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modelbuild.sh
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modelbuild.sh
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#!/bin/bash
# ARG_HELP([A qbatch enabled, optimal registration pyramid based re-implementaiton of antsMultivariateTemplateConstruction2.sh])
# ARG_OPTIONAL_SINGLE([output-dir],[],[Output directory for modelbuild],[output])
# ARG_OPTIONAL_SINGLE([gradient-step],[],[Gradient scaling step during template warping, can be a comma separated list same length as number of iterations],[0.25])
# ARG_OPTIONAL_SINGLE([starting-target],[],[Starting target, dumb average (dumb), align all inputs using their center-of-mass before averaging (com) use the first input (first), or an external file (provide path)],[first])
# ARG_OPTIONAL_SINGLE([starting-target-mask],[],[Mask for starting target if a file],[])
# ARG_OPTIONAL_SINGLE([starting-average-resolution],[],[If no starting target is provided, an average is constructed from all inputs, resample average to a target resolution MxNxO before modelbuild],[])
# ARG_OPTIONAL_SINGLE([iterations],[],[Number of iterations of model building per stage],[4])
# ARG_OPTIONAL_SINGLE([convergence],[],[Convergence limit during registration calls],[1e-7])
# ARG_OPTIONAL_SINGLE([syn-shrink-factors],[],[Shrink factors for Non-linear (SyN) stages, provide to override automatic generation, must be provided with sigmas and convergence],[])
# ARG_OPTIONAL_SINGLE([syn-smoothing-sigmas],[],[Smoothing sigmas for Non-linear (SyN) stages, provide to override automatic generation, must be provided with shrinks and convergence],[])
# ARG_OPTIONAL_SINGLE([syn-convergence],[],[Convergence levels for Non-linear (SyN) stages, provide to override automatic generation, must be provided with shrinks and sigmas],[])
# ARG_OPTIONAL_SINGLE([syn-control],[],[Non-linear (SyN) gradient and regularization parameters, not checked for correctness],[0.1,3,0])
# ARG_OPTIONAL_SINGLE([linear-shrink-factors],[],[Shrink factors for linear stages, provide to override automatic generation, must be provided with sigmas and convergence],[])
# ARG_OPTIONAL_SINGLE([linear-smoothing-sigmas],[],[Smoothing sigmas for linear stages, provide to override automatic generation, must be provided with shrinks and convergence],[])
# ARG_OPTIONAL_SINGLE([linear-convergence],[],[Convergence levels for linear stages, provide to override automatic generation, must be provided with shrinks and sigmas],[])
# ARG_OPTIONAL_BOOLEAN([float],[],[Use float instead of double for calculations (reduce memory requirements)],[])
# ARG_OPTIONAL_BOOLEAN([fast],[],[Run SyN registration with Mattes instead of CC],[])
# ARG_OPTIONAL_SINGLE([average-type],[],[Type of averaging to apply during modelbuild],[mean])
# ARG_OPTIONAL_SINGLE([average-prog],[],[Software to use for averaging images and transforms\n python with SimpleITK needed for trimmed_mean, efficient_trimean, and huber],[ANTs])
# ARG_OPTIONAL_BOOLEAN([average-norm],[],[Normalize images by their mean before averaging],[on])
# ARG_OPTIONAL_BOOLEAN([nlin-shape-update],[],[Perform nlin shape update, disable to switch to a forward-only modelbuild],[on])
# ARG_OPTIONAL_BOOLEAN([affine-shape-update],[],[Scale template by inverse of average affine transforms during shape update step],[on])
# ARG_OPTIONAL_BOOLEAN([scale-affines],[],[Apply gradient step scaling factor to average affine during shape update step, requires python with VTK and SimpleITK],[])
# ARG_OPTIONAL_BOOLEAN([rigid-update],[],[Include rigid component of transform when performing shape update on template (disable if template drifts in translation or orientation)],[])
# ARG_TYPE_GROUP_SET([averagetype],[AVERAGE],[average-type],[mean,median,trimmed_mean,efficient_trimean,huber])
# ARG_TYPE_GROUP_SET([averageprogtype],[PROG],[average-prog],[ANTs,python])
# ARG_OPTIONAL_SINGLE([sharpen-type],[],[Type of sharpening applied to average during modelbuild],[unsharp])
# ARG_TYPE_GROUP_SET([sharptypetype],[SHARPEN],[sharpen-type],[none,laplacian,unsharp])
# ARG_OPTIONAL_SINGLE([masks],[],[File containing mask filenames, one file per line],[])
# ARG_OPTIONAL_BOOLEAN([mask-extract],[],[Use masks to extract images before registration],[])
# ARG_OPTIONAL_SINGLE([mask-merge-threshold],[],[Threshold to combine masks during averaging],[0.5])
# ARG_OPTIONAL_SINGLE([stages],[],[Stages of modelbuild used (comma separated options: 'rigid' 'similarity' 'affine' 'nlin' 'nlin-only','volgenmodel-nlin'), append a number in brackets 'rigid[n]' to override global iteration setting],[rigid,similarity,affine,nlin])
# ARG_OPTIONAL_BOOLEAN([reuse-affines],[],[Reuse affines from previous stage/iteration to initialize next stage],[off])
# ARG_OPTIONAL_SINGLE([final-target],[],[Perform a final registration between the average and final target, used in postprocessing],[none])
# ARG_OPTIONAL_SINGLE([final-target-mask],[],[Mask for the final target used in postprocessing],[none])
# ARG_OPTIONAL_SINGLE([walltime-short],[],[Walltime for short running stages (averaging, resampling)],[00:30:00])
# ARG_OPTIONAL_SINGLE([walltime-linear],[],[Walltime for linear registration stages],[0:45:00])
# ARG_OPTIONAL_SINGLE([walltime-nonlinear],[],[Walltime for nonlinear registration stages],[4:30:00])
# ARG_OPTIONAL_SINGLE([jobname-prefix],[],[Prefix to add to front of job names, used by twolevel wrapper],[])
# ARG_OPTIONAL_SINGLE([job-predepend],[],[Job name dependency pattern to prepend to all jobs, used by twolevel wrapper],[])
# ARG_OPTIONAL_BOOLEAN([skip-file-checks],[],[Skip preflight checking of existence of files, used by twolevel wrapper],[])
# ARG_OPTIONAL_BOOLEAN([block],[],[For SGE, PBS and SLURM, blocks execution until jobs are finished.],[])
# ARG_OPTIONAL_BOOLEAN([debug],[],[Debug mode, print all commands to stdout],[])
# ARG_OPTIONAL_BOOLEAN([dry-run],[],[Dry run, don't run any commands, implies debug],[])
# ARG_POSITIONAL_INF([inputs],[Input text file, one line per input],[1])
# ARGBASH_SET_INDENT([ ])
# ARGBASH_GO()
# needed because of Argbash --> m4_ignore([
### START OF CODE GENERATED BY Argbash v2.10.0 one line above ###
# Argbash is a bash code generator used to get arguments parsing right.
# Argbash is FREE SOFTWARE, see https://argbash.io for more info
die()
{
local _ret="${2:-1}"
test "${_PRINT_HELP:-no}" = yes && print_help >&2
echo "$1" >&2
exit "${_ret}"
}
# validators
averagetype()
{
local _allowed=("mean" "median" "trimmed_mean" "efficient_trimean" "huber") _seeking="$1"
for element in "${_allowed[@]}"
do
test "$element" = "$_seeking" && echo "$element" && return 0
done
die "Value '$_seeking' (of argument '$2') doesn't match the list of allowed values: 'mean', 'median', 'trimmed_mean', 'efficient_trimean' and 'huber'" 4
}
averageprogtype()
{
local _allowed=("ANTs" "python") _seeking="$1"
for element in "${_allowed[@]}"
do
test "$element" = "$_seeking" && echo "$element" && return 0
done
die "Value '$_seeking' (of argument '$2') doesn't match the list of allowed values: 'ANTs' and 'python'" 4
}
sharptypetype()
{
local _allowed=("none" "laplacian" "unsharp") _seeking="$1"
for element in "${_allowed[@]}"
do
test "$element" = "$_seeking" && echo "$element" && return 0
done
die "Value '$_seeking' (of argument '$2') doesn't match the list of allowed values: 'none', 'laplacian' and 'unsharp'" 4
}
begins_with_short_option()
{
local first_option all_short_options='h'
first_option="${1:0:1}"
test "$all_short_options" = "${all_short_options/$first_option/}" && return 1 || return 0
}
# THE DEFAULTS INITIALIZATION - POSITIONALS
_positionals=()
_arg_inputs=('' )
# THE DEFAULTS INITIALIZATION - OPTIONALS
_arg_output_dir="output"
_arg_gradient_step="0.25"
_arg_starting_target="first"
_arg_starting_target_mask=
_arg_starting_average_resolution=
_arg_iterations="4"
_arg_convergence="1e-7"
_arg_syn_shrink_factors=
_arg_syn_smoothing_sigmas=
_arg_syn_convergence=
_arg_syn_control="0.1,3,0"
_arg_linear_shrink_factors=
_arg_linear_smoothing_sigmas=
_arg_linear_convergence=
_arg_float="off"
_arg_fast="off"
_arg_average_type="mean"
_arg_average_prog="ANTs"
_arg_average_norm="on"
_arg_nlin_shape_update="on"
_arg_affine_shape_update="on"
_arg_scale_affines="off"
_arg_rigid_update="off"
_arg_sharpen_type="unsharp"
_arg_masks=
_arg_mask_extract="off"
_arg_mask_merge_threshold="0.5"
_arg_stages="rigid,similarity,affine,nlin"
_arg_reuse_affines="off"
_arg_final_target="none"
_arg_final_target_mask="none"
_arg_walltime_short="00:30:00"
_arg_walltime_linear="0:45:00"
_arg_walltime_nonlinear="4:30:00"
_arg_jobname_prefix=
_arg_job_predepend=
_arg_skip_file_checks="off"
_arg_block="off"
_arg_debug="off"
_arg_dry_run="off"
print_help()
{
printf '%s\n' "A qbatch enabled, optimal registration pyramid based re-implementaiton of antsMultivariateTemplateConstruction2.sh"
printf 'Usage: %s [-h|--help] [--output-dir <arg>] [--gradient-step <arg>] [--starting-target <arg>] [--starting-target-mask <arg>] [--starting-average-resolution <arg>] [--iterations <arg>] [--convergence <arg>] [--syn-shrink-factors <arg>] [--syn-smoothing-sigmas <arg>] [--syn-convergence <arg>] [--syn-control <arg>] [--linear-shrink-factors <arg>] [--linear-smoothing-sigmas <arg>] [--linear-convergence <arg>] [--(no-)float] [--(no-)fast] [--average-type <AVERAGE>] [--average-prog <PROG>] [--(no-)average-norm] [--(no-)nlin-shape-update] [--(no-)affine-shape-update] [--(no-)scale-affines] [--(no-)rigid-update] [--sharpen-type <SHARPEN>] [--masks <arg>] [--(no-)mask-extract] [--mask-merge-threshold <arg>] [--stages <arg>] [--(no-)reuse-affines] [--final-target <arg>] [--final-target-mask <arg>] [--walltime-short <arg>] [--walltime-linear <arg>] [--walltime-nonlinear <arg>] [--jobname-prefix <arg>] [--job-predepend <arg>] [--(no-)skip-file-checks] [--(no-)block] [--(no-)debug] [--(no-)dry-run] <inputs-1> [<inputs-2>] ... [<inputs-n>] ...\n' "$0"
printf '\t%s\n' "<inputs>: Input text file, one line per input"
printf '\t%s\n' "-h, --help: Prints help"
printf '\t%s\n' "--output-dir: Output directory for modelbuild (default: 'output')"
printf '\t%s\n' "--gradient-step: Gradient scaling step during template warping, can be a comma separated list same length as number of iterations (default: '0.25')"
printf '\t%s\n' "--starting-target: Starting target, dumb average (dumb), align all inputs using their center-of-mass before averaging (com) use the first input (first), or an external file (provide path) (default: 'first')"
printf '\t%s\n' "--starting-target-mask: Mask for starting target if a file (no default)"
printf '\t%s\n' "--starting-average-resolution: If no starting target is provided, an average is constructed from all inputs, resample average to a target resolution MxNxO before modelbuild (no default)"
printf '\t%s\n' "--iterations: Number of iterations of model building per stage (default: '4')"
printf '\t%s\n' "--convergence: Convergence limit during registration calls (default: '1e-7')"
printf '\t%s\n' "--syn-shrink-factors: Shrink factors for Non-linear (SyN) stages, provide to override automatic generation, must be provided with sigmas and convergence (no default)"
printf '\t%s\n' "--syn-smoothing-sigmas: Smoothing sigmas for Non-linear (SyN) stages, provide to override automatic generation, must be provided with shrinks and convergence (no default)"
printf '\t%s\n' "--syn-convergence: Convergence levels for Non-linear (SyN) stages, provide to override automatic generation, must be provided with shrinks and sigmas (no default)"
printf '\t%s\n' "--syn-control: Non-linear (SyN) gradient and regularization parameters, not checked for correctness (default: '0.1,3,0')"
printf '\t%s\n' "--linear-shrink-factors: Shrink factors for linear stages, provide to override automatic generation, must be provided with sigmas and convergence (no default)"
printf '\t%s\n' "--linear-smoothing-sigmas: Smoothing sigmas for linear stages, provide to override automatic generation, must be provided with shrinks and convergence (no default)"
printf '\t%s\n' "--linear-convergence: Convergence levels for linear stages, provide to override automatic generation, must be provided with shrinks and sigmas (no default)"
printf '\t%s\n' "--float, --no-float: Use float instead of double for calculations (reduce memory requirements) (off by default)"
printf '\t%s\n' "--fast, --no-fast: Run SyN registration with Mattes instead of CC (off by default)"
printf '\t%s\n' "--average-type: Type of averaging to apply during modelbuild. Can be one of: 'mean', 'median', 'trimmed_mean', 'efficient_trimean' and 'huber' (default: 'mean')"
printf '\t%s\n' "--average-prog: Software to use for averaging images and transforms
python with SimpleITK needed for trimmed_mean, efficient_trimean, and huber. Can be one of: 'ANTs' and 'python' (default: 'ANTs')"
printf '\t%s\n' "--average-norm, --no-average-norm: Normalize images by their mean before averaging (on by default)"
printf '\t%s\n' "--nlin-shape-update, --no-nlin-shape-update: Perform nlin shape update, disable to switch to a forward-only modelbuild (on by default)"
printf '\t%s\n' "--affine-shape-update, --no-affine-shape-update: Scale template by inverse of average affine transforms during shape update step (on by default)"
printf '\t%s\n' "--scale-affines, --no-scale-affines: Apply gradient step scaling factor to average affine during shape update step, requires python with VTK and SimpleITK (off by default)"
printf '\t%s\n' "--rigid-update, --no-rigid-update: Include rigid component of transform when performing shape update on template (disable if template drifts in translation or orientation) (off by default)"
printf '\t%s\n' "--sharpen-type: Type of sharpening applied to average during modelbuild. Can be one of: 'none', 'laplacian' and 'unsharp' (default: 'unsharp')"
printf '\t%s\n' "--masks: File containing mask filenames, one file per line (no default)"
printf '\t%s\n' "--mask-extract, --no-mask-extract: Use masks to extract images before registration (off by default)"
printf '\t%s\n' "--mask-merge-threshold: Threshold to combine masks during averaging (default: '0.5')"
printf '\t%s\n' "--stages: Stages of modelbuild used (comma separated options: 'rigid' 'similarity' 'affine' 'nlin' 'nlin-only','volgenmodel-nlin'), append a number in brackets 'rigid[n]' to override global iteration setting (default: 'rigid,similarity,affine,nlin')"
printf '\t%s\n' "--reuse-affines, --no-reuse-affines: Reuse affines from previous stage/iteration to initialize next stage (off by default)"
printf '\t%s\n' "--final-target: Perform a final registration between the average and final target, used in postprocessing (default: 'none')"
printf '\t%s\n' "--final-target-mask: Mask for the final target used in postprocessing (default: 'none')"
printf '\t%s\n' "--walltime-short: Walltime for short running stages (averaging, resampling) (default: '00:30:00')"
printf '\t%s\n' "--walltime-linear: Walltime for linear registration stages (default: '0:45:00')"
printf '\t%s\n' "--walltime-nonlinear: Walltime for nonlinear registration stages (default: '4:30:00')"
printf '\t%s\n' "--jobname-prefix: Prefix to add to front of job names, used by twolevel wrapper (no default)"
printf '\t%s\n' "--job-predepend: Job name dependency pattern to prepend to all jobs, used by twolevel wrapper (no default)"
printf '\t%s\n' "--skip-file-checks, --no-skip-file-checks: Skip preflight checking of existence of files, used by twolevel wrapper (off by default)"
printf '\t%s\n' "--block, --no-block: For SGE, PBS and SLURM, blocks execution until jobs are finished. (off by default)"
printf '\t%s\n' "--debug, --no-debug: Debug mode, print all commands to stdout (off by default)"
printf '\t%s\n' "--dry-run, --no-dry-run: Dry run, don't run any commands, implies debug (off by default)"
}
parse_commandline()
{
_positionals_count=0
while test $# -gt 0
do
_key="$1"
case "$_key" in
-h|--help)
print_help
exit 0
;;
-h*)
print_help
exit 0
;;
--output-dir)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_output_dir="$2"
shift
;;
--output-dir=*)
_arg_output_dir="${_key##--output-dir=}"
;;
--gradient-step)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_gradient_step="$2"
shift
;;
--gradient-step=*)
_arg_gradient_step="${_key##--gradient-step=}"
;;
--starting-target)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_starting_target="$2"
shift
;;
--starting-target=*)
_arg_starting_target="${_key##--starting-target=}"
;;
--starting-target-mask)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_starting_target_mask="$2"
shift
;;
--starting-target-mask=*)
_arg_starting_target_mask="${_key##--starting-target-mask=}"
;;
--starting-average-resolution)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_starting_average_resolution="$2"
shift
;;
--starting-average-resolution=*)
_arg_starting_average_resolution="${_key##--starting-average-resolution=}"
;;
--iterations)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_iterations="$2"
shift
;;
--iterations=*)
_arg_iterations="${_key##--iterations=}"
;;
--convergence)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_convergence="$2"
shift
;;
--convergence=*)
_arg_convergence="${_key##--convergence=}"
;;
--syn-shrink-factors)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_syn_shrink_factors="$2"
shift
;;
--syn-shrink-factors=*)
_arg_syn_shrink_factors="${_key##--syn-shrink-factors=}"
;;
--syn-smoothing-sigmas)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_syn_smoothing_sigmas="$2"
shift
;;
--syn-smoothing-sigmas=*)
_arg_syn_smoothing_sigmas="${_key##--syn-smoothing-sigmas=}"
;;
--syn-convergence)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_syn_convergence="$2"
shift
;;
--syn-convergence=*)
_arg_syn_convergence="${_key##--syn-convergence=}"
;;
--syn-control)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_syn_control="$2"
shift
;;
--syn-control=*)
_arg_syn_control="${_key##--syn-control=}"
;;
--linear-shrink-factors)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_linear_shrink_factors="$2"
shift
;;
--linear-shrink-factors=*)
_arg_linear_shrink_factors="${_key##--linear-shrink-factors=}"
;;
--linear-smoothing-sigmas)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_linear_smoothing_sigmas="$2"
shift
;;
--linear-smoothing-sigmas=*)
_arg_linear_smoothing_sigmas="${_key##--linear-smoothing-sigmas=}"
;;
--linear-convergence)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_linear_convergence="$2"
shift
;;
--linear-convergence=*)
_arg_linear_convergence="${_key##--linear-convergence=}"
;;
--no-float|--float)
_arg_float="on"
test "${1:0:5}" = "--no-" && _arg_float="off"
;;
--no-fast|--fast)
_arg_fast="on"
test "${1:0:5}" = "--no-" && _arg_fast="off"
;;
--average-type)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_average_type="$(averagetype "$2" "average-type")" || exit 1
shift
;;
--average-type=*)
_arg_average_type="$(averagetype "${_key##--average-type=}" "average-type")" || exit 1
;;
--average-prog)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_average_prog="$(averageprogtype "$2" "average-prog")" || exit 1
shift
;;
--average-prog=*)
_arg_average_prog="$(averageprogtype "${_key##--average-prog=}" "average-prog")" || exit 1
;;
--no-average-norm|--average-norm)
_arg_average_norm="on"
test "${1:0:5}" = "--no-" && _arg_average_norm="off"
;;
--no-nlin-shape-update|--nlin-shape-update)
_arg_nlin_shape_update="on"
test "${1:0:5}" = "--no-" && _arg_nlin_shape_update="off"
;;
--no-affine-shape-update|--affine-shape-update)
_arg_affine_shape_update="on"
test "${1:0:5}" = "--no-" && _arg_affine_shape_update="off"
;;
--no-scale-affines|--scale-affines)
_arg_scale_affines="on"
test "${1:0:5}" = "--no-" && _arg_scale_affines="off"
;;
--no-rigid-update|--rigid-update)
_arg_rigid_update="on"
test "${1:0:5}" = "--no-" && _arg_rigid_update="off"
;;
--sharpen-type)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_sharpen_type="$(sharptypetype "$2" "sharpen-type")" || exit 1
shift
;;
--sharpen-type=*)
_arg_sharpen_type="$(sharptypetype "${_key##--sharpen-type=}" "sharpen-type")" || exit 1
;;
--masks)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_masks="$2"
shift
;;
--masks=*)
_arg_masks="${_key##--masks=}"
;;
--no-mask-extract|--mask-extract)
_arg_mask_extract="on"
test "${1:0:5}" = "--no-" && _arg_mask_extract="off"
;;
--mask-merge-threshold)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_mask_merge_threshold="$2"
shift
;;
--mask-merge-threshold=*)
_arg_mask_merge_threshold="${_key##--mask-merge-threshold=}"
;;
--stages)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_stages="$2"
shift
;;
--stages=*)
_arg_stages="${_key##--stages=}"
;;
--no-reuse-affines|--reuse-affines)
_arg_reuse_affines="on"
test "${1:0:5}" = "--no-" && _arg_reuse_affines="off"
;;
--final-target)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_final_target="$2"
shift
;;
--final-target=*)
_arg_final_target="${_key##--final-target=}"
;;
--final-target-mask)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_final_target_mask="$2"
shift
;;
--final-target-mask=*)
_arg_final_target_mask="${_key##--final-target-mask=}"
;;
--walltime-short)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_walltime_short="$2"
shift
;;
--walltime-short=*)
_arg_walltime_short="${_key##--walltime-short=}"
;;
--walltime-linear)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_walltime_linear="$2"
shift
;;
--walltime-linear=*)
_arg_walltime_linear="${_key##--walltime-linear=}"
;;
--walltime-nonlinear)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_walltime_nonlinear="$2"
shift
;;
--walltime-nonlinear=*)
_arg_walltime_nonlinear="${_key##--walltime-nonlinear=}"
;;
--jobname-prefix)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_jobname_prefix="$2"
shift
;;
--jobname-prefix=*)
_arg_jobname_prefix="${_key##--jobname-prefix=}"
;;
--job-predepend)
test $# -lt 2 && die "Missing value for the optional argument '$_key'." 1
_arg_job_predepend="$2"
shift
;;
--job-predepend=*)
_arg_job_predepend="${_key##--job-predepend=}"
;;
--no-skip-file-checks|--skip-file-checks)
_arg_skip_file_checks="on"
test "${1:0:5}" = "--no-" && _arg_skip_file_checks="off"
;;
--no-block|--block)
_arg_block="on"
test "${1:0:5}" = "--no-" && _arg_block="off"
;;
--no-debug|--debug)
_arg_debug="on"
test "${1:0:5}" = "--no-" && _arg_debug="off"
;;
--no-dry-run|--dry-run)
_arg_dry_run="on"
test "${1:0:5}" = "--no-" && _arg_dry_run="off"
;;
*)
_last_positional="$1"
_positionals+=("$_last_positional")
_positionals_count=$((_positionals_count + 1))
;;
esac
shift
done
}
handle_passed_args_count()
{
local _required_args_string="'inputs'"
test "${_positionals_count}" -ge 1 || _PRINT_HELP=yes die "FATAL ERROR: Not enough positional arguments - we require at least 1 (namely: $_required_args_string), but got only ${_positionals_count}." 1
}
assign_positional_args()
{
local _positional_name _shift_for=$1
_positional_names="_arg_inputs "
_our_args=$((${#_positionals[@]} - 1))
for ((ii = 0; ii < _our_args; ii++))
do
_positional_names="$_positional_names _arg_inputs[$((ii + 1))]"
done
shift "$_shift_for"
for _positional_name in ${_positional_names}
do
test $# -gt 0 || break
eval "$_positional_name=\${1}" || die "Error during argument parsing, possibly an Argbash bug." 1
shift
done
}
parse_commandline "$@"
handle_passed_args_count
assign_positional_args 1 "${_positionals[@]}"
# OTHER STUFF GENERATED BY Argbash
# Validation of values
### END OF CODE GENERATED BY Argbash (sortof) ### ])
# [ <-- needed because of Argbash
set -uo pipefail
set -eE -o functrace
# Load up helper scripts and define helper variables
# shellcheck source=helpers.sh
source "$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)/helpers.sh"
# Set magic variables for current file, directory, os, etc.
__file="${__dir}/$(basename "${BASH_SOURCE[${__b3bp_tmp_source_idx:-0}]}")"
__base="$(basename "${__file}" .sh)"
# shellcheck disable=SC2034,SC2015
__invocation="$(printf %q "${__file}")$( (($#)) && printf ' %q' "$@" || true)"
# Setup a directory which contains all commands run
# for this invocation
mkdir -p ${_arg_output_dir}/jobs/${__datetime}
export QBATCH_SCRIPT_FOLDER="${_arg_output_dir}/qbatch/${__datetime}"
# Store the full command line for each run
echo ${__invocation} >${_arg_output_dir}/jobs/${__datetime}/invocation
info "Checking input files"
# Load input file into array
if [[ ! -s ${_arg_inputs[0]} ]]; then
failure "Input file ${_arg_inputs[0]} is non-existent or zero size"
else
mapfile -t _arg_inputs <${_arg_inputs[0]}
fi
input_filenames_for_dup_check=()
for file in "${_arg_inputs[@]}"; do
input_filenames_for_dup_check+=($(basename ${file}))
if [[ ${_arg_skip_file_checks} == "off" ]]; then
if [[ ! -s ${file} ]]; then
failure "Input file ${file} is non-existent or zero size"
fi
fi
done
#Check for duplicate filenames
duplicates=$(IFS=$'\n' ; sort <<<"${input_filenames_for_dup_check[*]}" | uniq -d)
if [[ ! -z ${duplicates} ]]; then
failure "The following filenames are duplicated in the input file, file names must be unique \n ${duplicates}"
fi
# Fill up array of masks
if [[ -z ${_arg_masks} ]]; then
_arg_masks=()
for file in "${_arg_inputs[@]}"; do
_arg_masks+=('')
done
else
mapfile -t _arg_masks <${_arg_masks}
info "Checking mask files"
if [[ ${_arg_skip_file_checks} == "off" ]]; then
for file in "${_arg_masks[@]}"; do
if [[ ! -s ${file} ]]; then
failure "Mask file ${file} is non-existent or zero size"
fi
done
fi
fi
# If target mask is specified use it
target_mask=${_arg_starting_target_mask}
if [[ -n ${target_mask} && ! -s ${target_mask} ]]; then
failure "Starting target mask ${target_mask} is non-existant or zero size"
fi
# Enable fast mode in antsRegistration_affine_SyN.sh
if [[ ${_arg_fast} == "on" ]]; then
_arg_fast="--fast"
else
_arg_fast="--no-fast"
fi
# Enable mask extraction in antsRegistration_affine_SyN.sh
if [[ ${_arg_mask_extract} == "on" ]]; then
_arg_mask_extract="--mask-extract"
else
_arg_mask_extract="--no-mask-extract"
fi
# Enable float mode for ants commands
if [[ ${_arg_float} == "on" ]]; then
_arg_float="--float"
else
_arg_float=""
fi
# Handle registration overrides
if [[ -n ${_arg_linear_convergence} && -n ${_arg_linear_shrink_factors} && -n ${_arg_linear_smoothing_sigmas} ]]; then
_arg_linear_convergence="--linear-convergence ${_arg_linear_convergence}"
_arg_linear_shrink_factors="--linear-shrink-factors ${_arg_linear_shrink_factors}"
_arg_linear_smoothing_sigmas="--linear-smoothing-sigmas ${_arg_linear_smoothing_sigmas}"
fi
if [[ -n ${_arg_syn_convergence} && -n ${_arg_syn_shrink_factors} && -n ${_arg_syn_smoothing_sigmas} ]]; then
_arg_syn_convergence="--syn-convergence ${_arg_syn_convergence}"
_arg_syn_shrink_factors="--syn-shrink-factors ${_arg_syn_shrink_factors}"
_arg_syn_smoothing_sigmas="--syn-smoothing-sigmas ${_arg_syn_smoothing_sigmas}"
fi
# Include rigid component in affine when updating template
if [[ ${_arg_rigid_update} == "on" ]]; then
AVERAGE_AFFINE_PROGRAM="AverageAffineTransform"
else
AVERAGE_AFFINE_PROGRAM="AverageAffineTransformNoRigid"
fi
# Enable block for qbatch job submission
if [[ ${_arg_block} == "on" ]]; then
_arg_block="--block"
else
_arg_block=""
fi
# Job predependency from wrapper
if [[ ! -z ${_arg_job_predepend} ]]; then
_arg_job_predepend="--depend ${_arg_job_predepend}*"
fi
# Prefight check for required programs
for program in AverageImages ImageSetStatistics ResampleImage qbatch ImageMath \
ThresholdImage ExtractRegionFromImageByMask antsAI ConvertImage \
antsApplyTransforms AverageAffineTransform AverageAffineTransformNoRigid \
antsRegistration_affine_SyN.sh parallel; do
if ! command -v ${program} &>/dev/null; then
failure "Required program ${program} not found!"
fi
done
# Check for valid average choices
if [[ ${_arg_average_prog} == "ANTs" ]]; then
case ${_arg_average_type} in
trimmed_mean|efficient_trimean|huber)
failure "Average method ${_arg_average_type} is not supported in ANTs, use --average-prog python"
;;
esac
fi
# Check that python code will run
if [[ ${_arg_average_prog} == "python" ]]; then
${__dir}/sitk_image_math.py -h &>/dev/null || failure "sitk_image_math.py failed to run, check python version and dependencies"
${__dir}/sitk_average_affine_transforms.py -h &>/dev/null || failure "sitk_average_affine_transforms.py failed to run, check python version and dependencies"
fi
# Check that interpolator works if requested
if [[ ${_arg_scale_affines} == "on" ]]; then
${__dir}/interp_transform.py -h &>/dev/null || failure "interp_transform.py failed to run, check python version and dependencies"
fi
if [[ ${_arg_average_norm} == "off" ]]; then
unset _arg_average_norm
else
_arg_average_norm=2
fi
# Averaging function
average_images () {
local output=$1
shift
local avg_inputs=("$@")
if [[ ${_arg_average_prog} == "ANTs" ]]; then
case ${_arg_average_type} in
mean)
echo AverageImages 3 ${output} \
${_arg_average_norm:-0} \
"${avg_inputs[@]}"
;;
median)
printf '%s\n' "${avg_inputs[@]}" > $(dirname ${output})/$(basename ${output} .nii.gz)_medianinput.txt
echo ImageSetStatistics 3 $(dirname ${output})/$(basename ${output} .nii.gz)_medianinput.txt \
${output} 0
;;
esac
else
echo ${__dir}/sitk_image_math.py \
-o ${output} \
--method ${_arg_average_type} \
${_arg_average_norm:+--normalize} \
--file-list "${avg_inputs[@]}"
fi
}
# If no starting target is supplied, create one
if [[ ! -s ${_arg_starting_target} ]]; then
if [[ ! -s ${_arg_output_dir}/initialaverage/initialtarget.nii.gz ]]; then
mkdir -p ${_arg_output_dir}/initialaverage
if [[ ${_arg_starting_target} == "dumb" ]]; then
info "Generating initial average of all subjects using ${_arg_average_type} method"
average_images ${_arg_output_dir}/initialaverage/initialtarget.nii.gz "${_arg_inputs[@]}" \
>${_arg_output_dir}/jobs/${__datetime}/initialaverage
if [[ -n ${_arg_starting_average_resolution} ]]; then
echo ResampleImage 3 ${_arg_output_dir}/initialaverage/initialtarget.nii.gz \
${_arg_output_dir}/initialaverage/initialtarget.nii.gz \
${_arg_starting_average_resolution} 0 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage
fi
debug "$(cat ${_arg_output_dir}/jobs/${__datetime}/initialaverage)"
if [[ ${_arg_dry_run} == "off" ]]; then
qbatch ${_arg_block} --logdir ${_arg_output_dir}/logs/${__datetime} \
--walltime ${_arg_walltime_short} \
-N ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage \
${_arg_job_predepend} \
-- bash ${_arg_output_dir}/jobs/${__datetime}/initialaverage
fi
last_round_job="--depend ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage"
elif [[ ${_arg_starting_target} == "com" ]]; then
info "Generating initial average of all subjects using ${_arg_average_type} and center-of-mass alignment"
# Bootstrap COM alignment with a normalized mean
echo AverageImages 3 ${_arg_output_dir}/initialaverage/initialtarget_dumb.nii.gz 2 \
"${_arg_inputs[@]}" \
>${_arg_output_dir}/jobs/${__datetime}/initialaverage_dumb
echo ImageMath 3 ${_arg_output_dir}/initialaverage/initialtarget_dumb.nii.gz \
PadImage ${_arg_output_dir}/initialaverage/initialtarget_dumb.nii.gz 20 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_dumb
echo ThresholdImage 3 ${_arg_output_dir}/initialaverage/initialtarget_dumb.nii.gz \
${_arg_output_dir}/initialaverage/bgmask.nii.gz Otsu 4 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_dumb
echo ThresholdImage 3 ${_arg_output_dir}/initialaverage/bgmask.nii.gz \
${_arg_output_dir}/initialaverage/bgmask.nii.gz 0.5 Inf 1 0 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_dumb
echo ExtractRegionFromImageByMask 3 ${_arg_output_dir}/initialaverage/initialtarget_dumb.nii.gz \
${_arg_output_dir}/initialaverage/initialtarget_dumb_recrop.nii.gz \
${_arg_output_dir}/initialaverage/bgmask.nii.gz 1 20 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_dumb
echo cp -f ${_arg_output_dir}/initialaverage/initialtarget_dumb_recrop.nii.gz \
${_arg_output_dir}/initialaverage/initialtarget_dumb.nii.gz \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_dumb
debug "$(cat ${_arg_output_dir}/jobs/${__datetime}/initialaverage_dumb)"
if [[ ${_arg_dry_run} == "off" ]]; then
qbatch ${_arg_block} --logdir ${_arg_output_dir}/logs/${__datetime} \
--walltime ${_arg_walltime_short} \
-N ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage_dumb \
${_arg_job_predepend} \
-- bash ${_arg_output_dir}/jobs/${__datetime}/initialaverage_dumb
fi
# Center-of-mass align the files onto the average, create an average and repeat
for file in "${_arg_inputs[@]}"; do
echo antsAI -d 3 --convergence 0 \
-m Mattes[${_arg_output_dir}/initialaverage/initialtarget_dumb.nii.gz,${file},32,None] \
-o ${_arg_output_dir}/initialaverage/$(basename ${file} | extension_strip).mat \
-t AlignCentersOfMass >>${_arg_output_dir}/jobs/${__datetime}/initialaverage_reg_com
done
for file in "${_arg_inputs[@]}"; do
echo antsApplyTransforms -d 3 -i ${file} -r ${_arg_output_dir}/initialaverage/initialtarget_dumb.nii.gz \
-t ${_arg_output_dir}/initialaverage/$(basename ${file} | extension_strip).mat \
-o ${_arg_output_dir}/initialaverage/$(basename ${file} | extension_strip).nii.gz >>${_arg_output_dir}/jobs/${__datetime}/initialaverage_resample_com
done
average_images ${_arg_output_dir}/initialaverage/initialtarget_com.nii.gz \
$(for j in "${!_arg_inputs[@]}"; do echo -n "${_arg_output_dir}/initialaverage/$(basename ${_arg_inputs[${j}]} | extension_strip).nii.gz "; done) \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
echo ImageMath 3 ${_arg_output_dir}/initialaverage/initialtarget_com.nii.gz \
PadImage ${_arg_output_dir}/initialaverage/initialtarget_com.nii.gz 20 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
echo ThresholdImage 3 ${_arg_output_dir}/initialaverage/initialtarget_com.nii.gz \
${_arg_output_dir}/initialaverage/bgmask.nii.gz Otsu 4 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
echo ThresholdImage 3 ${_arg_output_dir}/initialaverage/bgmask.nii.gz \
${_arg_output_dir}/initialaverage/bgmask.nii.gz 0.5 Inf 1 0 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
echo ExtractRegionFromImageByMask 3 ${_arg_output_dir}/initialaverage/initialtarget_com.nii.gz \
${_arg_output_dir}/initialaverage/initialtarget_com_recrop.nii.gz \
${_arg_output_dir}/initialaverage/bgmask.nii.gz 1 20 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
echo mv -f ${_arg_output_dir}/initialaverage/initialtarget_com_recrop.nii.gz \
${_arg_output_dir}/initialaverage/initialtarget_com.nii.gz \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
if [[ -n ${_arg_starting_average_resolution} ]]; then
echo ResampleImage 3 ${_arg_output_dir}/initialaverage/initialtarget_com.nii.gz \
${_arg_output_dir}/initialaverage/initialtarget.nii.gz ${_arg_starting_average_resolution} 0 \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
else
echo cp -f ${_arg_output_dir}/initialaverage/initialtarget_com.nii.gz \
${_arg_output_dir}/initialaverage/initialtarget.nii.gz \
>>${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
fi
debug "$(cat ${_arg_output_dir}/jobs/${__datetime}/initialaverage_reg_com)"
debug "$(cat ${_arg_output_dir}/jobs/${__datetime}/initialaverage_resample_com)"
debug "$(cat ${_arg_output_dir}/jobs/${__datetime}/initialaverage_com)"
if [[ ${_arg_dry_run} == "off" ]]; then
qbatch ${_arg_block} --logdir ${_arg_output_dir}/logs/${__datetime} \
--walltime ${_arg_walltime_short} \
-N ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage_reg_com \
${_arg_job_predepend} --depend ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage_dumb \
${_arg_output_dir}/jobs/${__datetime}/initialaverage_reg_com
qbatch ${_arg_block} --logdir ${_arg_output_dir}/logs/${__datetime} \
--walltime ${_arg_walltime_short} \
-N ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage_resample_com \
${_arg_job_predepend} --depend ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage_reg_com \
${_arg_output_dir}/jobs/${__datetime}/initialaverage_resample_com
qbatch ${_arg_block} --logdir ${_arg_output_dir}/logs/${__datetime} \
--walltime ${_arg_walltime_short} \
-N ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage_com \
${_arg_job_predepend} --depend ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage_resample_com \
-- bash ${_arg_output_dir}/jobs/${__datetime}/initialaverage_com
fi
last_round_job="--depend ${_arg_jobname_prefix}modelbuild_${__datetime}_initialaverage_com"
elif [[ ${_arg_starting_target} == "first" ]]; then
info "Using the first input image "${_arg_inputs[0]}" as initalization target"
cp -f ${_arg_inputs[0]} ${_arg_output_dir}/initialaverage/initialtarget.nii.gz
last_round_job=""
else
error "Starting target setting ${_arg_starting_target} unknown"
fi
else
last_round_job=""
fi
ln -srf ${_arg_output_dir}/initialaverage/initialtarget.nii.gz ${_arg_output_dir}/initialtarget.nii.gz
target=${_arg_output_dir}/initialtarget.nii.gz
else
if [[ ${_arg_skip_file_checks} == "on" ]]; then
ln -srf ${_arg_starting_target} ${_arg_output_dir}/initialtarget.nii.gz
else
info "Checking starting target"
if [[ ! -s ${_arg_starting_target} ]]; then
failure "Starting target ${_arg_starting_target} is non-existant or zero size"
fi
cp -f ${_arg_starting_target} ${_arg_output_dir}/initialtarget.nii.gz
fi
target=${_arg_output_dir}/initialtarget.nii.gz
last_round_job=""
fi
walltime_reg=${_arg_walltime_linear}
#Convert comma-seperated options into array
IFS=',' read -r -a _arg_stages <<<${_arg_stages}
#Read gradient schedule into array
IFS=',' read -r -a _arg_gradient_step <<<${_arg_gradient_step}
# Looping over different stages of modelbuilding
for reg_type in "${_arg_stages[@]}"; do
stage_iterations=$(grep -E -o '[0-9]+' <<<${reg_type} || echo ${_arg_iterations})
reg_type=$(sed -r 's/\[[0-9]+\]//g' <<<${reg_type})
k=0
if [[ "${reg_type}" == *volgenmodel* ]]; then
tmpdir=$(mktemp -d)
info "Calculating maximum image feature dimension of template for volgenmodel iterations"
ThresholdImage 3 ${_arg_output_dir}/initialtarget.nii.gz ${tmpdir}/bgmask.h5 1e-12 Inf 1 0
ThresholdImage 3 ${_arg_output_dir}/initialtarget.nii.gz ${tmpdir}/otsu.h5 Otsu 4 ${tmpdir}/bgmask.h5 &> /dev/null
ThresholdImage 3 ${tmpdir}/otsu.h5 ${tmpdir}/otsu.h5 2 Inf 1 0
LabelGeometryMeasures 3 ${tmpdir}/otsu.h5 none ${tmpdir}/geometry.csv &> /dev/null
volgenmodel_fixed_maximum_resolution=$(python -c "print(max([ a*b for a,b in zip( [ a-b for a,b in zip( [float(x) for x in \"$(tail -1 ${tmpdir}/geometry.csv | cut -d, -f 14,16,18)\".split(\",\") ],[float(x) for x in \"$(tail -1 ${tmpdir}/geometry.csv | cut -d, -f 13,15,17)\".split(\",\") ])],[abs(x) for x in [float(x) for x in \"$(PrintHeader ${_arg_output_dir}/initialtarget.nii.gz 1)\".split(\"x\")]])]))")
info "Calculating minimum image feature dimension of template for volgenmodel iterations"
volgenmodel_fixed_minimum_resolution=$(python -c "print(min([abs(x) for x in [float(x) for x in \"$(PrintHeader ${_arg_output_dir}/initialtarget.nii.gz 1)\".split(\"x\")]]))")
volgenmodel_iterations=$(ants_generate_iterations.py --min ${volgenmodel_fixed_minimum_resolution} --max ${volgenmodel_fixed_maximum_resolution} | grep shrink | grep -o x | wc -l)
info "volgenmodel registration will perform ${volgenmodel_iterations} levels with ${stage_iterations} repeats at each level"
rm -rf ${tmpdir}
else
volgenmodel_iterations=0
fi
while ((k <= volgenmodel_iterations)); do
i=0
if [[ "${reg_type}" == *volgenmodel* ]]; then
reg_type=volgenmodel-nlin_${k}
IFS=: read h m s <<<"${_arg_walltime_nonlinear%.*}"
walltime_reg=$((10#$s+10#$m*60+10#$h*3600))
walltime_reg=$(calc "int(${walltime_reg}*8^(${k}/${volgenmodel_iterations} - 1))")
if ((walltime_reg < 900)); then
walltime_reg=900
fi
walltime_reg=$(date -d@${walltime_reg} -u +%H:%M:%S)
fi
while ((i < stage_iterations)); do
info "Computing ${reg_type} stage iteration $((i + 1)) jobs"
if [[ ! -z ${_arg_gradient_step[i]:-} ]]; then
gradient_step=${_arg_gradient_step[i]}
else
gradient_step=${_arg_gradient_step[-1]}
fi
if [[ ${target} == ${_arg_output_dir}/initialtarget.nii.gz ]]; then
use_histogram=""
else
use_histogram="--histogram-matching"
fi
if [[ ! -s ${_arg_output_dir}/${reg_type}/${i}/average/template_sharpen_shapeupdate.nii.gz ]]; then
mkdir -p ${_arg_output_dir}/${reg_type}/${i}/{transforms,resample,average}
mkdir -p ${_arg_output_dir}/${reg_type}/${i}/resample/masks
# Empty files
>${_arg_output_dir}/jobs/${__datetime}/${reg_type}_${i}_reg
>${_arg_output_dir}/jobs/${__datetime}/${reg_type}_${i}_maskresample
>${_arg_output_dir}/jobs/${__datetime}/${reg_type}_${i}_maskaverage
# Register images to target
for j in "${!_arg_inputs[@]}"; do
# Check for existence of moving mask, if it exists, add option
if [[ -s ${_arg_masks[${j}]} ]]; then
_mask="--moving-mask ${_arg_masks[${j}]}"
else
_mask=""
fi
# If target mask is defined, add to the registration command
if [[ -n ${target_mask} ]]; then
_mask+=" --fixed-mask ${target_mask}"
fi
# If three was a previous round of modelbuilding, bootstrap registration with its affine (if enabled), also do so for nlin-only stages
if [[ $(basename ${target}) == "template_sharpen_shapeupdate.nii.gz" && $(dirname $(dirname $(dirname $(dirname ${target})))) == "${_arg_output_dir}" && ${_arg_reuse_affines} == "on" ]]; then
bootstrap="--initial-transform $(dirname $(dirname ${target}))/transforms/$(basename ${_arg_inputs[${j}]} | extension_strip)_0GenericAffine.mat"
else
bootstrap=""
fi
if [[ ! -s ${_arg_output_dir}/${reg_type}/${i}/resample/$(basename ${_arg_inputs[${j}]} | extension_strip).nii.gz ]]; then
if [[ ${reg_type} =~ ^(rigid|similarity|affine)$ ]]; then
# Linear stages of registration
walltime_reg=${_arg_walltime_linear}
echo antsRegistration_affine_SyN.sh --clobber \
${_arg_float} ${_arg_fast} \
${use_histogram} \
${_arg_linear_convergence} \
${_arg_linear_shrink_factors} \
${_arg_linear_smoothing_sigmas} \
${_arg_syn_convergence} \
${_arg_syn_shrink_factors} \
${_arg_syn_smoothing_sigmas} \
--skip-nonlinear --linear-type ${reg_type} \
${_arg_mask_extract} ${_mask} \
${bootstrap} \
--convergence ${_arg_convergence} \
-o ${_arg_output_dir}/${reg_type}/${i}/resample/$(basename ${_arg_inputs[${j}]} | extension_strip).nii.gz \
${_arg_inputs[${j}]} ${target} \
${_arg_output_dir}/${reg_type}/${i}/transforms/$(basename ${_arg_inputs[${j}]} | extension_strip)_ \
>>${_arg_output_dir}/jobs/${__datetime}/${reg_type}_${i}_reg
elif [[ ${reg_type} == "nlin" ]]; then
# Full regisration affine + nlin