#!/bin/sh -e

#   fsl_motion_outliers - detect motion outliers (timepoints) and create EVs to 
#	eliminate these images from the GLM
#
#   Mark Jenkinson, FMRIB Image Analysis Group
#
#   Copyright (C) 2008 University of Oxford
#
#   Part of FSL - FMRIB's Software Library
#   http://www.fmrib.ox.ac.uk/fsl
#   fsl@fmrib.ox.ac.uk
#   
#   Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance
#   Imaging of the Brain), Department of Clinical Neurology, Oxford
#   University, Oxford, UK
#   
#   
#   LICENCE
#   
#   FMRIB Software Library, Release 5.0 (c) 2012, The University of
#   Oxford (the "Software")
#   
#   The Software remains the property of the University of Oxford ("the
#   University").
#   
#   The Software is distributed "AS IS" under this Licence solely for
#   non-commercial use in the hope that it will be useful, but in order
#   that the University as a charitable foundation protects its assets for
#   the benefit of its educational and research purposes, the University
#   makes clear that no condition is made or to be implied, nor is any
#   warranty given or to be implied, as to the accuracy of the Software,
#   or that it will be suitable for any particular purpose or for use
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#   the Software.
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export LC_NUMERIC=C

usage()
{
    echo "Usage: `basename $0` -i <input 4D image> -o <output confound file> [options]"
    echo "   (old version)  `basename $0` <unfiltered 4D image> <number of dummy scans> <output confound file>"
    echo " "
    echo "Options: -m <mask image>      use supplied mask image for calculating metric"
    echo "         -s <filename>        save metric values (e.g. DVARS) as text into specified file"
    echo "         -p <filename>        save metric values (e.g. DVARS) as a graphical plot (png format)"
    echo "         -t <path>            [Optional] Path to the location where temporary files should be created. Defaults to /tmp"
    echo "         --refrms             use RMS intensity difference to reference volume as metric [default metric]"
    echo "         --dvars              use DVARS as metric"
    echo "         --refmse             Mean Square Error version of --refrms (used in original version of fsl_motion_outliers)"
    echo "         --fd                 use FD (framewise displacement) as metric"
    echo "         --fdrms              use FD with RMS matrix calculation as metric"
    echo "         --thresh=<val>       specify absolute threshold value (otherwise use box-plot cutoff = P75 + 1.5*IQR)"
    echo "         --nomoco             do not run motion correction (assumed already done)"
    echo "         --dummy=<val>        number of dummy scans to delete (before running anything and creating EVs)"
    echo "         -v                   verbose mode"
    echo " "
}


get_opt1() {
    arg=`echo $1 | sed 's/=.*//'`
    echo $arg
}


get_arg1() {
    if [ X`echo $1 | grep '='` = X ] ; then 
	echo "Option $1 requires an argument" 1>&2
	exit 1
    else 
	arg=`echo $1 | sed 's/.*=//'`
	if [ X$arg = X ] ; then
	    echo "Option $1 requires an argument" 1>&2
	    exit 1
	fi
	echo $arg
    fi
}


get_arg2() {
    if [ X$2 = X ] ; then
	echo "Option $1 requires an argument" 1>&2
	exit 1
    fi
    echo $2
}


# default options
mask=
abs_thresh=
do_moco=yes;
use_abs_thresh=no;
metric=refrms;
do_make_mask=yes;
verbose=no;
ndel=0;
cleanup=yes;
sqrtcom="-sqrt";
savefile="";
plotfile="";
tmppath=""

if [ $# -eq 0 ] ; then usage; exit 0; fi
if [ $# -lt 3 ] ; then usage; exit 1; fi
niter=0;
while [ $# -ge 1 ] ; do
    niter=`echo $niter + 1 | bc`;
    iarg=`get_opt1 $1`;
    case "$iarg"
	in
	-i)
	    mcf=`get_arg2 $1 $2`;
	    shift 2;;
	-o)
	    outfile=`get_arg2 $1 $2`;
	    shift 2;;
	-m)
	    do_make_mask=no;
	    mask=`get_arg2 $1 $2`;
	    shift 2;;
	-s)
	    savefile=`get_arg2 $1 $2`;
	    shift 2;;
	-p)
	    plotfile=`get_arg2 $1 $2`;
	    shift 2;;
	-t)
	    tmppath=`get_arg2 $1 $2`;
	    shift 2;;
	--nomoco)
	    do_moco=no;
	    shift;;
	--nocleanup)
	    cleanup=no;
	    shift;;
	--refrms)
	    metric=refrms;
	    shift;;
	--refmse)
	    metric=refrms;
	    sqrtcom=""
	    shift;;
	--dvars)
	    metric=dvars;
	    shift;;
	--fd)
	    metric=fd;
	    shift;;
	--fdrms)
	    metric=fdrms;
	    shift;;
	--dummy)
	    ndel=`get_arg1 $1`;
	    shift;;
	--thresh)
	    use_abs_thresh=yes;
	    abs_thresh=`get_arg1 $1`;
	    shift;;
	-v)
	    verbose=yes; 
	    shift;;
	-h)
	    usage;
	    exit 0;;
	*)
	    if [ `echo $1 | sed 's/^\(.\).*/\1/'` = "-" ] ; then 
		if [ $niter = 1 -a $# -eq 3 ] ; then
		    mcf=$1;
		    ndel=$2;
		    outfile=$3;
		    shift 2;
		else
		    usage;
		    echo "Unrecognised option $1" 1>&2
		    exit 1
		fi
	    fi
	    shift;;
    esac
done




#### PARSE OPTIONS
mcf=`$FSLDIR/bin/remove_ext $mcf`;
outfile=`$FSLDIR/bin/remove_ext $outfile`;
if [ X$ndel = X ] ; then ndel=0; fi
if [ $do_make_mask = no ] ; then mask=`$FSLDIR/bin/remove_ext $mask`; fi
if [ $verbose = yes ] ; then echo "mcf = $mcf ; outfile = $outfile ; ndel = $ndel ; mask = $mask ; do_moco = $do_moco ; thresh = $abs_thresh ; use_thresh = $use_abs_thresh ; metric = $metric"; fi

# sanity checks
if [ $do_moco = no ] ; then
  if [ $metric = fd -o $metric = fdrms ] ; then
      echo "Cannot use metrics FD or FDRMS without motion correction";
      exit 2;
  fi
fi

# output dir creation
outdir=`$FSLDIR/bin/tmpnam`;

# If there is a preferred location for temporary files, use that, else default to /tmp (set by tmpnam)
if [ X${tmppath} != X ] ; then
  outdir=${tmppath}/`basename ${outdir}` 
fi

if [ X${outdir} = X ] ; then
  echo "Could not create tmp directory"
  exit 2;
fi
mkdir ${outdir}_mc


#### DELETE DUMMY SCANS
nvol=`$FSLDIR/bin/fslval $mcf dim4`;
nvol=`echo $nvol - $ndel | bc`;
if [ $ndel -gt 0 ] ; then
    $FSLDIR/bin/fslroi $mcf ${outdir}_mc/invol $ndel $nvol
    mcf=${outdir}_mc/invol
fi


#### MOTION CORRECTION
refnum=`$FSLDIR/bin/fslval $mcf dim4`;
refnum=`echo $refnum / 2 | bc`;
if [ $do_moco = yes ] ; then
    # run mcflirt
    $FSLDIR/bin/mcflirt -in $mcf -out ${outdir}_mc/fmri_mcf -mats -plots -refvol $refnum -rmsrel -rmsabs
else 
    $FSLDIR/bin/imcp $mcf ${outdir}_mc/fmri_mcf
fi
mcf=${outdir}_mc/fmri_mcf

tmax=`$FSLDIR/bin/fslval ${mcf} dim4`;
tmax1=`echo $tmax - 1 | bc`;


#### MASK and calculate intensity normalisation values
if [ $do_make_mask = yes ] ; then
    mask=${outdir}_mc/mask
    thr2=`$FSLDIR/bin/fslstats $mcf -P 2`;
    thr98=`$FSLDIR/bin/fslstats $mcf -P 98`;
    robthr=`echo "$thr2 + 0.1 * ( $thr98 - $thr2 )" | bc -l`;
    $FSLDIR/bin/fslmaths $mcf -Tmean -thr $robthr -bin $mask
else
    $FSLDIR/bin/fslmaths $mask -thr 0.5 -bin ${outdir}_mc/mask
    mask=${outdir}_mc/mask
fi
# normalise by percentage of mask voxels and by median value within the brain
brainmed=`$FSLDIR/bin/fslstats ${mcf} -k ${mask} -P 50`;
maskmean=`$FSLDIR/bin/fslstats ${mask} -m`;
if [ $verbose = yes ] ; then echo "brainmed = $brainmed ; maskmean = $maskmean" ; fi


#### CALCULATE METRIC 
#  The output is a 1x1x1x(N-1) nifti image called res_mse_diff
#  The jth point represents motion changes between timepoints j and (j+1)
#  After this the code will add a point at the start
if [ $metric = dvars ] ; then
    # generate DVARS
    $FSLDIR/bin/fslroi $mcf ${mcf}1 0 $tmax1
    $FSLDIR/bin/fslroi $mcf ${mcf}2 1 $tmax1
    $FSLDIR/bin/fslmaths ${mcf}2 -sub ${mcf}1 -mas ${mask} -sqr -Xmean -Ymean -Zmean -div $maskmean $sqrtcom ${outdir}_mc/res_mse_diff -odt float
    $FSLDIR/bin/fslmaths ${outdir}_mc/res_mse_diff -div $brainmed -mul 1000 ${outdir}_mc/res_mse_diff

elif [ $metric = refrms ] ; then
    # generate example functional image
    $FSLDIR/bin/fslroi $mcf ${outdir}_mc/exf $refnum 1
    exf=${outdir}_mc/exf
    # generate residual mean square error (average across each 3D volume)
    if [ $verbose = yes ] ; then echo "Generating residual mean square error"; fi
    $FSLDIR/bin/fslmaths $mcf -sub $exf -mas ${mask} -div $brainmed -sqr -Xmean -Ymean -Zmean -div $maskmean $sqrtcom ${outdir}_mc/res_mse -odt float
    # now form difference (to remove slow trends - still obvious in mse)
    $FSLDIR/bin/fslroi ${outdir}_mc/res_mse ${outdir}_mc/res_mse0 0 1 0 1 0 1 0 $tmax1
    $FSLDIR/bin/fslroi ${outdir}_mc/res_mse ${outdir}_mc/res_mse1 0 1 0 1 0 1 1 $tmax1
    $FSLDIR/bin/fslmaths ${outdir}_mc/res_mse1 -sub ${outdir}_mc/res_mse0 -abs ${outdir}_mc/res_mse_diff

elif [ $metric = fd ] ; then
    ${FSLDIR}/bin/fslascii2img ${outdir}_mc/fmri_mcf.par 1 1 $tmax 6 1 1 1 1 ${outdir}_mc/res_mse_par
    ${FSLDIR}/bin/fslroi ${outdir}_mc/res_mse_par ${outdir}_mc/res_mse_par_rot_full 0 3 
    ${FSLDIR}/bin/fslroi ${outdir}_mc/res_mse_par ${outdir}_mc/res_mse_par_trans_full 3 3
    # calculate time differences of all parameters
    ${FSLDIR}/bin/fslroi ${outdir}_mc/res_mse_par_rot_full ${outdir}_mc/res_mse_par_rot0 0 1 0 1 0 $tmax1
    ${FSLDIR}/bin/fslroi ${outdir}_mc/res_mse_par_rot_full ${outdir}_mc/res_mse_par_rot1 0 1 0 1 1 $tmax1
    ${FSLDIR}/bin/fslmaths ${outdir}_mc/res_mse_par_rot1 -sub ${outdir}_mc/res_mse_par_rot0 ${outdir}_mc/res_mse_par_rot
    ${FSLDIR}/bin/fslroi ${outdir}_mc/res_mse_par_trans_full ${outdir}_mc/res_mse_par_trans0 0 1 0 1 0 $tmax1
    ${FSLDIR}/bin/fslroi ${outdir}_mc/res_mse_par_trans_full ${outdir}_mc/res_mse_par_trans1 0 1 0 1 1 $tmax1
    ${FSLDIR}/bin/fslmaths ${outdir}_mc/res_mse_par_trans1 -sub ${outdir}_mc/res_mse_par_trans0 ${outdir}_mc/res_mse_par_trans
    # multiply rots (radians) by 50mm and add up with abs translations to get FD in Power et al, 2011
    ${FSLDIR}/bin/fslmaths ${outdir}_mc/res_mse_par_rot -abs -mul 50 ${outdir}_mc/res_mse_par_rot
    ${FSLDIR}/bin/fslmaths ${outdir}_mc/res_mse_par_rot -Tmean -mul 3 ${outdir}_mc/res_mse_par_rotsum
    ${FSLDIR}/bin/fslmaths ${outdir}_mc/res_mse_par_trans -abs -Tmean -mul 3 ${outdir}_mc/res_mse_par_transsum
    ${FSLDIR}/bin/fslmaths ${outdir}_mc/res_mse_par_transsum -add ${outdir}_mc/res_mse_par_rotsum ${outdir}_mc/res_mse_diffZ
    ${FSLDIR}/bin/fsl2ascii ${outdir}_mc/res_mse_diffZ ${outdir}_mc/res_mse_diff.txt
    grep [0-9] ${outdir}_mc/res_mse_diff.txt0* > ${outdir}_mc/res_mse_diff.txt
    ${FSLDIR}/bin/fslascii2img ${outdir}_mc/res_mse_diff.txt 1 1 1 $tmax1 1 1 1 1 ${outdir}_mc/res_mse_diff

elif [ $metric = fdrms ] ; then
    ${FSLDIR}/bin/fslascii2img ${outdir}_mc/fmri_mcf_rel.rms 1 1 1 $tmax1 1 1 1 1 ${outdir}_mc/res_mse_diff

else
    echo "Metric $metric is not supported"
    exit 1;
fi


### SAVE VALUES AND/OR PLOT
# Need to add a zero at the start in each case (see full explanation below)
if [ X${savefile} != X ] ; then
    $FSLDIR/bin/fsl2ascii ${outdir}_mc/res_mse_diff ${outdir}_mc/vals.txt
    echo "0" > ${savefile}
    cat ${outdir}_mc/vals.txt[0-9]* | grep [0-9] >> ${savefile}
    rm ${outdir}_mc/vals.txt[0-9]*
fi
if [ X${plotfile} != X ] ; then
    $FSLDIR/bin/fsl2ascii ${outdir}_mc/res_mse_diff ${outdir}_mc/vals.txt
    echo "0" > ${outdir}_mc/vals.txt
    cat ${outdir}_mc/vals.txt[0-9]* | grep [0-9] >> ${outdir}_mc/vals.txt
    rm ${outdir}_mc/vals.txt[0-9]*
    $FSLDIR/bin/fsl_tsplot -i ${outdir}_mc/vals.txt -t "Motion outlier metric: $metric" -x "time" -y "metric value" -o ${plotfile}
fi

#### CALCULATING OUTLIERS
if [ $verbose = yes ] ; then echo "Calculating outliers"; fi
# Calculate thresholds
if [ $use_abs_thresh = yes ] ; then
    threshv=$abs_thresh
else
    # calculate box-plot outlier limits
    pv=`$FSLDIR/bin/fslstats ${outdir}_mc/res_mse_diff -p 25 -p 75`;
    p25=`echo $pv | awk '{ print $1 }'`;
    p75=`echo $pv | awk '{ print $2 }'`;
    threshv=`echo "$p75 + 1.5 * ( $p75 - $p25 )" | bc -l`
fi
if [ $verbose = yes ] ; then echo "Range of metric values: `$FSLDIR/bin/fslstats ${outdir}_mc/res_mse_diff -R`" ; fi

$FSLDIR/bin/fslmaths ${outdir}_mc/res_mse_diff -thr $threshv -bin ${outdir}_mc/outliers
# Add a point at the start to fix timing (as inputs from previous section contain forward diffs)
# If there is a step change then the induced intensity artefact will be associated with the first timepoint _after_ the change, so a change between timepoints j and (j+1) should create a confound spike at timepoint j+1
#      e.g.  3 1 2 696 1  =>  0 0 1 1 for res_mse 
#              => 0 0 0 1 0  and   0 0 0 0 1  as EVs 
# the following lines put a zero at the start of outliers
$FSLDIR/bin/fslroi ${outdir}_mc/outliers ${outdir}_mc/one 0 1 0 1 0 1 0 1
$FSLDIR/bin/fslmaths ${outdir}_mc/one -mul 0 ${outdir}_mc/zero
$FSLDIR/bin/fslmerge -t ${outdir}_mc/outliers ${outdir}_mc/zero ${outdir}_mc/outliers
nmax=`$FSLDIR/bin/fslstats ${outdir}_mc/outliers -V | awk '{ print $1 }'`
if [ $verbose = yes ] ; then echo "Found $nmax outliers over $threshv"; fi


#### GENERATE EVs (one spike per EV)
if [ $verbose = yes ] ; then echo "Generating EVs"; fi
# get index values of all non-zero events in res_mse
if [ -f $outfile ] ; then rm -f $outfile ; fi
nvals="";
n=0;
while [ $n -lt $tmax ] ; do
  $FSLDIR/bin/fslmaths ${outdir}_mc/outliers -roi 0 1 0 1 0 1 $n 1 ${outdir}_mc/stp
  val=`$FSLDIR/bin/fslstats ${outdir}_mc/stp -V | awk '{ print $1 }'`;
  if [ $val -gt 0 ] ; then
      nvals="$nvals $n";
      $FSLDIR/bin/fslmeants -i ${outdir}_mc/stp -o ${outdir}_mc/singleev;
      if [ -f $outfile ] ; then	  
	  paste -d ' ' $outfile ${outdir}_mc/singleev > ${outfile}2
	  cp ${outfile}2 $outfile
	  rm -f ${outfile}2
      else
	  cp ${outdir}_mc/singleev $outfile
      fi
  fi
  n=`echo "$n + 1" | bc`;
done

if [ $verbose = yes ] ; then echo "Found spikes at $nvals"; fi


# CLEANUP
if [ $cleanup = yes ] ; then
    if [ X${outdir}_mc != X ] ; then
	if [ -d ${outdir}_mc ] ; then
	    rm -rf ${outdir}_mc
	fi
	if [ X${outdir} != X ] ; then
           if [ -e ${outdir} ] ; then
 	     rm ${outdir}
 	   fi  
	fi
    fi
fi