#!/bin/sh

#   feat_gm_prepare - take structurals and prepare GM-density-based higher-level FEAT confound regressor
#
#   Stephen Smith, FMRIB Image Analysis Group
#
#   Copyright (C) 2008 University of Oxford
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#   Imaging of the Brain), Department of Clinical Neurology, Oxford
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#  -> find all _original_ brain-extracted structurals (outside FEAT directories)
#     -> run FAST and keep GM only
#  -> find warp files from FEAT directories and apply to GM
#  -> concatenate -> 4D -> demean

Usage() {
    echo "Usage: feat_gm_prepare <4D-GM-output> <list of first-level FEAT output directories>"
    echo "Note: these all have to have had registration completed in them"
    exit 1
}

[ "$2" = "" ] && Usage

OUT=`${FSLDIR}/bin/remove_ext $1`
shift

# estimate how much we will need to smooth the structurals by, in the end
echo Estimating smoothness of functional data...
func_smoothing=`grep "fmri(smooth)" $1/design.fsf | tail -n 1 | awk '{print $3}'`
standard_space_resolution=`${FSLDIR}/bin/fslval $1/reg/standard pixdim1`
struc_smoothing=`${FSLDIR}/bin/match_smoothing $1/example_func $func_smoothing $1/reg/highres $standard_space_resolution`
echo Structural-space GM PVE images will be smoothed by sigma=${struc_smoothing}mm to match the standard-space functional data

# run segmentations, smoothing, and standard-space transformation
CWD=`pwd`
/bin/rm -rf ${OUT}.log
mkdir ${OUT}.log
for f in $@ ; do
  ${FSLDIR}/bin/fslecho "cd ${f}/reg; $FSLDIR/bin/fast -R 0.3 -H 0.1 -o grot highres; $FSLDIR/bin/immv grot_pve_1 highresGM; /bin/rm grot*; $FSLDIR/bin/fslmaths highresGM -s $struc_smoothing highresGMs; \c" >> ${OUT}.log/featseg1
  if [ `${FSLDIR}/bin/imtest ${f}/reg/highres2standard_warp` = 1 ] ; then
      ${FSLDIR}/bin/fslecho "${FSLDIR}/bin/applywarp --ref=standard --in=highresGMs --out=highresGMs2standard --warp=highres2standard_warp; \c" >> ${OUT}.log/featseg1
  else
      ${FSLDIR}/bin/fslecho "${FSLDIR}/bin/flirt -in highresGMs -out highresGMs2standard -ref standard -applyxfm -init highres2standard.mat; \c" >> ${OUT}.log/featseg1
  fi 
  echo "cd $CWD" >> ${OUT}.log/featseg1
  GMlist="$GMlist ${f}/reg/highresGMs2standard"
done
chmod a+x ${OUT}.log/featseg1
echo Running segmentations...
featseg1_id=`$FSLDIR/bin/fsl_sub -T 30 -N featseg1 -l ./${OUT}.log -t ./${OUT}.log/featseg1`

# concatenate and de-mean GM images
echo "${FSLDIR}/bin/fslmerge -t $OUT $GMlist; ${FSLDIR}/bin/fslmaths $OUT -Tmean -mul -1 -add $OUT $OUT" > ${OUT}.log/featseg2
echo Running concatenation of all standard space GM images
$FSLDIR/bin/fsl_sub -T 10 -N featseg2 -l ./${OUT}.log -j $featseg1_id -t ./${OUT}.log/featseg2 > /dev/null

echo "Once this is all complete you may want to add additional smoothing to $OUT in order to ameliorate possible effects of mis-registrations between functional and structural data, and to lessen the effect of the additional confound regressors"