#!/bin/sh
#   Copyright (C) 2012 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
#   under any specific conditions. Furthermore, the University disclaims
#   all responsibility for the use which is made of the Software. It
#   further disclaims any liability for the outcomes arising from using
#   the Software.
#   
#   The Licensee agrees to indemnify the University and hold the
#   University harmless from and against any and all claims, damages and
#   liabilities asserted by third parties (including claims for
#   negligence) which arise directly or indirectly from the use of the
#   Software or the sale of any products based on the Software.
#   
#   No part of the Software may be reproduced, modified, transmitted or
#   transferred in any form or by any means, electronic or mechanical,
#   without the express permission of the University. The permission of
#   the University is not required if the said reproduction, modification,
#   transmission or transference is done without financial return, the
#   conditions of this Licence are imposed upon the receiver of the
#   product, and all original and amended source code is included in any
#   transmitted product. You may be held legally responsible for any
#   copyright infringement that is caused or encouraged by your failure to
#   abide by these terms and conditions.
#   
#   You are not permitted under this Licence to use this Software
#   commercially. Use for which any financial return is received shall be
#   defined as commercial use, and includes (1) integration of all or part
#   of the source code or the Software into a product for sale or license
#   by or on behalf of Licensee to third parties or (2) use of the
#   Software or any derivative of it for research with the final aim of
#   developing software products for sale or license to a third party or
#   (3) use of the Software or any derivative of it for research with the
#   final aim of developing non-software products for sale or license to a
#   third party, or (4) use of the Software to provide any service to an
#   external organisation for which payment is received. If you are
#   interested in using the Software commercially, please contact Isis
#   Innovation Limited ("Isis"), the technology transfer company of the
#   University, to negotiate a licence. Contact details are:
#   innovation@isis.ox.ac.uk quoting reference DE/9564.
Usage () {
    echo ""
    echo "Usage: tbss_x <listOfScalarDirectories> <listOfVectorDirectories>"
    echo "e.g. tbss_x F1 F2 D1 D2"
    echo ""
    exit 1
}


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

echo [`date`] [`hostname`] [`uname -a`] [`pwd`] [$0 $@] >> .tbsslog

# session-specific random number
suf=$$

# here we count how many inputs we have
cnt=0
for d in $@ ; do    
    cnt=`echo "$cnt+1" | bc -l`
done

# only accept an even number of inputs
if [ $((cnt % 2)) -eq 1 ];then
    echo "Number of inputs must be even"
    echo "Exit without doing anything"
    exit 1
fi
let "cnt/=2"

# distinguish cases where tbss_reg -T and -n
postaffine=""
if [ -f FA/target_to_MNI152.mat ] ; then
    postaffine="--postmat=../FA/target_to_MNI152.mat"
    best=`cat FA/best.msf`
else
    best="target"
fi

# #######################################################
#            RESAMPLE SCALARS AND VECTORS
# #######################################################

echo "upsampling scalar images into standard space"
for ((i=1;i<=$cnt;i++)) ; do
     m=$1
     scalist="$scalist $m"
     cd $m
     echo $m
     for f in `$FSLDIR/bin/imglob *` ; do
 	ff=`$FSLDIR/bin/remove_ext $f`
 	echo $ff 
	if [ "$postaffine" != "" ];then
	    $FSLDIR/bin/applywarp -i $f -o ../FA/${ff}_to_target_${m} -r ../FA/target_to_MNI152 -w ../FA/${ff}_FA_to_${best}_warp $postaffine --interp=nn
	else
	    $FSLDIR/bin/applywarp -i $f -o ../FA/${ff}_to_target_${m} -r ../FA/target -w ../FA/${ff}_FA_to_${best}_warp $postaffine --interp=nn
	fi
     done
     cd ..
     shift
done 
echo "upsampling vector images into standard space"
for ((i=1;i<=$cnt;i++)) ; do
     m=$1
     veclist="$veclist $m"
     cd $m
     echo $m
     for f in `$FSLDIR/bin/imglob *` ; do
 	ff=`$FSLDIR/bin/remove_ext $f`
 	echo $ff 
  	if [ "$postaffine" != "" ];then
   	    convertwarp -o grot${suf}_${ff}_FA_to_target_warp_postmat -r ../FA/target_to_MNI152 -w ../FA/${ff}_FA_to_${best}_warp $postaffine
   	    $FSLDIR/bin/vecreg -i $f -o ../FA/${ff}_to_target_${m} -r ../FA/target_to_MNI152 -w grot${suf}_${ff}_FA_to_target_warp_postmat --interp=trilinear
 	    $FSLDIR/bin/imrm grot${suf}_${ff}_FA_to_target_warp_postmat 
   	else
   	    $FSLDIR/bin/vecreg -i $f -o ../FA/${ff}_to_target_${m} -r ../FA/target -w ../FA/${ff}_FA_to_target_warp --interp=trilinear
   	fi
     done
     cd ..
     shift
done 

# #####################################################
#         DONE RESAMPLING - NOW COMBINE SUBJECTS
# #####################################################

echo "merging scalar and vector images into single 4D images"
cd FA
for m in $scalist ; do
    echo $m
    $FSLDIR/bin/fslmerge -t ../stats/all_${m} `$FSLDIR/bin/imglob *_to_target_${m}.*`
    $FSLDIR/bin/fslmaths ../stats/all_${m} -mas ../stats/mean_FA_mask ../stats/all_${m}
done
for m in $veclist ; do
    echo $m
    i=0
    for xyz in x y z;do
	for f in `$FSLDIR/bin/imglob *_to_target_${m}.*` ; do
	    echo $f
	    fslroi ${f} `$FSLDIR/bin/remove_ext ${f}`_${xyz} ${i} 1
	done
	$FSLDIR/bin/fslmerge -t ../stats/all_${m}_${xyz} `$FSLDIR/bin/imglob *_to_target_${m}_${xyz}.*`
	$FSLDIR/bin/fslmaths ../stats/all_${m}_${xyz} -mas ../stats/mean_FA_mask ../stats/all_${m}_${xyz}
	$FSLDIR/bin/imrm `$FSLDIR/bin/imglob *_to_target_${m}_${xyz}.*`
	let "i+=1"
    done
done

# ####################################
#     SKELETON PROJECTION
# ####################################

echo "projecting onto mean FA skeleton"
cd ../stats
thresh=`cat thresh.txt`
for m in $scalist ; do
    echo $m
    $FSLDIR/bin/tbss_skeleton -i mean_FA -p $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_${m}_skeletonised -a all_$m    
     # save some disk space
    $FSLDIR/bin/imrm all_$m
done
for m in $veclist ; do
    for xyz in x y z ; do
  	echo $xyz
 	$FSLDIR/bin/tbss_skeleton -i mean_FA -p $thresh mean_FA_skeleton_mask_dst ${FSLDIR}/data/standard/LowerCingulum_1mm all_FA all_${m}_${xyz}_skeletonised -a all_${m}_$xyz
	# save some disk space
	$FSLDIR/bin/imrm all_${m}_$xyz
    done
done

# #########################################################
#    CREATE VARIOUS TEMPORARY TEXT FILES
# #########################################################

echo "creating files and textfiles for voxewise reassignments"
/bin/rm -f .scalist*.txt
for m in $scalist ; do
    $FSLDIR/bin/fslsplit all_${m}_skeletonised all_${m}_skeletonised_
    for im in `$FSLDIR/bin/imglob all_${m}_skeletonised_????.*` ; do
	n=`echo $im | sed s/all_"${m}"_skeletonised_//g`
	echo $im >> .scalist${n}.txt
    done
done
/bin/rm -f .veclist*.txt
for m in $veclist ; do
    for xyz in x y z ; do
	echo $xyz
	$FSLDIR/bin/fslsplit all_${m}_${xyz}_skeletonised  all_${m}_${xyz}_skeletonised_ 
    done
    for im in `$FSLDIR/bin/imglob all_${m}_x_skeletonised_????.*` ; do
	n=`echo $im | sed s/all_"${m}"_x_skeletonised_//g`
	$FSLDIR/bin/fslmerge -t all_${m}_skeletonised_$n all_${m}_x_skeletonised_$n all_${m}_y_skeletonised_$n all_${m}_z_skeletonised_$n
	
	echo all_${m}_skeletonised_$n >> .veclist${n}.txt
    done
done

# #############################################################
#   VOXELWISE REASSIGNMENTS (A.K.A. SPATIAL REGULARISATION)
# #############################################################

echo "Voxelwise reassignments"
for list in .scalist????.txt ; do
    n=`echo $list | sed s/.scalist//g | sed s/.txt//g`
    subjscalist=.scalist${n}.txt
    subjveclist=.veclist${n}.txt    
    # calculate initmask (places where there are no crossing fibres stay the same)
    fslmaths mean_FA_skeleton_mask mfibresmask
    for f in `cat $subjscalist` ; do
	fslmaths $f -thr .1 -bin -mas mfibresmask mfibresmask
    done
    fslmaths mfibresmask -sub 1 -abs -mas mean_FA_skeleton_mask -bin initmask$n
    $FSLDIR/bin/swap_voxelwise --mode=voxels -s $subjscalist -v $subjveclist --initmask=initmask$n -m mean_FA_skeleton_mask -b voxelwise_realigned_$n 
    $FSLDIR/bin/imrm all_*_skeletonised_${n}.*
done
# save some disk space
$FSLDIR/bin/imrm all_*_{x,y,z}_skeletonised.*

# ########################################################
#    CREATE MORE TEMPORARY TEXT FILES
# ########################################################

echo "creating textfiles for subjectwise reassignments"
rm -f .scalist.txt
for m in $scalist ; do
    echo .scalist${m}_subjects.txt >> .scalist.txt
done
rm -f .veclist.txt
for m in $veclist ; do
    echo .veclist${m}_subjects.txt >> .veclist.txt
done
for i in .scalist????.txt ; do
    n=`echo $i | sed s/.scalist//g | sed s/.txt//g`
    mm=1
    for m in $scalist ; do
	echo voxelwise_realigned_${n}_scalars${mm} >> .scalist${m}_subjects.txt
	let "mm+=1"
    done
    mm=1
    for m in $veclist ; do
	echo voxelwise_realigned_${n}_vectors${mm} >> .veclist${m}_subjects.txt
	let "mm+=1"
    done
done

# ##############################################################
#     SUBJECTWISE REASSIGNMENTS 
# ##############################################################

echo "Subjectwise reassignments"
$FSLDIR/bin/swap_subjectwise -m mean_FA_skeleton_mask -r .veclist.txt -f .scalist.txt -b subjectwise_realigned -v

# ########################################################
#     FINAL STEP + CLEANUP
# ########################################################

echo "merging final results"
i=1
for m in $scalist ; do
    echo $m
    $FSLDIR/bin/fslmerge -t all_${m}_x_skeletonised subjectwise_realigned_voxelwise_realigned_????_scalars${i}.*
    let "i+=1"
done
# save some disk space
for m in $scalist;do 
    $FSLDIR/bin/imrm all_${m}_skeletonised
done
$FSLDIR/bin/imrm *voxelwise_realigned*
rm .scalist*.txt .veclist*.txt
rm initmask????.*

cd ..
echo "Now run randomise on the newly created files: all_F1_x_skeletonised etc."