#!/bin/sh

#   first_flirt - initial standard space registration before running the main part of FIRST
#
#   Brian Patenaude, Courtney Bishop and Mark Jenkinson, FMRIB Image Analysis Group
#
#   Copyright (C) 2006-2010 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
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#   or that it will be suitable for any particular purpose or for use
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export LC_NUMERIC=C

Usage() {
    echo ""
    echo "Usage:   first_flirt <input_image> <output_basename> [options]"
    echo ""
    echo "-b        : input is already brain extracted"
    echo "-d        : debug (don't delete intermediate files)"
    echo "-inweight : use a weighting mask on the first registration"
    echo "-strucweight <maskimage> : use a specific structure weighting mask (in standard space) for an (optional) third-stage registration step"
    echo "-cort : use a weighting mask of the whole brain on the first registration (for specific models)"
    echo "-cost <costfunction> : specify the costfunction to be used by all FLIRT calls"
    echo ""
    echo "e.g.:    first_flirt subject10rawT1 subject10rawT1_to_std_sub"
    echo ""
    exit 1
}

[ "$2" = "" ] && Usage
[ `${FSLDIR}/bin/imtest $1` = 0 ] && Usage
A=`${FSLDIR}/bin/remove_ext $1`
B=`${FSLDIR}/bin/remove_ext $2`
shift 2
refim=MNI152_T1_1mm
debug=0
doCortAlignment=0

inweightCom=""
strucweight=""
costCom=""
while [ _$1 != _ ] ; do
    if [ $1 = -d ] ; then
        debug=1
        shift
    elif [ $1 = -b ] ; then
	refim=MNI152_T1_1mm_brain
        shift
	elif [ $1 = "-cort" ] ; then
		 doCortAlignment=1
		 shift
    elif [ $1 = -cost ] ; then
        costCom="${1} ${2}"
        shift 2
    elif [ $1 = -inweight ] ; then
        inweightCom="${1} ${2}"
        shift 2
    elif [ $1 = -strucweight ] ; then
        strucweight="${2}"
        shift 2
    fi
done

echo "initial registration $doCortAlignment"
${FSLDIR}/bin/flirt -in $A -out ${B}_tmp_stage1 -ref ${FSLDIR}/data/standard/${refim} -omat ${B}_tmp_stage1.mat $inweightCom $costCom

echo "Stage 2: use subcortical mask"
#do subcortical alignment
${FSLDIR}/bin/flirt -in ${B}_tmp_stage1 -out ${B}_tmp_stage2 -ref ${FSLDIR}/data/standard/${refim} -omat ${B}_tmp_stage2.mat -nosearch -refweight ${FSLDIR}/data/standard/MNI152lin_T1_1mm_subbr_mask $costCom
${FSLDIR}/bin/convert_xfm -omat ${B}.mat -concat ${B}_tmp_stage2.mat ${B}_tmp_stage1.mat 


#generate registered images
${FSLDIR}/bin/flirt -in ${A} -out ${B} -ref ${FSLDIR}/data/standard/${refim} -applyxfm -init ${B}.mat 

if [ $doCortAlignment -eq 1 ] ; then 
    #do hemisphere/cerebellum alignment
    echo "Alternate Stage 2: Use brain mask"
    ${FSLDIR}/bin/flirt -in ${B}_tmp_stage1 -out ${B}_tmp_cort_stage2 -ref ${FSLDIR}/data/standard/${refim} -omat ${B}_tmp_cort_stage2.mat -nosearch -refweight ${FSLDIR}/data/standard/MNI152_T1_1mm_first_brain_mask.nii.gz $costCom
    
    ${FSLDIR}/bin/convert_xfm -omat ${B}_cort.mat -concat ${B}_tmp_cort_stage2.mat ${B}_tmp_stage1.mat 
    
    ${FSLDIR}/bin/flirt -in ${A} -out ${B}_cort -ref ${FSLDIR}/data/standard/${refim} -applyxfm -init ${B}_cort.mat
fi

if [ X$strucweight != X ] ; then
    ${FSLDIR}/bin/flirt -in ${A} -ref ${FSLDIR}/data/standard/${refim} -init ${B}.mat -out ${B} -omat ${B}_tmp_stage3.mat -refweight ${strucweight} -nosearch $costCom
    cp ${B}_tmp_stage3.mat ${B}.mat
fi



if [ $debug = 0 ] ; then
  /bin/rm ${B}_tmp_stage*
fi

exit 0

