default.sh

# MIRTK installation
mirtk="$appdir/bin/mirtk"  # MIRTK AppImage downloaded from bintray with executable bit set
if [ ! -x "$mirtk" ]; then
  mirtk=
fi
if [ -z "$mirtk" ]; then
  if [ -z "$MIRTK_DIR" ]; then
    MIRTK_DIR=`which mirtk`
    if [ $? -ne 0 ]; then
      echo "Could not find MIRTK, either set PATH or MIRTK_DIR in $BASH_SOURCE" 1>&2
      exit 1
    fi
    MIRTK_DIR="$(cd "$(dirname "$MIRTK_DIR")"/.. && pwd)"
  fi
  PATH="$MIRTK_DIR/lib/tools:$MIRTK_DIR/lib/mirtk/tools:$PATH"
  LD_LIBRARY_PATH="$MIRTK_DIR/lib:$MIRTK_DIR/lib/mirtk:$LD_LIBRARY_PATH"
  PYTHONPATH="$MIRTK_DIR/lib/python:$PYTHONPATH"
fi

export PATH="$appdir/bin:$PATH"
export LD_LIBRARY_PATH="$appdir/lib:$LD_LIBRARY_PATH"
export PYTHONPATH="$appdir/lib/python:$PYTHONPATH"


# input settings
topdir="`cd $appdir && pwd`"          # absolute path of top-level working directory

pardir="`dirname "$BASH_SOURCE"`"     # directory containing configuration files
pardir="`cd $pardir && pwd`"          # - make path absolute
pardir="${pardir/$topdir\//}"         # - make path relative to working directory

agelst="$pardir/ages.csv"             # CSV table of image IDs and associated ages
sublst="$pardir/subjects.lst"         # List of image IDs, one per line

imgdir="../images"                    # directory of anatomical brain images
imgpre=""                             # brain image file name prefix
imgsuf=".nii.gz"                      # brain image file name suffix
bgvalue=0                             # background value of skull-stripped images

lbldir="../labels"                    # base directory of available segmentations
lblpre="structures/"                  # file name prefix of structural segmentation label image
lblsuf=".nii.gz"                      # file name suffix of structural segmentation label image
clspre="tissues/"                     # file name prefix of tissue segmentations
clssuf=".nii.gz"                      # file name suffix of tissue segmentations
tissues=9                             # no. of tissue classes
structures=87                         # no. of structures

segdir="seg"                          # directory with binary segmentation masks
segpre=""                             # file name prefix of binary segmentation masks
segsuf=".nii.gz"                      # file name suffix of binary segmentation masks

# global normalization
refdir="etc/reference"                # directory of reference image
refpre=""                             # reference image file name prefix
refsuf=".nii.gz"                      # reference image file name suffix
refid=""                              # ID of reference image (optional)
                                      # - set reference ID to empty string to compute
                                      #   population specific linear average
refini=true                           # - false: use reference for global normalization
                                      # - true:  construct linear population reference
                                      #          and, when refid set, align this average
                                      #          image rigidly with the specified reference

# common settings
verbose=0                             # verbosity of output messages
threads=8                             # maximum no. of CPU cores to use
update=false                          # enable (true) or disable update of existing DAG files
binlnk=true                           # link (true) or copy (false) job executables

# registration parameters
resolution=0.5                        # highest image resolution at final level in mm
similarity="NMI"                      # image (dis-)similarity measure: SSD, NMI, NCC
radius=3                              # radius of NCC in number of voxels (0: global NCC)
bins=64                               # no. of bins to use for NMI
model="SVFFD"                         # free-form deformation model
mffd="None"                           # multi-level transformation model
levels=4                              # no. of resolution levels for deformable registration
spacing=2.0                           # control point spacing on finest level
bending=5e-3                          # weight of bending energy term
elasticity=0                          # weight of linear elasticity term
elasticity_lambda=0                   # lambda parameter of linear elasticity constraint
elasticity_mu=1                       # mu parameter of linear elasticity constraint
jacobian=1e-5                         # weight of Jacobian-based penalty term
symmetric=true                        # use symmetric registration (requires 'SVFFD' model)
pairwise=true                         # true:  construct template using pairwise deformable registrations
                                      # false: use initial affine average as initial template
useresdof=false                       # whether to compute and apply residual average deformation
                                      # when "pairwise" deformable registration are enabled
                                      # - only needed for non-inverse-consistent registration
                                      # - not considered by Serag et al., NeuroImage 2012
refine=10                             # no. of subject to template deformation refinement steps
inclbg=false                          # whether to include background during deformable registration
interpolation="Linear"                # image interpolation mode
[[ $inclbg == true ]] || interpolation="$interpolation with padding"
finalize=true                         # whether to create output atlas files
                                      # false: only perform registrations to compute transformations

# temporal kernel regression parameters
epsilon=0.001                         # kernel weight threshold
means=()                              # default list of atlas time points
[ -n "$sigma" ] || sigma=1            # default standard deviation of temporal kernel
kernel="$pardir/weights"              # directory containing temporal kernel files
krnpre="t"                            # kernel file name prefix
krnext="tsv"                          # kernel file name extension (excl. leading dot)

# averaging options
threshold=0.5                         # minimum accumulated normalized weight threshold
normalization="zscore"                # input normalization option of mirtk average-images
rescaling="1 100"                     # output rescaling option of mirtk average-images
sharpen=true                          # whether to enhance edges in average image

# default output settings
libdir="lib"                          # shared libraries required by job executables
bindir="$libdir/tools"                # symbolic links to / copy of job executable files
dagdir="dag"                          # workflow description as DAG files for HTCondor DAGMan
logdir="log"                          # directory of log files written by workflow jobs
dofdir="../dofs"                      # transformations computed during atlas construction
evldir="../eval"                      # directory of output files suitable for QC and evaluation
outdir="../atlas"                     # atlas output directory
tmpdir="../temp"                      # directory of intermediate average images

# HTCondor settings
notify_user=""
notification="Error"
requirements='Arch == "X86_64" && OpSysShortName == "Ubuntu" && OpSysMajorVer >= 16'
log="progress.log"

# utility function to set pardir in custom configuration
set_pardir_from_file_path()
{
  pardir="`dirname "$1"`"
  if [ -L "$1" ]; then
    pardir="$pardir/`readlink "$1"`"
    pardir="`dirname "$pardir"`"
  fi
  pardir="`cd $pardir && pwd`"
  pardir="${pardir/$topdir\//}"
}

# load default custom configuration
# (e.g., link to configuration otherwise specified with -config option of commands)
if [ -f "$topdir/$pardir/custom.sh" ]; then
  source "$topdir/$pardir/custom.sh"
fi