#!/bin/tcsh -f
# fs-synthmorph-reg - sources
if(-e $FREESURFER_HOME/sources.csh) then
  source $FREESURFER_HOME/sources.csh
endif

if($?FSMNI152DIR == 0) setenv FSMNI152DIR $FREESURFER/average/mni_icbm152_nlin_asym_09c
unsetenv FS_LOCAL_PYTHONPATH

set VERSION = '$Id$';
set scriptname = `basename $0`

set outdir = ();
set subject = ();
set m3z = ();
set m3zinv = ()
set invol = ()
set targvol = ()
set lta2 = ()
set vgthresh = 1e-4
set StripInput = 0
set StripTarget = 0
set ReRun = 0

set threads = 1
set ForceUpdate = 0
set antsreg = antsRegistrationSyNQuick.sh
set UseQuick = 0
set CropInput = 1
set CropTarget = 1
set MNITarget = 1
# Synthmorph uses 1mm internally, so useing target res=1mm does not
# slow things down or take more mem and it is probably gives a little
# bit better registration.  ANTs speed and performance will be
# affected.
set MNITargetRes = 1.0mm 
set MNIOutputRes = 1.0mm
set DoCBIG = 0
set DoTest = 0
set dim = 3
set UseAnts = 0 # 0 means use synthmorph
set ComputeInverse = 1
set PitStr = ""
set AffineOnly = 0

set tmpdir = ();
set cleanup = 1;
set LF = ();

set inputargs = ($argv);
set PrintHelp = 0;
if($#argv == 0) goto usage_exit;
set n = `echo $argv | grep -e -help | wc -l` 
if($n != 0) then
  set PrintHelp = 1;
  goto usage_exit;
endif
set n = `echo $argv | grep -e -version | wc -l` 
if($n != 0) then
  echo $VERSION
  exit 0;
endif
goto parse_args;
parse_args_return:
goto check_params;
check_params_return:

set StartTime = `date`;
set tSecStart = `date '+%s'`;
set year  = `date +%Y`
set month = `date +%m`
set day   = `date +%d`
set hour   = `date +%H`
set min    = `date +%M`

if($#outdir) then
  mkdir -p $outdir/log
else
  set outdir = `dirname $m3z`
  mkdir -p $outdir
endif
pushd $outdir > /dev/null
set outdir = `pwd`;
popd > /dev/null

if($#tmpdir == 0) set tmpdir = $outdir/tmp
mkdir -p $tmpdir

# Set up log file
if($#LF == 0) set LF = $outdir/log/fs-synthmorph-reg.Y$year.M$month.D$day.H$hour.M$min.log
if($LF != /dev/null) rm -f $LF
echo "Log file for fs-synthmorph-reg" >> $LF
date  | tee -a $LF
echo "" | tee -a $LF
echo "setenv SUBJECTS_DIR $SUBJECTS_DIR" | tee -a $LF
echo "cd `pwd`"  | tee -a $LF
echo $0 $inputargs | tee -a $LF
ls -l $0  | tee -a $LF
echo "" | tee -a $LF
cat $FREESURFER_HOME/build-stamp.txt | tee -a $LF
echo $VERSION | tee -a $LF
uname -a  | tee -a $LF
echo "pid $$" | tee -a $LF
if($?PBS_JOBID) then
  echo "pbsjob $PBS_JOBID"  >> $LF
endif
if($?SLURM_JOB_ID) then
  echo SLURM_JOB_ID $SLURM_JOB_ID >> $LF
endif

#========================================================
# Note: Ants might not be deterministc with threads
setenv OMP_NUM_THREADS $threads
setenv ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS $threads

if($StripInput) then
  #set involstripped = $tmpdir/invol.stripped.nii.gz # breaks header
  set involstripped = $tmpdir/invol.stripped.mgz
  set ud = `UpdateNeeded $involstripped $invol`
  if($ud || $ForceUpdate) then
    set cmd = (mri_synthstrip -i $invol -o $involstripped  -t $threads)
    echo $cmd | tee -a $LF
    $cmd | tee -a $LF
    if($status) exit 1
  endif
  set invol = $involstripped
endif
if($StripTarget) then
  #set targvolstripped = $tmpdir/targ.stripped.nii.gz  # breaks header
  set targvolstripped = $tmpdir/targ.stripped.mgz
  set ud = `UpdateNeeded $targvolstripped $targvol`
  if($ud || $ForceUpdate) then
    set cmd = (mri_synthstrip -i $targvol -o $targvolstripped -t $threads)
    echo $cmd | tee -a $LF
    $cmd | tee -a $LF
    if($status) exit 1
  endif
  set targvol = $targvolstripped
endif

if($CropInput) then # Crop for speed
  # Input volume
  set involcrop = $tmpdir/invol.crop.nii.gz
  set ud = `UpdateNeeded $involcrop $invol`
  if($ud || $ForceUpdate) then
    set cmd = (mri_mask -bb 3 $invol $invol $involcrop)
    echo $cmd | tee -a $LF
    $cmd | tee -a $LF
    if($status) exit 1
  endif
  # To get back to the full FoV
  set regcroptoinvol = $tmpdir/reg.crop-to-invol.lta
  set ud = `UpdateNeeded $regcroptoinvol $involcrop $invol`
  if($ud || $ForceUpdate) then
    set cmd = (lta_convert --inlta identity.nofile --src $involcrop \
      --trg $invol  --outlta $regcroptoinvol)
    echo $cmd | tee -a $LF
    $cmd |& tee -a $LF
    if($status) exit 1
  endif
else
  set involcrop = $invol
  set regcroptoinvol = ()
endif

if($CropTarget) then
  if(! $MNITarget) then
    # Target vol
    set targvolcrop = $tmpdir/targvol.crop.nii.gz
    set ud = `UpdateNeeded $targvolcrop $targvol`
    if($ud || $ForceUpdate) then
      set cmd = (mri_mask -crop 3 $targvol $targvol $targvolcrop)
      echo $cmd | tee -a $LF
      $cmd | tee -a $LF
      if($status) exit 1
    endif
    # To get back to the full FoV
    set regcroptotarg = $tmpdir/reg.crop-to-targ.lta
    set ud = `UpdateNeeded $regcroptotarg $targvolcrop $targvol`
    if($ud || $ForceUpdate) then
      set cmd = (lta_convert --inlta identity.nofile --src $targvolcrop \
        --trg $targvol  --outlta $regcroptotarg)
      echo $cmd | tee -a $LF
      $cmd |& tee -a $LF
      if($status) exit 1
    endif
  else
    set targvolcrop   = $FSMNI152DIR/reg-targets/mni152.${MNITargetRes}$PitStr.cropped.nii.gz
    set regcroptotarg = $FSMNI152DIR/reg-targets/reg.${MNITargetRes}.cropped.to.${MNIOutputRes}.lta
    # Note that lta does not have PitStr
  endif
else
  set targvolcrop = $targvol
  set regcroptotarg = ()
endif

if($UseAnts) then
# Compute both the affine and the warp with ANTs. The Affine goes from
# the input croped space to the target cropped space. The warp goes
# from target cropped to target cropped.
set warp      = $tmpdir/reg.1Warp.nii.gz
set affinemat = $tmpdir/reg.0GenericAffine.mat
set ud = `UpdateNeeded $warp $involcrop $targvol`
if($ud || $ForceUpdate) then
  date | tee -a $LF
  pushd $tmpdir # this program can crash if stuff in the current dir
  if(! $DoCBIG) then
    set cmd = ($antsreg -d $dim -m $involcrop -f $targvolcrop -o reg. -n $threads)
  else
  set cmd = (antsRegistration --dimensionality $dim \
      --output [reg.,reg.Warped.nii.gz,reg.InverseWarped.nii.gz] \
      --initial-moving-transform [ $involcrop, $targvolcrop, 1 ] \
      --collapse-output-transforms 1 \
      --use-histogram-matching 1  \
      --use-estimate-learning-rate-once 1 \
      --metric mattes[ $fixed, $moving, 1, 32, regular, 0.3] \
        --transform affine[ 0.1 ] \
        --convergence [ 100x100x200, 1.e-8, 20 ] \
        --smoothing-sigmas  4x2x1vox \
        --shrink-factors 3x2x1 -l 1 \
      -metric cc[ $fixed, $moving, 1, 4] \
        --transform SyN[ .20, 3, 0] \
        --convergence [ 100x100x50, 0, 5 ] \
        --smoothing-sigmas  1x0.5x0vox \
        --shrink-factors 4x2x1)
  endif
  echo "\n\n"| tee -a $LF 
  echo $cmd | tee -a $LF 
  fs_time $cmd |& tee -a $LF
  if($status) goto error_exit
  echo "\n\n"| tee -a $LF 
  if($CropInput || $CropTarget) then
    # Somehow ANTs will change the geom slightly, so map it back to the
    # the target space. This is a bit of a hack that seems to work, but
    # it is not principled (ie, it was derived by trial and error, so
    # there is a danger that it will not work all the time).
    set cmd = (mri_vol2vol --regheader --targ $targvolcrop --mov $warp --o $warp)
    echo "\n\n"| tee -a $LF 
    echo $cmd | tee -a $LF 
    fs_time $cmd |& tee -a $LF
    if($status) goto error_exit
    echo "\n\n"| tee -a $LF 
  endif
  popd
endif

# Convert the ANTs affine to txt file (maps involcrop to the input of the targvolcrop space)
set affinetxt = $tmpdir/reg.0GenericAffine.txt
set ud = `UpdateNeeded $affinetxt $affinemat`
if($ud || $ForceUpdate) then
  date | tee -a $LF
  set cmd = (ConvertTransformFile $dim $affinemat $affinetxt --hm --ras)
  echo "\n\n"| tee -a $LF 
  echo $cmd | tee -a $LF 
  fs_time $cmd |& tee -a $LF
  if($status) goto error_exit
  echo "\n\n"| tee -a $LF 
endif

# Convert the ANTs affine to an LTA
set affinelta = $tmpdir/reg.0GenericAffine.lta
set ud = `UpdateNeeded $affinelta $affinetxt`
if($ud || $ForceUpdate) then
  date | tee -a $LF
  set cmd = (lta_convert --src $involcrop --trg $targvolcrop --outlta $affinelta)
  if($dim == 2) set cmd = ($cmd --inniftyreg2d $affinetxt);
  if($dim == 3) set cmd = ($cmd --inniftyreg   $affinetxt);
  echo "\n\n"| tee -a $LF 
  echo $cmd | tee -a $LF 
  fs_time $cmd |& tee -a $LF
  if($status) goto error_exit
  echo "\n\n"| tee -a $LF 
endif

# Create one lta that maps from the uncropped input vol space to the taret space
if($CropInput || $CropTarget) then
  set regcroptargtocropinvol = $tmpdir/reg.croptarg_to_cropinvol.lta
  set ud = `UpdateNeeded $regcroptargtocropinvol $affinelta $regcroptoinvol`
  if($ud || $ForceUpdate) then
    date | tee -a $LF
    set cmd = (mri_concatenate_lta -invert1 -invertout $affinelta $regcroptoinvol $regcroptargtocropinvol)
    echo "\n\n"| tee -a $LF 
    echo $cmd | tee -a $LF 
    fs_time $cmd |& tee -a $LF
    if($status) goto error_exit
    echo "\n\n"| tee -a $LF 
  endif
else
  set regcroptargtocropinvol = $affinelta
endif

# Concatenate the affines and the warp (ANTS)
set ud = `UpdateNeeded $m3z $warp $targvolcrop $regcroptargtocropinvol $regcroptotarg `
if($ud || $ForceUpdate) then
  date | tee -a $LF
  set cmd = (mri_warp_convert --initk $warp --insrcgeom $targvolcrop \
    --outfswarp $m3z --vg-thresh $vgthresh)
  if($CropInput) set cmd = ($cmd --lta1-inv $regcroptargtocropinvol )
  if($#regcroptotarg) set cmd = ($cmd --lta2 $regcroptotarg)
  echo "\n\n"| tee -a $LF 
  echo $cmd | tee -a $LF 
  fs_time $cmd |& tee -a $LF
  if($status) goto error_exit
  echo "\n\n"| tee -a $LF 
endif

else # End ANTS ================= else Use synthmorph

set gpuopt = ""
# Compute both the affine, maps from involcrop to targvolcrop
set affinelta = $outdir/aff.lta
set ud = `UpdateNeeded $affinelta $involcrop $targvolcrop`
if($ud || $ForceUpdate) then
  date | tee -a $LF
  set cmd = (mri_synthmorph -m affine -t $affinelta $involcrop $targvolcrop  -j $threads $gpuopt)
  echo "\n\n"| tee -a $LF 
  echo $cmd | tee -a $LF 
  fs_time $cmd |& tee -a $LF
  if($status) goto error_exit
endif

# Create one lta that maps from the uncropped input vol space to the (cropped) target space
set regtargtoinvol = $outdir/reg.targ_to_invol.lta
set reginvoltotarg = $outdir/reg.invol_to_targ.lta
if($CropInput || $CropTarget) then
  set reginvoltocroptarg = $tmpdir/reg.invol_to_croptarg.lta 
  set ud = `UpdateNeeded $reginvoltocroptarg $affinelta $regcroptoinvol`
  if($ud || $ForceUpdate) then
    date | tee -a $LF
    set cmd = (mri_concatenate_lta -invert1 -invertout $affinelta $regcroptoinvol $reginvoltocroptarg)
    echo "\n\n"| tee -a $LF 
    echo $cmd | tee -a $LF 
    fs_time $cmd |& tee -a $LF
    if($status) goto error_exit
    echo "\n\n"| tee -a $LF 
  endif
  if($MNITarget) then
    # Create one lta that maps from the uncropped input vol space to the uncropped target space
    # This produces a linear tranform that can be used to map from target to input volume just
    # like the nonlinear transform
    set ud = `UpdateNeeded $regtargtoinvol $reginvoltocroptarg`
    if($ud || $ForceUpdate) then
      set regtargtocropped = $FSMNI152DIR/reg-targets/reg.$MNIOutputRes.to.$MNITargetRes.cropped.lta
      set cmd = (mri_concatenate_lta -invert2 $regtargtocropped $reginvoltocroptarg $regtargtoinvol)
      echo $cmd | tee -a $LF 
      fs_time $cmd |& tee -a $LF
      if($status) goto error_exit
      echo "\n\n"| tee -a $LF 
    endif
  endif
  # Compute the inverse: invol-to-targ
  set ud = `UpdateNeeded $reginvoltotarg $regtargtoinvol`
  if($ud || $ForceUpdate) then
    set cmd = (lta_convert --invert --inlta $regtargtoinvol --outlta $reginvoltotarg)
    echo $cmd | tee -a $LF 
    fs_time $cmd |& tee -a $LF
    if($status) goto error_exit
    echo "\n\n"| tee -a $LF 
  endif
else
  pushd $tmpdir
  ln -fs aff.lta reg.invol_to_targ.lta
  popd
  set reginvoltocroptarg = $affinelta
  set reginvoltotarg = $affinelta
  # Compute target to invol
  set ud = `UpdateNeeded $regtargtoinvol $reginvoltotarg`
  if($ud || $ForceUpdate) then
    set cmd = (lta_convert --invert --inlta $reginvoltotarg --outlta $regtargtoinvol)
    echo $cmd | tee -a $LF 
    fs_time $cmd |& tee -a $LF
    if($status) goto error_exit
    echo "\n\n"| tee -a $LF 
  endif

endif

if($MNITarget) then
  # Create an xfm file which can be used as the taliarch.xfm
  set xfm = $outdir/reg.invol_to_targ.xfm
  set ud = `UpdateNeeded $xfm $reginvoltotarg`
  if($ud) then
    set cmd = (lta_convert --inlta $reginvoltotarg --outmni $xfm)
    echo $cmd | tee -a $LF 
    $cmd |& tee -a $LF
    if($status) goto error_exit
    echo "\n\n"| tee -a $LF 
  endif
endif

echo ""   | tee -a $LF
echo "To check affine registration"  | tee -a $LF
echo "tkregisterfv --mov $invol --targ $targvol --reg $reginvoltotarg"  | tee -a $LF
echo ""   | tee -a $LF

if($AffineOnly) then
  echo "AffineOnly specified, so exiting now" | tee -a $LF
  goto done
endif

# Now compute the nonlinear part
set deform = $tmpdir/deform.mgz
set smvol = $tmpdir/synthmorph.out.mgz
set ud = `UpdateNeeded $deform $affinelta $involcrop $targvolcrop`
if($ud) then
  set cmd = (mri_synthmorph -m deform -t $deform -i $affinelta $involcrop $targvolcrop -j $threads $gpuopt)
  if($DoTest) set cmd = ($cmd -o $smvol); # can be a pain when you want to rerun to create test output
  echo "\n\n" | tee -a $LF
  echo $cmd | tee -a $LF
  fs_time $cmd |& tee -a $LF
  if($status) goto error_exit
endif

# Compute warp to the full FoV of the input (synthmorph)
set ud = `UpdateNeeded $m3z $deform $targvolcrop $reginvoltocroptarg $regcroptotarg`
if($ud || $ForceUpdate) then
  # This call is not intuitive to me. It appears that the insrcgeom
  # will set the vox2ras for the image-side of the warp. The warp
  # maps from target voxel to cropped input RAS. The insrcgeom
  # indicates how to go from that RAS to a CRS in the cropped input,
  # then the lta1 indicates how to go from the cropped CRS to the
  # uncropped CRS.
  set cmd = (mri_warp_convert --inras $deform --insrcgeom $involcrop\
     --outfswarp $m3z --vg-thresh $vgthresh)
  if($CropInput) set cmd = ($cmd --lta1-inv $regcroptoinvol)
  if($#regcroptotarg) set cmd = ($cmd --lta2 $regcroptotarg)
  echo "\n\n$cmd" | tee -a $LF
  fs_time $cmd |& tee -a $LF
  if($status) goto error_exit
endif

endif # Synthmorph

if($ComputeInverse) then
  set ud = `UpdateNeeded $m3zinv $m3z`
  if($ud || $ForceUpdate) then
    set cmd = (mri_ca_register -invert-and-save $m3z $m3zinv)
    echo "\n\n$cmd" | tee -a $LF
    fs_time $cmd |& tee -a $LF
    if($status) goto error_exit
  endif
endif

# Test against output generated by the registration program
if($DoTest) then
  if($UseAnts) then
    set mvol = $tmpdir/reg.Warped.nii.gz
  else
    set mvol = $smvol
  endif
  if($CropInput || $CropTarget) then
    # Ants will output to the cropped target space, need to resample
    # to the full uncropped space.
    set mvol2 = $tmpdir/morph.out.nii.gz
    set ud = `UpdateNeeded $mvol2 $mvol $targvol`
    if($ud || $ForceUpdate) then
      set cmd = (mri_vol2vol --regheader --mov $mvol --targ $targvol --o $mvol2)
      echo $cmd | tee -a $LF
      fs_time $cmd |& tee -a $LF
      if($status) exit 1
    endif
    set mvol = $mvol2
  endif

  set ud = `UpdateNeeded $testvol $invol $m3z $mvol`
  if($ud || $ForceUpdate) then
    set cmd = (mri_convert -rt nearest $invol -at $m3z $testvol)
    echo $cmd | tee -a $LF
    fs_time $cmd |& tee -a $LF
    if($status) exit 1
    set cmd = (mri_diff --po $testvol $mvol)
    echo $cmd | tee -a $LF
    $cmd | tee $tmpdir/test.diff.dat |& tee -a $LF
  endif
  echo "tkmeditfv -f $targvol -aux $testvol"  |& tee -a $LF
endif

#========================================================

done:

# Cleanup
if($cleanup) rm -rf $tmpdir

# Done
echo " " |& tee -a $LF
set tSecEnd = `date '+%s'`;
@ tSecRun = $tSecEnd - $tSecStart;
set tRunMin = `echo $tSecRun/60|bc -l`
set tRunMin = `printf %5.2f $tRunMin`
set tRunHours = `echo $tSecRun/3600|bc -l`
set tRunHours = `printf %5.2f $tRunHours`
echo "Started at $StartTime " |& tee -a $LF
echo "Ended   at `date`" |& tee -a $LF
echo "Fs-Synthmorph-Reg-Run-Time-Sec $tSecRun" |& tee -a $LF
echo "Fs-Synthmorph-Reg-Run-Time-Min $tRunMin" |& tee -a $LF
echo "Fs-Synthmorph-Reg-Run-Time-Hours $tRunHours" |& tee -a $LF
echo " " |& tee -a $LF
echo "fs-synthmorph-reg Done" |& tee -a $LF
exit 0

###############################################

############--------------##################
error_exit:
echo "ERROR:"

exit 1;
###############################################

############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )

  set flag = $argv[1]; shift;
  
  switch($flag)

    case "--i":
      if($#argv < 1) goto arg1err;
      set invol = $argv[1]; shift;
      if(! -e $invol) then
        echo "ERROR: cannot find $invol"
        exit 1
      endif
      set invol = `getfullpath $invol`
      breaksw

    case "--t":
      if($#argv < 1) goto arg1err;
      set targvol = $argv[1]; shift;
      if(! -e $targvol) then
        echo "ERROR: cannot find $targvol"
        exit 1
      endif
      set targvol = `getfullpath $targvol`
      set MNITarget = 0
      set Crop = 1
      breaksw

    case "--warp":
    case "--m3z":
      if($#argv < 1) goto arg1err;
      set m3z = $argv[1]; shift;
      breaksw

    case "--affine-only":
      set AffineOnly = 1
      breaksw

    case "--o":
      if($#argv < 1) goto arg1err;
      set outdir = $argv[1]; shift;
      breaksw

    case "--s":
      if($#argv < 1) goto arg1err;
      set subject = $argv[1]; shift;
      breaksw

    case "--sd":
      if($#argv < 1) goto arg1err;
      setenv SUBJECTS_DIR $argv[1]; shift;
      breaksw

    case "--threads":
      if($#argv < 1) goto arg1err;
      set threads = $argv[1]; shift;
      breaksw

    case "--vg-thresh":
      if($#argv < 1) goto arg1err;
      set vgthresh = $argv[1]; shift;
      breaksw

    case "--synthmorph":
      set UseAnts = 0
      breaksw
    case "--ants":
      set UseAnts = 1
      breaksw

    case "--test":
      set DoTest = 1
      breaksw
    case "--no-test":
      set DoTest = 0
      breaksw

    case "--2d":
      set dim = 2
      set DoTest = 0
      breaksw

    case "--quick":
      set antsreg = antsRegistrationSyNQuick.sh
      set UseQuick = 1
      breaksw
    case "--no-quick":
    case "--syn":
      set antsreg = antsRegistrationSyN.sh
      set UseQuick = 0
      breaksw

    case "--crop":
     set CropInput = 1
     set CropTarget = 1
     breaksw
    case "--no-crop":
     set CropInput = 0
     set CropTarget = 0
     breaksw

    case "--strip":
     set StripInput = 1
     set StripTarget = 1
     breaksw
    case "--no-strip":
     set StripInput = 0
     set StripTarget = 0
     breaksw
    case "--strip-input":
     set StripInput = 1
     breaksw
    case "--no-strip-input":
     set StripInput = 0
     breaksw
    case "--strip-target":
     set StripTarget = 1
     breaksw
    case "--no-strip-target":
     set StripTarget = 0
     breaksw

    case "--inv":
     set ComputeInverse = 1
     breaksw
    case "--no-inv":
     set ComputeInverse = 0
     breaksw

    case "--mni":
     set MNITarget = 1
     breaksw
    case "--no-nmni":
     set MNITarget = 0
     breaksw

    case "--mni-res":
    case "--mni-int-res":
    case "--mni-targ-res":
      if($#argv < 1) goto arg1err;
      set MNITargetRes = $argv[1]; shift;
      if($MNITargetRes != 1.0mm && $MNITargetRes != 1.5mm && $MNITargetRes != 2.0mm) then
        echo "ERROR: --mni-res must be 1.0mm, 1.5mm, or 2.0mm"
        exit 1
      endif
      set MNITarget = 1
      breaksw

    case "--mni-output-res":
    case "--mni-out-res":
      if($#argv < 1) goto arg1err;
      set MNIOutputRes = $argv[1]; shift;
      if($MNIOutputRes != 1.0mm && $MNIOutputRes != 1.5mm && $MNIOutputRes != 2.0mm && $MNIOutputRes != conformed) then
        echo "ERROR: --mni-out-res must be 1.0mm, 1.5mm, 2.0mm, or conformed"
        exit 1
      endif
      set MNITarget = 1
      breaksw

    case "--mni-1":
      set MNIOutputRes = 1.0mm
      set MNITarget = 1
      breaksw

    case "--mni-1.5":
      set MNIOutputRes = 1.5mm
      set MNITarget = 1
      breaksw

    case "--mni-2":
      set MNIOutputRes = 2.0mm
      set MNITarget = 1
      breaksw

    case "--mni-conformed":
      set MNIOutputRes = conformed
      set MNITarget = 1
      breaksw

    case "--pituitary":
      set PitStr = ".pit"
      breaksw

    case "--cbig":
     set DoCBig = 1
     breaksw
    case "--no-cbig":
     set DoCBig = 0
     breaksw

    case "--force":
     set ForceUpdate = 1
     breaksw
    case "--rerun":
     # Prevents it from bailing out on the first check. This can be
     # handy when debugging and you want it to get into the interior
     # of the code.
     set ReRun = 1
     breaksw

    case "--log":
      if($#argv < 1) goto arg1err;
      set LF = $argv[1]; shift;
      breaksw

    case "--nolog":
    case "--no-log":
      set LF = /dev/null
      breaksw

    case "--tmp":
    case "--tmpdir":
      if($#argv < 1) goto arg1err;
      set tmpdir = $argv[1]; shift;
      set cleanup = 0;
      breaksw

    case "--nocleanup":
      set cleanup = 0;
      breaksw

    case "--cleanup":
      set cleanup = 1;
      breaksw

    case "--debug":
      set verbose = 1;
      set echo = 1;
      breaksw

    default:
      echo ERROR: Flag $flag unrecognized. 
      echo $cmdline
      exit 1
      breaksw
  endsw

end

goto parse_args_return;
############--------------##################

############--------------##################
check_params:

if($UseAnts == -1) then
  echo "ERROR: must spec either --ants or --synthmorph"
  exit 1
endif

# This will keep the temp stuff from being deleted
if($#outdir && $#tmpdir == 0) then
  set tmpdir = $outdir
  set cleanup = 0
endif

if($#subject) then
  set sd = $SUBJECTS_DIR/$subject
  if(! -e $sd) then
    echo "ERROR: cannot find $subject"
    exit 1;
  endif
  if($#invol == 0)  set invol = $sd/mri/norm.mgz
  if($#outdir == 0 && $MNITarget) then
    if($UseAnts) then
      set outdir = $sd/mri/transforms/ants.warp.$MNITargetRes.$MNIOutputRes$PitStr
    else
      set outdir = $sd/mri/transforms/synthmorph.$MNITargetRes.$MNIOutputRes$PitStr
    endif
    #don't create particular files in the transform dir
    #set m3z = $outdir.nii.gz
    #set m3zinv = $outdir.inv.nii.gz # Just in case the invert is requested
  endif
endif

# This is too complicated now as it is not just setting the target volume to 
# the cropped; have to set the reg-crop-to-target too
#if($MNITarget) set CropTarget = 0; 

if(! $MNITarget) then
  # Could get this to work, but not really needed
  set CropTarget = 0; 
  set CropInput = 0; 
endif

if($#outdir == 0) then
  echo "ERROR: must spec output dir"
  exit 1
endif
if($#invol == 0) then
  echo "ERROR: must spec input volume"
  exit 1
endif
foreach f ($invol $targvol) 
  if(! -e $f) then
    echo "ERROR: cannot find $f"
    exit 1
  endif
end

mkdir -p $outdir
set outdir = `getfullpath $outdir`
if($#m3z == 0) then
  if($MNITarget) then
     # Lose ants vs synthseg distinction in the output
     set m3z = $outdir/warp.to.mni152.${MNITargetRes}.${MNIOutputRes}.nii.gz
     set m3zinv = $outdir/warp.to.mni152.${MNITargetRes}.${MNIOutputRes}.inv.nii.gz
  else
     set m3z = $outdir/warp.nii.gz
     set m3zinv = $outdir/warp.inv.nii.gz
  endif
endif 

if($ComputeInverse && $#m3zinv == 0) then
  set stem = `fname2stem $m3z`
  set ext  = `fname2ext $m3z`
  set m3zinv = $stem.inv.$ext
endif

if($#targvol && $MNITarget) then
  echo "ERROR: cannot specify both target volume and mni target"
  exit 1
endif

# MNI is already skull stripped
if($MNITarget) set targvol = $FSMNI152DIR/reg-targets/mni152.${MNIOutputRes}${PitStr}.nii.gz

if($UseQuick) then
  set antsreg = antsRegistrationSyNQuick.sh
else
  set antsreg = antsRegistrationSyN.sh
endif

set testvol = ()
if($DoTest) set testvol = $outdir/test.nii.gz

set ud1 = `UpdateNeeded $m3z $targvol $invol`
set ud2 = 0
if($ComputeInverse) set ud2 = `UpdateNeeded $m3zinv $targvol $invol`
if($ReRun == 0 && $ud1 == 0 && $ud2 == 0 && $ForceUpdate == 0) then
  echo "fs-synthmorph-reg: update not needed"
  exit 0
endif

goto check_params_return;
############--------------##################

############--------------##################
arg1err:
  echo "ERROR: flag $flag requires one argument"
  exit 1
############--------------##################
arg2err:
  echo "ERROR: flag $flag requires two arguments"
  exit 1
############--------------##################

############--------------##################
usage_exit:
  echo ""
  echo "fs-synthmorph-reg -- frontend for running mri_synthmorph (24GB)"
  echo "  --i invol"
  echo "  --t targetvol"
  echo "  --warp warp.{m3z,mgz,nii.gz} : output warp file (or save in outdir)"
  echo "  --o outdir"
  echo "  --s subject (invol=norm.mgz, warp=mri/transforms/synthmorph.1.0mm.1.0mm.nii.gz  targ=MNI152.1mm)"
  echo "  --threads threads"
  echo "  --mni-targ-res 1.0mm, 1.5mm, 2.0mm (default is 1.0mm)"
  echo "  --mni-out-res 1.0mm, 1.5mm, 2.0mm, conformed (default is 1.0mm)"
  echo "  --no-inv : do not compute warp inverse (computed by default)"
  echo "  --affine-only : only perform the affine registration part"
  echo "  --strip : skull strip input and target"
  echo "  --strip-input : skull strip input"
  echo "  --strip-target : skull strip target"
  echo "  --crop/--no-crop (default is $CropInput, but no-crop if not registering to mni)"
  echo "  --pituitary : select the MNI target volume that does not mask out the pituitary"
  echo "  --test : resample the input volume to the output space and store as test.nii.gz"
  echo "  --vg-thresh vgthresh : threshold for testing diffs in volume geom"
  echo "  --ants : use ANTs registration intstead of synthmorph"
  echo "  --force : regenerate all output "
  echo "  --rerun : for debugging only, when you want it to get into the inteiror of the code"
  echo "  --tmp tmpdir"
  echo "  "


  if(! $PrintHelp) exit 1;
  echo $VERSION
  cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'
exit 1;

#---- Everything below here is printed out as part of help -----#
BEGINHELP

This is a frontend for running mri_synthmorph, especially for
registering to mni152 space.  For typical usage, it will consume less
than 15GB of memory. For affine only it requires less than 7GB.

Simple usage:

fs-synthmorph-reg --i inputvol.nii.gz --o synthmorphdir

This will register to the mni152 saving output files in synthmorphdir. The nonlinear 
warp will be outdir/warp.to.mni152.1.0mm.1.0mm.nii.gz which can be applied like:

mri_convert inputvol.nii.gz -at warp.to.mni152.1.0mm.1.0mm.nii.gz inputvol.mni152.nii.gz

which can be checked with

freeview inputvol.mni152.nii.gz $FREESURFER/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz 

If you have created the warp from a FreeSurfer subject space (either with --s or passing a 
conformed volume), then you can apply the warp to the surfaces, eg,

mris_apply_reg --warp lh.white warp.to.mni152.1.0mm.1.0mm.inv.nii.gz lh.warp.mni152

which you can check with

freeview inputvol.mni152.nii.gz $FREESURFER/average/mni_icbm152_nlin_asym_09c/reg-targets/mni152.1.0mm.nii.gz -f lh.warp.mni152

Skull stripping: mri_synthmorph is quite robust to the presence or
absence of skull stripping, but there will be some differences, so, to
be on the safe side, we recommend that images be skull stripped prior
to registration. When registering to the mni152, it will automatically
use a skull stripped volume. If you want fs-synthmorph-reg to skull
strip for you, then add --strip (uses mri_synthstrip). Note that if
you pass a FS subject (--s), it will use the norm.mgz volume, which is
already skull stripped. Note that ANTs performance and speed will be
very sensitive to stripping.

Cropping: internally, fs-synthmorph-reg will crop the input to a
minimal window around non-zero voxels in the image. In the end, this
probably does not have much of an effect for synthmorph as it will
sample to 256^3 internally. For ANTs, this can speed up the program
dramatically and reduce its memory footprint. fs-synthmorph-reg will
manage all of the transforms so that they all reference the uncropped
space, ie, the user is completely insulated from the cropping process
and its implications. To turn off cropping, use --no-crop. If you are
not stripping, it probably does not make sense to crop. 

Target and Output MNI Resolution: the first 1.0mm in the warp file
name means that the registration is done to a version of the mni152
with an isotropic resolution of 1.0mm (this will be how finely the
warp field is sampled). The second 1.0mm means that the warp file will
actually warp to the the mni152 with an isotropic resolution of 1.0mm.
You can change the resolution of the warp field with the
--mni-targ-res flag (options are 1.0mm, 1.5mm, 2.0mm), but,
internally, synthmorph uses 1mm, so this makes sense. You can change
the resolution of the output in several ways. From this program, you
can specify the output resolution with --mni-out-res (options are
1.0mm, 1.5mm, 2.0mm). You can also create an LTA file to the desired
output resolution and then use mri_warp_convert to change the warp.
Or you can create an LTA file to the desired resolution, and then use
mri_vol2vol --gcam to apply the warp and the LTA (instead of
mri_convert, which will only the the warp).

Affine and affine-only: by default, this script will perform a
non-linear registration to the target space. The first step of this
will be to perform an affine registration.  Sometimes, this is useful
too. This affine registration is stored in reg.targ_to_invol.lta.  If
you ONLY want the affine registration, then you can specify
--affine-only.

Arbitrary Targets: you can use fs-synthmorph-reg to register to target
volumes other than the mni152. To do this, simply specify --t
targetvol.  You can have fs-synthmorph-reg skull strip the target by
adding --strip-target. By default, the target will be cropped unless
--no-crop (see Cropping above).

Please cite SynthMorph:
Anatomy-specific acquisition-agnostic affine registration learned from
fictitious images
Hoffmann M, Hoopes A, Fischl B*, Dalca AV* (*equal contribution)
SPIE Medical Imaging: Image Processing, 12464, p 1246402, 2023
https://doi.org/10.1117/12.2653251
https://synthmorph.io/#papers (PDF)

SynthMorph: learning contrast-invariant registration without acquired images
Hoffmann M, Billot B, Greve DN, Iglesias JE, Fischl B, Dalca AV
IEEE Transactions on Medical Imaging, 41 (3), 543-558, 2022
https://doi.org/10.1109/TMI.2021.3116879

If you use SynthStrip in your analysis, please cite:
SynthStrip: Skull-Stripping for Any Brain Image
A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann
NeuroImage 206 (2022), 119474
https://doi.org/10.1016/j.neuroimage.2022.119474
Website: https://synthstrip.io