF -mul ${OUT}_tmp_betraw $OUT
${FSLDIR}/bin/fslmaths $OUT -bin ${OUT}_mask

#### remove eyes from original skull to produce final skull image
${FSLDIR}/bin/fslmaths ${OUT}_tmp_eyes7dil -ero -kernel 2D -ero -mul -1 -add 1 ${OUT}_tmp_eyes5dil_inv
${FSLDIR}/bin/fslmaths ${OUT}_tmp_betraw_skull -mas ${OUT}_tmp_eyes5dil_inv ${OUT}_skull

# }}}
elif [ $variation = 3 ] ; then
    # {{{ small FOV in Z

MINZFOV=100.0
get_dims $IN

npad=`echo "$MINZFOV $zpixdim / $zdim - 2 / 1 + p" | dc -`

if [ $npad -le 0 ] ; then
    echo "Image already has a greater Z FOV than $MINZFOV so not using padding"
    ${FSLDIR}/bin/bet2 $IN $OUT $bet2opts
    exit
fi

${FSLDIR}/bin/fslroi $IN ${OUT}_tmp_bottom 0 $xdim 0 $ydim 0 1
${FSLDIR}/bin/fslroi $IN ${OUT}_tmp_top    0 $xdim 0 $ydim `echo "$zdim 1 - p" | dc -` 1

n=1
while [ $n -le $npad ] ; do
    bottomlist="$bottomlist ${OUT}_tmp_bottom"
    toplist="$toplist ${OUT}_tmp_top"
    n=`echo "$n 1 + p" | dc -`
done

${FSLDIR}/bin/fslmerge -z ${OUT}_tmp $bottomlist $IN $toplist

${FSLDIR}/bin/bet2 ${OUT}_tmp $OUT $bet2opts

for f in `imglob ${OUT}*` ; do
    ${FSLDIR}/bin/fslroi $f $f 0 $xdim 0 $ydim $npad $zdim
done

# }}}
elif [ $variation = 4 ] ; then
    # {{{ FMRI

${FSLDIR}/bin/fslroi $IN ${OUT}_tmp 0 1
${FSLDIR}/bin/bet2 ${OUT}_tmp ${OUT}_tmp_brain -m -n -f 0.3 $bet2opts
${FSLDIR}/bin/fslmaths ${OUT}_tmp_brain_mask -dilF ${OUT}_mask
${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT

# }}}
elif [ $variation = 5 ] ; then
    # {{{ bet2 + betsurf (T1 only)

# register T1 to standard space
${FSLDIR}/bin/flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm -in $IN -omat ${OUT}_tmp_T1_to_std.mat

# run brain extraction and save brain mesh
${FSLDIR}/bin/bet2 $IN $OUT -e $bet2opts

# find other surfaces
${FSLDIR}/bin/betsurf --t1only -o -m -s $IN ${OUT}_mesh.vtk ${OUT}_tmp_T1_to_std.mat $OUT

# }}}
elif [ $variation = 6 ] ; then
    # {{{ bet2 + betsurf (T1 & T2)

# register T2 to T1
${FSLDIR}/bin/flirt -in $IN2 -ref $IN -out ${OUT}_tmp_T2_to_T1 -omat ${OUT}_tmp_T2_to_T1.mat -interp sinc

# register T1 to standard space
${FSLDIR}/bin/flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm -in $IN -omat ${OUT}_tmp_T1_to_std.mat

# run brain extraction and save brain mesh
${FSLDIR}/bin/bet2 $IN $OUT -e $bet2opts

# find other surfaces
${FSLDIR}/bin/betsurf -o -m -s $IN ${OUT}_tmp_T2_to_T1 ${OUT}_mesh.vtk ${OUT}_tmp_T1_to_std.mat $OUT

# }}}
elif [ $variation = 7 ] ; then
    # {{{ SIENA bias field & neck cleanup

#### run betpremask
${FSLDIR}/bin/standard_space_roi $IN ${OUT}_tmp_premask -b -d

#### run FAST to get bias field
${FSLDIR}/bin/fast -b ${OUT}_tmp_premask >/dev/null 2>&1

#### apply bias correction to original
${FSLDIR}/bin/fslmaths $IN -div ${OUT}_tmp_premask_bias ${OUT}_tmp_unbiased

#### get skull if asked for
if [ $skull ] ; then
  ${FSLDIR}/bin/bet2 ${OUT}_tmp_unbiased ${OUT}_tmp_unbiased_forskull $bet2opts
  bet2opts=`echo $bet2opts | sed 's/-s//g'`
  ${FSLDIR}/bin/immv ${OUT}_tmp_unbiased_forskull_skull ${OUT}_skull
fi

#### re-run betpremask
${FSLDIR}/bin/standard_space_roi ${OUT}_tmp_unbiased ${OUT}_tmp_unbiased_premask -b -d

#### re-run in robust mode
${FSLDIR}/bin/bet ${OUT}_tmp_unbiased_premask $OUT -m $bet2opts -R -d

# }}}
elif [ $variation = 8 ] ; then
    # {{{ Two-image extraction

if [ $verbose = 1 ] ; then
    echo "Starting multispectral BET"
fi

# run bet on IN2 in robust mode
${FSLDIR}/bin/bet $IN2 ${OUT}_tmp_I2_brain $bet2opts -m -n -R -d

# register IN2 to IN, outputting mask
${FSLDIR}/bin/flirt -dof 6 -cost mutualinfo -searchcost mutualinfo -in $IN2 -ref $IN -omat ${OUT}_tmp_I2_to_I.mat

# register mask to IN
${FSLDIR}/bin/flirt -in ${OUT}_tmp_I2_brain_mask -ref $IN -applyxfm -init ${OUT}_tmp_I2_to_I.mat -out ${OUT}_mask

# register IN2 skull to IN
if [ $skull = 1 ] ; then
	${FSLDIR}/bin/flirt -in ${OUT}_tmp_I2_brain_skull -ref $IN -applyxfm -init ${OUT}_tmp_I2_to_I.mat -out ${OUT}_skull
fi

# apply mask
if [ ! $dil = 0 ] ; then
    ${FSLDIR}/bin/imcp ${OUT}_mask ${OUT}_mask_dil
    while [ ! $dil = 0 ]; do
        ${FSLDIR}/bin/fslmaths ${OUT}_mask_dil -dilM ${OUT}_mask_dil -odt input
    done
    ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask_dil $OUT
else
    ${FSLDIR}/bin/fslmaths $IN -mas ${OUT}_mask $OUT
fi

if [ $fast = 1 ] ; then
    # register IN2 brain to IN space
    ${FSLDIR}/bin/flirt -in ${OUT}_tmp_I2_brain -ref ${IN} -applyxfm -init ${OUT}_tmp_I2_to_I.mat -out ${IN2}_brain_in_I
    # do brain/nonbrain segmentation
    ${FSLDIR}/bin/fast -N -S 2 -g -n 2 ${IN2}_brain_in_I ${IN} >> report.sienax 2>&1
    # apply mask to outputs
    ${FSLDIR}/bin/fslmaths ${IN}_seg_1 -mul ${OUT} ${OUT}
    ${FSLDIR}/bin/fslmaths ${IN}_seg_1 -mul ${OUT}_mask ${OUT}_mask
fi
# }}}
fi

# }}}

if [ $png = 1 ]; then
    slicer_nw -overlay "1 0 -c $IN -a ${OUT}_mask 0.9 1.1 ${OUT}_skull 0.9 1.1 overlay" -in overlay.nii.gz -out bet
fi

# {{{ cleanup temporary files

if [ $debug = 0 ] ; then
    /bin/rm -f ${OUT}_tmp*
fi

# }}}