#!/bin/bash

##
##  Copyright 2004-2014 SRI International
##
##  Copyright 1997-2011 Torsten Rohlfing
##
##  This file is part of the Computational Morphometry Toolkit.
##
##  http://www.nitrc.org/projects/cmtk/
##
##  The Computational Morphometry Toolkit is free software: you can
##  redistribute it and/or modify it under the terms of the GNU General Public
##  License as published by the Free Software Foundation, either version 3 of
##  the License, or (at your option) any later version.
##
##  The Computational Morphometry Toolkit is distributed in the hope that it
##  will be useful, but WITHOUT ANY WARRANTY; without even the implied
##  warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
##  GNU General Public License for more details.
##
##  You should have received a copy of the GNU General Public License along
##  with the Computational Morphometry Toolkit.  If not, see
##  <http://www.gnu.org/licenses/>.
##
##  $Revision: 5370 $
##
##  $LastChangedDate: 2014-07-28 21:26:05 -0700 (Mon, 28 Jul 2014) $
##
##  $LastChangedBy: torsten_at_home $
##

RUNTEST=$1
CONFIG=$2
VALGRIND=$3

BUILDNAME=@BUILDNAME@
DATADIR=@CMTK_DATA_ROOT@/testing/inputs

BINDIR=@EXECUTABLE_OUTPUT_PATH@/${CONFIG}
if [ ! -d ${BINDIR}/. ]; then
    BINDIR=@EXECUTABLE_OUTPUT_PATH@
fi

BASELINE_DEFAULT=@CMTK_DATA_ROOT@/testing/baseline/${RUNTEST}
BASELINE=${BINDIR}/../testing/baseline/${RUNTEST}
if [ ! -d ${BASELINE} ]; then
    BASELINE=${BASELINE_DEFAULT}
fi

HOSTNAME=`uname -n`

NUMDIFF=@NUMDIFF_EXECUTABLE@

tmpdir=${BINDIR}/../testing/temporary/${HOSTNAME}/${RUNTEST}
if [ -e ${tmpdir} ]; then
    rm -rf ${tmpdir}
fi
mkdir -p ${tmpdir}

sqlite=${BINDIR}/sqlite
if [ ! -f ${sqlite} ]; then
    sqlite=sqlite3
fi

sed=/opt/local/bin/gsed
if [ ! -f ${sed} ]; then
    sed=sed
fi

cd ${DATADIR}

run()
{
    cmd=$*

    echo "pushd $PWD; ${BINDIR}/$cmd; popd" 1>&2
    if ${VALGRIND} ${BINDIR}/$cmd; then
	return
    else
	exit 1
    fi
}

run_expect_fail()
{
    cmd=$*

    echo "pushd $PWD; ${BINDIR}/$cmd; popd"
    if ${BINDIR}/$cmd; then
	exit 1
    else
	return
    fi
}

run_eval()
{
    cmd=$*

    echo "pushd $PWD; $cmd; popd"
    if eval "${VALGRIND} $cmd"; then
	return
    else
	exit 1
    fi
}

run_eval_expect_fail()
{
    cmd=$*

    echo "pushd $PWD; $cmd; popd"
    if eval "${VALGRIND} $cmd"; then
	exit 1
    else
	return
    fi
}

get_unzipped()
{
    if test -f ${1}.gz; then
	if [ "`uname`" = "Darwin" ]; then
	    local tmp=`mktemp /tmp/temp.XXXX`
	else
	    local tmp=`mktemp`
	fi
	gzip -cd ${1}.gz > ${tmp}
	echo ${tmp}
    else
	echo ${1}
    fi
}

remove_if_tempfile()
{
    for f in $*; do
	local dir=`dirname $f`
	if [ "${dir}" == "/tmp" ]; then
	    rm $f
	fi 
    done
}

check_result()
{
    baseline=`get_unzipped ${BASELINE}/$1`
    result=`get_unzipped ${tmpdir}/$1`

    if test ! -f ${result}; then
	echo "Results file ${result} does not exist"
	remove_if_tempfile ${baseline} ${result}
	exit 1
    fi

    if test ! -f ${baseline}; then
	echo "Baseline file ${baseline} does not exist"
	remove_if_tempfile ${baseline} ${result}
	exit 1
    fi

    local diff="cmp"
    if file ${result} | fgrep text; then
##	diff="diff --strip-trailing-cr"
	diff="${NUMDIFF} --relative-tolerance=1e-5 --absolute-tolerance=5e-7"
    fi

    echo "${diff} ${tmpdir}/$1 ${BASELINE}/$1"

    if ${diff} $result $baseline; then
	remove_if_tempfile ${baseline} ${result}
	return
    else
	remove_if_tempfile ${baseline} ${result}
	exit 1
    fi
}

check_results()
{
    for r in $*; do
	check_result $r
    done
}

check_image()
{
    baseline=${BASELINE}/$1
    result=${tmpdir}/$1
    
    abs_threshold=1e-5 ## if this is made much smaller, need to adjust "scale=" on next line:

    # see if maximum relative difference between images exceeds 1e-6
    difference=`${BINDIR}/similarity $baseline $result | fgrep SIMval | cut -f3`
    compare=`echo "SCALE; $difference > $abs_threshold" | sed 's/e/*10^/g;s/SCALE/scale=10/' | bc`

    echo difference=$difference compare=$compare

    if [ "${compare}" = "0" ]; then
	return
    else
	echo "Absolute image difference $difference exceeds threshold $abs_threshold"
    fi

    rel_threshold=1e-5 ## if this is made much smaller, need to adjust "scale=" on next line:

    difference=`${BINDIR}/similarity $baseline $result | fgrep SIMval | cut -f4`
    compare=`echo "SCALE; $difference > $rel_threshold" | sed 's/e/*10^/g;s/SCALE/scale=10/' | bc`

    echo difference=$difference compare=$compare

    if [ "${compare}" = "0" ]; then
	return
    else
	echo "Relative image difference $difference exceeds threshold $rel_threshold"
	exit 1
    fi
}

check_images()
{
    for r in $*; do
	check_image $r
    done
}

case ${RUNTEST} in
    average_imagesMean)
	run average_images -o ${tmpdir}/average.hdr spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results average.img
	;;
    average_imagesMeanNormPadd)
	run average_images -o ${tmpdir}/average.hdr --set-padding-value 0 --normalize-mean-stdev spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results average.img
	;;
    average_imagesMeanAbsLog)
	run average_images --set-padding-value 0 -o ${tmpdir}/average.hdr --abs --log spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results average.img
	;;
    average_imagesVariance)
	run average_images -o ${tmpdir}/variance.hdr --var spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results variance.img
	;;
    average_imagesStDev)
	run average_images -o ${tmpdir}/stdev.hdr --stdev spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results stdev.img
	;;
    average_imagesEntropy)
	run average_images -o ${tmpdir}/entropy.hdr --entropy spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results entropy.img
	;;
    average_imagesZScore)
	run average_images -o ${tmpdir}/zscore.hdr --zscore spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results zscore.img
	;;
    avg_admDefault2)
        run avg_adm --output ${tmpdir}/avg.hdr --output-warp ${tmpdir}/avg.warp spgr_brain_12_warp.list
	check_results avg.img avg.warp
	;;
    avg_admDefault3)
        run avg_adm --output ${tmpdir}/avg.hdr --output-warp ${tmpdir}/avg.warp spgr_brain_12_warp.list spgr_brain_13_warp.list
	check_results avg.img avg.warp
	;;
    avg_admJacobianFloat)
        run avg_adm --jacobian --float --output ${tmpdir}/avg.hdr --output-warp ${tmpdir}/avg.warp spgr_brain_12_warp.list spgr_brain_13_warp.list
	check_results avg.img avg.warp
	;;
    avg_admLabels)
        run avg_adm --nn --label --replace-from spgr_brain_ --replace-to parc --output ${tmpdir}/avg.hdr --output-warp ${tmpdir}/avg.warp spgr_brain_12_warp.list spgr_brain_13_warp.list
	check_results avg.img avg.warp
	;;
    avg_admPaddOutZeroNN)
        run avg_adm --nn --pad-out 0 --output ${tmpdir}/avg.hdr --output-warp ${tmpdir}/avg.warp spgr_brain_12_warp.list spgr_brain_13_warp.list
	check_results avg.img avg.warp
	;;
    avg_admNoReferenceModelCubic)
        run avg_adm --byte --cubic --output ${tmpdir}/avg.hdr --output-warp ${tmpdir}/avg.warp --no-ref-model spgr_brain_12_warp.list spgr_brain_13_warp.list
	check_results avg.img avg.warp
	;;
    avg_admNoScaleModelAutoScale)
        run avg_adm --byte --output ${tmpdir}/avg.hdr --output-warp ${tmpdir}/avg.warp --no-scale-model --auto-scale spgr_brain_12_warp.list spgr_brain_13_warp.list
	check_results avg.img avg.warp
	;;
    avg_admWithAffineNoRefData)
        run avg_adm --byte --output ${tmpdir}/avg.hdr --output-warp ${tmpdir}/avg.warp --no-ref-data --with-affine spgr_brain_12_warp.list spgr_brain_13_warp.list
	check_results avg.img avg.warp
	;;
    concat_affineABA)
	run concat_affine -o ${tmpdir}/concat.xform affineA.xform affineB.xform affineA.xform
	check_results concat.xform
	;;
    concat_affineABAInvert)
	run concat_affine --invert-output -o ${tmpdir}/concat.xform affineA.xform affineB.xform affineA.xform
	check_results concat.xform
	;;
    concat_affineAB1A)
	run concat_affine -o ${tmpdir}/concat.xform affineA.xform --inverse affineB.xform affineA.xform
	check_results concat.xform
	;;
    concat_affineAA1)
	run concat_affine -o ${tmpdir}/concat.xform affineA.xform --inverse affineA.xform
	check_results concat.xform
	;;
    concat_affineA1A)
	run concat_affine -o ${tmpdir}/concat.xform -- --inverse affineA.xform affineA.xform
	check_results concat.xform
	;;
    convert_warpFractional)
	run convert_warp --fractional 0.5 vol001_mr_t0t1_warp.xform ${tmpdir}/fractional.xform
	check_results fractional.xform
	;;
    convert_warpDeformation)
	run convert_warp --deformation-only vol001_mr_t0t1_warp.xform ${tmpdir}/deformation.xform
	check_results deformation.xform
	;;
    convertxType)
        run convertx --byte --char --float --double --int --uint --short --ushort spgr_brain_1.hdr ${tmpdir}/convert.nii
	check_results convert.nii
	;;
    convertxLabels)
        run convertx --labels binary_mask.nii ${tmpdir}/convert.nii
	check_results convert.nii
	;;
    convertxBinarize)
        run convertx --binarize-thresh 100 spgr_brain_1.hdr ${tmpdir}/thresh.hdr
	check_results thresh.img
	;;
    convertxBinarizeOtsu)
        run convertx --otsu-thresh --byte phantom_ax.nii ${tmpdir}/binary.nii
	check_results binary.nii
	;;
    convertxBinarizeOtsuNBins)
        run convertx --otsu-thresh-nbins 128 --byte phantom_ax.nii ${tmpdir}/binary.nii
	check_results binary.nii
	;;
    convertxPruneHighLow)
        run convertx --prune-histogram 16 pat001_pet.hdr ${tmpdir}/prune.nii
	check_results prune.nii
	;;
    convertxPruneHigh)
        run convertx --prune-histogram-high 16 pat001_pet.hdr ${tmpdir}/prune.nii
	check_results prune.nii
	;;
    convertxPruneLow)
        run convertx --prune-histogram-low 16 pat001_pet.hdr ${tmpdir}/prune.nii
	check_results prune.nii
	;;
    convertxBoundaryMap)
	run convertx --boundary-map parc1.hdr ${tmpdir}/boundary_map.hdr
	check_results boundary_map.img
	;;
    convertxConnectedComponents)
        run convertx --connected-components binary_mask.nii ${tmpdir}/connected.hdr
	check_results connected.img
	;;
    convertxDistanceUnsigned)
        run convertx --distance-map parc1_bin.hdr ${tmpdir}/dmap.hdr
	check_results dmap.img
	;;
    convertxLaplace)
        run convertx --float --laplace-filter spgr_brain_1.hdr ${tmpdir}/laplace.hdr
	check_results laplace.img
	;;
    convertxMapValues)
        run convertx --map-values 82,86:254 --map-values 16:255 --set-padding 128 --map-values 0 parc3.hdr ${tmpdir}/mapped.hdr
	check_results mapped.img
        ;;
    convertxMapValues2)
        run convertx --set-padding 128 --map-values 82,86:254+16:255+0 parc3.hdr ${tmpdir}/mapped.hdr
	check_results mapped.img
        ;;
    convertxMapValues3)
        run convertx --set-padding 128 --map-values 16:255+82,86:254+0 parc3.hdr ${tmpdir}/mapped.hdr
	check_results mapped.img
        ;;
    convertxMapValuesOnly)
        run convertx  --set-padding 255 --map-values-only 82,86:1 parc3.hdr ${tmpdir}/mapped.hdr
	check_results mapped.img
        ;;
    convertxMapValuesOnly2)
        run convertx  --set-padding 255 --map-values-only 82:1+86:1 parc3.hdr ${tmpdir}/mapped.hdr
	check_results mapped.img
        ;;
    convertxRevert)
        run convertx --revert parc1_bin.hdr ${tmpdir}/revert.hdr
	check_results revert.img
        run convertx --revert parc1.hdr ${tmpdir}/revert.hdr
	check_results revert.img
	;;
    convertxDistanceSigned)
        run convertx --signed-distance-map parc1_bin.hdr ${tmpdir}/dmap.hdr
	check_results dmap.img
	;;
    convertxDistanceSigned2)
        run convertx --signed-distance-map parc1.hdr ${tmpdir}/dmap.hdr
	check_results dmap.img
	;;
    convertxBoundaryMapMultiValue)
	run convertx --multi-boundary-map parc1.hdr ${tmpdir}/boundary_map_multi.hdr
	check_results boundary_map_multi.img
	;;
    convertxCropThresholdWriteRegion)
        run_eval "${BINDIR}/convertx --crop-by-threshold-write-region 1 spgr_brain_1.hdr ${tmpdir}/cropped.nii > ${tmpdir}/crop.txt"
	check_results cropped.nii crop.txt
	;;
    convertxCropRegion1)
        run_eval "${BINDIR}/convertx --crop-by-index 2,2,2,12,12,12 spgr_brain_1.hdr ${tmpdir}/cropped.nii"
	check_results cropped.nii
	;;
    convertxCropRegion2)
        run_eval "${BINDIR}/convertx --crop-by-index 10,10,10,-10,-10,-10 spgr_brain_1.hdr ${tmpdir}/cropped.nii"
	check_results cropped.nii
	;;
    convertxResample)
	run convertx --resample 1.0 phantom_ax.nii ${tmpdir}/resample.nii
	check_results resample.nii
	;;
    convertxResampleExactLabels)
	run convertx --resample-exact 10 lvote_atlas_l0.nii ${tmpdir}/resample.nii
	check_results resample.nii
	;;
    convertxDownsample)
	run convertx --downsample-average 8,4,1 phantom_ax.hdr ${tmpdir}/downsample.hdr
	check_results downsample.hdr downsample.img
	;;
    convertxDownsampleNiftiSform)
	run convertx --downsample-average 8,4,1 phantom_ax_sform.nii ${tmpdir}/downsample_ax.nii
	run convertx --downsample-average 1,8,4 phantom_sa_sform.nii ${tmpdir}/downsample_sa.nii
	run convertx --downsample-average 4,1,8 phantom_co_sform.nii ${tmpdir}/downsample_co.nii
	check_results downsample_ax.nii downsample_sa.nii downsample_co.nii
	;;
    convertxDownsampleNiftiQform)
	run convertx --downsample-average 8,4,1 phantom_ax_qform.nii ${tmpdir}/downsample_ax.nii
	run convertx --downsample-average 1,8,4 phantom_sa_qform.nii ${tmpdir}/downsample_sa.nii
	run convertx --downsample-average 4,1,8 phantom_co_qform.nii ${tmpdir}/downsample_co.nii
	check_results downsample_ax.nii downsample_sa.nii downsample_co.nii
	;;
    convertxDownsampleNiftiQformSform)
	run convertx --downsample-average 8,4,1 phantom_ax_qform_sform.nii ${tmpdir}/downsample_ax.nii
	run convertx --downsample-average 1,8,4 phantom_sa_qform_sform.nii ${tmpdir}/downsample_sa.nii
	run convertx --downsample-average 4,1,8 phantom_co_qform_sform.nii ${tmpdir}/downsample_co.nii
	check_results downsample_ax.nii downsample_sa.nii downsample_co.nii
	;;
    convertxDownsampleNrrd)
	run convertx --downsample-average 8,4,1 phantom_ax.nhdr ${tmpdir}/downsample.nhdr
	check_results downsample.nhdr downsample.raw
	;;
    convertxDownsampleSelect)
	run convertx --downsample-select 8,4,1 phantom_ax.hdr ${tmpdir}/downsample.hdr
	check_results downsample.hdr downsample.img
	;;
    convertxDownsampleSelectNrrd)
	run convertx --downsample-select 8,4,1 phantom_ax.nhdr ${tmpdir}/downsample.nhdr
	check_results downsample.nhdr downsample.raw
	;;
    convertxFlipX)
        run convertx --flip-x parc1_bin.hdr ${tmpdir}/flip.hdr
	check_results flip.img
	;;
    convertxFlipYZ)
        run convertx --flip-y --flip-z parc1_bin.hdr ${tmpdir}/flip.hdr
	check_results flip.img
	;;
    convertxErodeDilateErode)
	run convertx --erode 1 --dilate 2 --erode 1 parc1_bin.hdr ${tmpdir}/parc1_ede.img
	check_results parc1_ede.img
	;;
    convertxDilateErodeDilate)
	run convertx --dilate 1 --erode 2 --dilate 1 parc1_bin.hdr ${tmpdir}/parc1_ded.img
	check_results parc1_ded.img
	;;
    convertxErodeByDistance)
	run convertx --erode-distance 10 parc1_bin.hdr ${tmpdir}/parc1_erode.nii
	check_results parc1_erode.nii
	;;
    convertxErodeByDistanceMultiLabel)
	run convertx --erode-distance-multilabel 10 lvote_atlas_l0.nii ${tmpdir}/erode.nii
	check_results erode.nii
	;;
    convertxDilateByDistance)
	run convertx --dilate-distance 10 parc1_bin.hdr ${tmpdir}/parc1_dilate.nii
	check_results parc1_dilate.nii
	;;
    convertxGaussianFilterSigma)
	run convertx --gaussian-filter-sigma 5.0 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxGaussianFilterFWHM)
        run convertx --gaussian-filter-fwhm 10.0 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxHistogramEqualization)
        run convertx --histogram-equalization spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxHistogramEqualizationNBins)
        run convertx --histogram-equalization-nbins 32 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxMatchMeanSDev)
        run convertx --match-mean-sdev spgr_brain_2.hdr spgr_brain_1.hdr ${tmpdir}/match.nii
        check_results match.nii
        ;;
    convertxMatchHistograms)
        run convertx --match-histograms spgr_brain_2.hdr spgr_brain_1.hdr ${tmpdir}/match.nii
        check_results match.nii
        ;;
    convertxMask)
	run convertx --mask spgr_3t_mask.hdr spgr_3t.hdr ${tmpdir}/masked.hdr
	check_results masked.img
	;;
    convertxMaskInverse)
	run convertx --mask-inverse spgr_3t_mask.hdr spgr_3t.hdr ${tmpdir}/masked.hdr
	check_results masked.img
	;;
    convertxMedianFilter1)
	run convertx --median-filter 1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxMedianFilter2)
	run convertx --median-filter 2 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxMedianFilterXYZ)
	run convertx --median-filter 2,2,1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxMeanFilter)
	run convertx --float --mean-filter 1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxFastMean0Filter)
	run convertx --float --fast-mean-filter 0 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxFastMean1Filter)
	run convertx --float --fast-mean-filter 1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxFastMean2Filter)
	run convertx --float --fast-mean-filter 2 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxFastMean2PadFilter)
	run convertx --set-padding 0 --float --fast-mean-filter 2 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxVarianceFilter)
	run convertx --float --variance-filter 1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxFastVariance0Filter)
	run convertx --float --fast-variance-filter 0 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxFastVariance1Filter)
	run convertx --float --fast-variance-filter 1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxFastVariance2Filter)
	run convertx --float --fast-variance-filter 2 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxFastVariance2PadFilter)
	run convertx --set-padding 0 --float --fast-variance-filter 2 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxThirdMomentFilter)
	run convertx --float --third-moment-filter 1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxStandardDeviationFilter)
	run convertx --float --standard-deviation-filter 1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxSmoothnessFilter)
	run convertx --float --smoothness-filter 1 spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.img
	;;
    convertxNiftiToAnalyze)
	run convertx spgr_brain_1.nii ${tmpdir}/spgr_brain_1.hdr
	check_results spgr_brain_1.hdr spgr_brain_1.img
	;;
    convertxNiftiToMetaImage)
	run convertx spgr_brain_1.nii ${tmpdir}/spgr_brain_1.mha
	check_results spgr_brain_1.mha
	;;
    convertxAnalyzeToNifti)
	run convertx spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.nii
	check_results spgr_brain_1.nii
	;;
    convertxAnalyzeToNiftiRAS)
        export CMTK_LEGACY_WRITE_IMAGES_RAS=1
	run convertx spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.nii
	unset CMTK_LEGACY_WRITE_IMAGES_RAS
	check_results spgr_brain_1.nii	
	;;
    convertxNiftiDetachedToNifti)
	run convertx spgr_brain_nifti.hdr ${tmpdir}/spgr_brain_1.nii
	check_results spgr_brain_1.nii
	;;
    convertxAnalyzeToNiftiDetached)
	run convertx spgr_brain_1.hdr ${tmpdir}/spgr_brain_1.img
	check_results spgr_brain_1.hdr spgr_brain_1.img
	;;
    convertxUncompressedNIFTI1)
        export CMTK_WRITE_UNCOMPRESSED=1
        run convertx parc1_bin.hdr ${tmpdir}/out.nii
	unset CMTK_WRITE_UNCOMPRESSED
	if [ ! -e ${tmpdir}/out.nii ]; then exit 1; fi
	;;
    convertxUncompressedNIFTI2)
        export CMTK_WRITE_UNCOMPRESSED=1
        run convertx parc1_bin.hdr ${tmpdir}/out.nii.gz
	unset CMTK_WRITE_UNCOMPRESSED
	if [ ! -e ${tmpdir}/out.nii.gz ]; then exit 1; fi
	;;
    convertxUncompressedNIFTI3)
        unset CMTK_WRITE_UNCOMPRESSED
        run convertx parc1_bin.hdr ${tmpdir}/out.nii
	if [ ! -e ${tmpdir}/out.nii.gz ]; then exit 1; fi
	;;
    convertxUncompressedNIFTI4)
        unset CMTK_WRITE_UNCOMPRESSED
        run convertx parc1_bin.hdr ${tmpdir}/out.nii.gz
	if [ ! -e ${tmpdir}/out.nii.gz ]; then exit 1; fi
	;;
    convertxThresholdBelow)
	run convertx --set-padding 0 --thresh-below 100 spgr_brain_1.hdr ${tmpdir}/thresh.hdr
	check_results thresh.img
	;;
    convertxThresholdAbove)
        run convertx --set-padding 0 --thresh-above 100 spgr_brain_1.hdr ${tmpdir}/thresh.hdr
	check_results thresh.img
	;;
    convertxThresholdBelowToPadding)
	run convertx --set-padding 0 --thresh-below-to-padding 100 spgr_brain_1.hdr ${tmpdir}/thresh.hdr
	check_results thresh.img
	;;
    convertxThresholdAboveToPadding)
        run convertx --set-padding 0 --thresh-above-to-padding 100 spgr_brain_1.hdr ${tmpdir}/thresh.hdr
	check_results thresh.img
	;;
    convertxScaleToRange)
	run convertx --scale-to-range 128:192 spgr_brain_1.hdr ${tmpdir}/scaled.hdr
	check_results scaled.img
	;;
    convertxReplacePadding)
	run convertx --byte --set-padding 0 --replace-padding 255 spgr_brain_1.hdr ${tmpdir}/replaced.hdr
	check_results replaced.img
        ;;
    convertxReplaceInfNaN)
	run convertx --replace-inf-nan 255 infinite.nii ${tmpdir}/replaced.hdr
	check_results replaced.img
        ;;
    dbtool_AddImages)
      run dbtool add_images ${tmpdir}/db.sqlite image1 image2
      ${sqlite} ${tmpdir}/db.sqlite "SELECT * FROM images ORDER BY path ASC" > ${tmpdir}/images
      check_results images
      ;;
    dbtool_AddImages2)
      run dbtool add_images ${tmpdir}/db.sqlite image1 image2 image3 image3
      ${sqlite} ${tmpdir}/db.sqlite "SELECT * FROM images ORDER BY path ASC" > ${tmpdir}/images
      check_results images
      ;;
    dbtool_ListSpace)
      run_eval "${BINDIR}/dbtool list_space images.sqlite image1c > ${tmpdir}/list.txt"
      check_results list.txt
      ;;
    dbtool_GetXform1)
      run_eval "${BINDIR}/dbtool get_xform imagesSingleXform.sqlite image1.nii image2.nii > ${tmpdir}/xform.txt"
      check_results xform.txt
      ;;
    dbtool_GetXform2)
      run_eval "${BINDIR}/dbtool get_xform imagesSingleXform.sqlite image2.nii image1.nii > ${tmpdir}/xform.txt"
      check_results xform.txt
      ;;
    dbtool_GetXform3)
      run_eval "${BINDIR}/dbtool get_xform imagesMultiXforms.sqlite image1.nii image2.nii > ${tmpdir}/xform.txt"
      check_results xform.txt
      ;;
    dbtool_GetXform4)
      run_eval "${BINDIR}/dbtool get_xform imagesMultiXforms.sqlite image2.nii image1.nii > ${tmpdir}/xform.txt"
      check_results xform.txt
      ;;
    dbtool_GetXform5)
      run_eval "${BINDIR}/dbtool get_xform --all imagesMultiXforms.sqlite image1.nii image2.nii > ${tmpdir}/xform.txt"
      check_results xform.txt
      ;;
    dbtool_GetXform6)
      run_eval "${BINDIR}/dbtool get_xform --all imagesMultiXforms.sqlite image2.nii image1.nii > ${tmpdir}/xform.txt"
      check_results xform.txt
      ;;
    dcm2image)
	run dcm2image -O ${tmpdir}/00%n.hdr dcm/
	check_results 001.hdr 001.img 002.hdr 002.img 003.hdr 003.img
	;;
    dcm2imageSubs)
        run dcm2image -O ${tmpdir}/%D_%R_%E%N.nii dcm/
	check_results 3-plane-localizer_5.104_1.52-1.nii 3-plane-localizer_5.104_1.52-2.nii 3-plane-localizer_5.104_1.52-3.nii
	;;
    dcm2imageZ)
	run dcm2image -O ${tmpdir}/00%n.nii dcmz/
	check_results 001.nii 002.nii 003.nii
	;;
    dcm2imageNrrd)
	run dcm2image -O ${tmpdir}/00%n.nhdr dcm/
	check_results 001.nhdr 001.raw 002.nhdr 002.raw 003.nhdr 003.raw
	;;
    dcm2imageEmbedPatientNameAnalyze)
	run dcm2image --embed PatientName -O ${tmpdir}/00%n.hdr dcm/
	check_results 001.hdr 002.hdr 003.hdr
	;;
    dcm2imageEmbedPatientNameNifti)
	run dcm2image --embed PatientName -O ${tmpdir}/00%n.nii dcm/
	check_results 001.nii 002.nii 003.nii
	;;
    dcm2imageEmbedSeriesDescriptionNifti)
	run dcm2image --embed SeriesDescription -O ${tmpdir}/00%n.nii dcm/
	check_results 001.nii 002.nii 003.nii
	;;
    dcm2imageEmbedStudyIDDateNifti)
        run dcm2image --embed StudyID_StudyDate -O ${tmpdir}/00%n.nii dcm/
	check_results 001.nii
	;;
    dcm2imageEmbedPatientNameNrrd)
	run dcm2image --embed PatientName -O ${tmpdir}/00%n.nhdr dcm/
	check_results 001.nhdr 002.nhdr 003.nhdr
	;;
    dcm2imageMosaic)
	run dcm2image -x --include-identifiers -O ${tmpdir}/00.nii mr-mosaic/
	check_results 00.nii 00.nii.xml
	;;
    dcm2imageMosaicPACS)
	run dcm2image -x --include-identifiers -O ${tmpdir}/00.nii mr-mosaic-pacs/
	check_results 00.nii 00.nii.xml
	;;
    dcm2imageDiffusionGEXML)
        run dcm2image -x --tolerance 1e-4 --include-identifiers -O ${tmpdir}/%n.nii mr-dwi-ge/
	check_results 1.nii 1.nii.xml 2.nii 2.nii.xml
	;;
    dcm2imageDiffusionSiemensXML)
        run dcm2image -x --include-identifiers -O ${tmpdir}/%n.nii mr-dwi-siemens/
	check_results 1.nii 1.nii.xml 2.nii 2.nii.xml 3.nii 3.nii.xml 4.nii 4.nii.xml
	;;
    dcm2imageMosaicAnon)
	run dcm2image -x -O ${tmpdir}/00.nii mr-mosaic/
	check_results 00.nii 00.nii.xml
	;;
    dcm2imageMosaicPACSAnon)
	run dcm2image -x -O ${tmpdir}/00.nii mr-mosaic-pacs/
	check_results 00.nii 00.nii.xml
	;;
    dcm2imageDiffusionGEXMLAnon)
        run dcm2image -x --tolerance 1e-4 -O ${tmpdir}/%n.nii mr-dwi-ge/
	check_results 1.nii 1.nii.xml 2.nii 2.nii.xml
	;;
    dcm2imageDiffusionSiemensXMLAnon)
        run dcm2image -x -O ${tmpdir}/%n.nii mr-dwi-siemens/
	check_results 1.nii 1.nii.xml 2.nii 2.nii.xml 3.nii 3.nii.xml 4.nii 4.nii.xml
	;;
    dcm2imageExclude)
        run dcm2image --exclude ImageOrientationPatient=1\\-0\\0\\-0\\1\\0 -O ${tmpdir}/image%n.nii dcm/
	check_results image1.nii image2.nii
	;;
    dcm2imageInclude)
        run dcm2image --filter ImageOrientationPatient=1\\-0\\0\\-0\\1\\0 -O ${tmpdir}/image%n.nii dcm/
	check_results image.nii
	;;
    dcm2imageSubsDirName)
        run dcm2image -x --tolerance 1e-4 --include-identifiers -O ${tmpdir}/%1/%0.nii mr-dwi-ge/ mr-dwi-siemens/
	check_results mr-dwi-ge/I0150.dcm.nii mr-dwi-ge/I0150.dcm.nii.xml mr-dwi-ge/I0280.dcm.nii mr-dwi-ge/I0280.dcm.nii.xml
	check_results mr-dwi-siemens/I0001.dcm.nii mr-dwi-siemens/I0001.dcm.nii.xml mr-dwi-siemens/I0002.dcm.nii mr-dwi-siemens/I0002.dcm.nii.xml 
	check_results mr-dwi-siemens/I0003.dcm.nii mr-dwi-siemens/I0003.dcm.nii.xml mr-dwi-siemens/I0004.dcm.nii mr-dwi-siemens/I0004.dcm.nii.xml
	;;
    describeEmpty)
	run_eval "${BINDIR}/describe -m empty.nii > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMountPoints)
        run_eval "CMTK_MOUNTPOINTS=INPUTS=${DATADIR} ${BINDIR}/describe -m INPUTS/spgr_brain_1.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMountPointsMulti)
        run_eval "CMTK_MOUNTPOINTS=DUMMY=/fs/dummy,INPUTS=${DATADIR} ${BINDIR}/describe -m INPUTS/spgr_brain_1.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMountPointsPrefix)
        run_eval "CMTK_MOUNTPOINTS=^INPUTS=${DATADIR} ${BINDIR}/describe -m INPUTS/spgr_brain_1.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMountPointsPrefixInvalid)
        run_eval "CMTK_MOUNTPOINTS=^NPUTS=INVALID,^INPUTS=${DATADIR} ${BINDIR}/describe -m INPUTS/spgr_brain_1.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeDICOM)
	run_eval "${BINDIR}/describe -m dcm/I0007.dcm > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeDICOMZ)
	run_eval "${BINDIR}/describe -m dcmz/I0007.dcm > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMosaicDICOM)
	run_eval "${BINDIR}/describe -m mr-mosaic/fmri.dcm > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMosaicPACSDICOM)
	run_eval "${BINDIR}/describe -m mr-mosaic-pacs/image.dcm > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeVanderbilt)
	run_eval "${BINDIR}/describe -m vanderbilt/header.ascii > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeBZip2a)
        run_eval "${BINDIR}/describe -m bzip_test.nii > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeBZip2b)
        run_eval "${BINDIR}/describe -m bzip_test.nii.bz2 > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeLZMAa)
        run_eval "${BINDIR}/describe -m lzma_test.nii > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeLZMAb)
        run_eval "${BINDIR}/describe -m lzma_test.nii.lzma > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeXZa)
        run_eval "${BINDIR}/describe -m xz_test.nii > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeXZb)
        run_eval "${BINDIR}/describe -m xz_test.nii.xz > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMR1)
	run_eval "${BINDIR}/describe -m parc1_bin.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMR2)
	run_eval "${BINDIR}/describe -m phantom_ax.hdr phantom_co.hdr phantom_sa.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMR3)
	run_eval "${BINDIR}/describe -m header_only.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMR4)
	run_eval "${BINDIR}/describe -m phantom_ax.nii phantom_co.nii phantom_sa.nii > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeHuman)
	run_eval "${BINDIR}/describe --read-ras phantom_ax.nii phantom_co.nii phantom_sa.nii > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMRBiorad)
	run_eval "${BINDIR}/describe -m bioradvol.PIC > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMRBioradGz)
	run_eval "${BINDIR}/describe -m gz_bioradvol.PIC.gz > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMRNrrd1)
	run_eval "${BINDIR}/describe -m phantom_ax.nhdr phantom_co.nhdr phantom_sa.nhdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeMRNrrd2)
	run_eval "${BINDIR}/describe -m split_ax_0.nhdr split_ax_1.nhdr split_ax_2.nhdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeNrrdNoOrigin)
	run_eval "${BINDIR}/describe -m phantom_ax_noOrigin.nhdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeNiftiDetached348)
	run_eval "${BINDIR}/describe -m spgr_brain_nifti_hdr348.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeEmbedAnalyze)
	run_eval "${BINDIR}/describe -m embed_patient.hdr > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeEmbedNifti)
	run_eval "${BINDIR}/describe -m embed_patient.nii > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeEmbedNrrd)
	run_eval "${BINDIR}/describe -m embed_patient.nrrd > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeXform)
	run_eval "${BINDIR}/describe spgr_brain_12_warp.list vol001_mr_t0t1.list > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    describeXformMachine)
	run_eval "${BINDIR}/describe -m spgr_brain_12_warp.list vol001_mr_t0t1.list > ${tmpdir}/describe.txt"
	check_results describe.txt
	;;
    destripeDefault)
        run destripe -y stripes_crop_byte.nii ${tmpdir}/destripe.nii
	check_results destripe.nii
	;;
    destripeKernelFloat)
        run destripe -y --kernel-fwhm 5 --kernel-radius 2 --write-float stripes_crop_byte.nii ${tmpdir}/destripe.nii
	check_results destripe.nii
	;;
    detect_adni_phantomDefault)
        run detect_adni_phantom --write-labels ${tmpdir}/labels.nii --write-rigid ${tmpdir}/rigid.xform --write-affine ${tmpdir}/affine.xform spgr_magphan.nii ${tmpdir}/magphan.xml
        check_results labels.nii rigid.xform affine.xform magphan.xml
	;;
    detect_adni_phantomRefineXform)
        run detect_adni_phantom --tolerant --refine-xform --write-rigid ${tmpdir}/rigid.xform --write-affine ${tmpdir}/affine.xform spgr_magphan_lowcontrast.nii ${tmpdir}/magphan.xml
        check_results rigid.xform affine.xform magphan.xml
	;;
    detect_adni_phantomRefineOutliers)
        run detect_adni_phantom --tolerant --refine-outliers --write-rigid ${tmpdir}/rigid.xform --write-affine ${tmpdir}/affine.xform spgr_magphan_lowcontrast.nii ${tmpdir}/magphan.xml
        check_results rigid.xform affine.xform magphan.xml
	;;
    detect_adni_phantomExcludeOutliers)
        run detect_adni_phantom --tolerant --exclude-outliers --write-rigid ${tmpdir}/rigid.xform --write-affine ${tmpdir}/affine.xform spgr_magphan_lowcontrast.nii ${tmpdir}/magphan.xml
        check_results rigid.xform affine.xform magphan.xml
	;;
    detect_adni_phantomErodeNonStd)
        run detect_adni_phantom --erode-snr 20 --erode-cnr 2 spgr_magphan.nii ${tmpdir}/magphan.xml
        check_results magphan.xml
	;;
    detect_adni_phantomBadFOV)
        run_expect_fail detect_adni_phantom spgr_magphan_badFOV.nii ${tmpdir}/magphan.xml
	;;
    detect_adni_phantomTolerantBadFOV)
        run detect_adni_phantom --tolerant --write-labels ${tmpdir}/labels.nii spgr_magphan_badFOV.nii ${tmpdir}/magphan.xml
	check_results magphan.xml labels.nii
	;;
    detect_adni_phantomMissingSphere)
        run detect_adni_phantom --write-labels ${tmpdir}/labels.nii --write-rigid ${tmpdir}/rigid.xform --write-affine ${tmpdir}/affine.xform spgr_magphan_missingSphere.nii ${tmpdir}/magphan.xml
        check_results labels.nii rigid.xform affine.xform magphan.xml
	;;
    detect_adni_phantomBrokenSNR)
        run detect_adni_phantom --write-labels ${tmpdir}/labels.nii --write-rigid ${tmpdir}/rigid.xform --write-affine ${tmpdir}/affine.xform spgr_magphan_brokenSNR.nii ${tmpdir}/magphan.xml
        check_results labels.nii rigid.xform affine.xform magphan.xml
	;;
    detect_spheres_matched_filter)
        run detect_spheres_matched_filter --radius 15 --filter-margin 2 adni_phantom2mm.nii ${tmpdir}/filtered.nii
	run convertx --float --downsample-select 4,4,4 ${tmpdir}/filtered.nii ${tmpdir}/filtered.nii
	check_images filtered.nii
	;;
    detect_spheres_matched_filterNormalized)
        run detect_spheres_matched_filter --normalized --radius 15 --filter-margin 1 adni_phantom2mm.nii ${tmpdir}/filtered.nii
	run convertx --float --downsample-select 4,4,4 ${tmpdir}/filtered.nii ${tmpdir}/filtered.nii
	check_images filtered.nii
	;;
    dof2mat)
        run_eval "${BINDIR}/dof2mat parc1_parc2_9dof.xform > ${tmpdir}/matrix"
	check_results matrix
        ;;
    dof2matTranspose)
        run_eval "${BINDIR}/dof2mat --transpose parc1_parc2_9dof.xform > ${tmpdir}/matrix"
	check_results matrix
        ;;
    dof2matLegacy)
        run_eval "${BINDIR}/dof2mat vol001_mr_t0t1.list > ${tmpdir}/matrix"
	check_results matrix
        ;;    
    dof2matLegacyFwd)
        run_eval "${BINDIR}/dof2mat vol001_mr_t0t1_fwd.list > ${tmpdir}/matrix"
	check_results matrix
        ;;    
    dof2matFixed)
        run_eval "${BINDIR}/dof2mat vol001_mr_t0t1_fwd24.list > ${tmpdir}/matrix"
	check_results matrix
        ;;    
    dof2matSuffix)
        run_eval "${BINDIR}/dof2mat xform.ZYX > ${tmpdir}/matrix"
	check_results matrix
        ;;    
    dof2mat3x3)
        run_eval "${BINDIR}/dof2mat --matrix3x3 vol001_mr_t0t1_fwd24.list > ${tmpdir}/matrix"
	check_results matrix
        ;;    
    stream_pixels)
        run_eval "${BINDIR}/stream_pixels jacobian-01.nii jacobian-02.nii > ${tmpdir}/stream.raw"
	check_results stream.raw
	;;
    stream_pixelsConvert)
        run_eval "${BINDIR}/stream_pixels --convert int jacobian-01.nii jacobian-02.nii > ${tmpdir}/stream.raw"
	check_results stream.raw
	;;
    stream_pixelsReorient)
        run_eval "${BINDIR}/stream_pixels --reorient RIP jacobian-01.nii jacobian-02.nii > ${tmpdir}/stream.raw"
	check_results stream.raw
	;;
    stream_pixelsEndian)
        run_eval "${BINDIR}/stream_pixels --change-endian jacobian-01.nii jacobian-02.nii > ${tmpdir}/stream.raw"
	check_results stream.raw
	;;
    epiunwarp)
        export CMTK_NUM_THREADS=1
        run epiunwarp --no-init-shift-com --write-jacobian-fwd ${tmpdir}/jacobian.nii --folding-constraint-weight 0 --smooth-sigma-max 16 --smooth-sigma-min 0 --smooth-sigma-diff 1 --iterations 5 --smoothness-constraint-weight 1e4 --phase-encode-ap dwi_fwd.nii dwi_rev.nii ${tmpdir}/c1.nii ${tmpdir}/c2.nii ${tmpdir}/df.nrrd ${tmpdir}/df2.nrrd
        unset CMTK_NUM_THREADS
	check_images c1.nii c2.nii jacobian.nii
	check_results df.nrrd df2.nrrd
	;;
    epiunwarpInitShift)
        export CMTK_NUM_THREADS=1
        run epiunwarp --write-jacobian-fwd ${tmpdir}/jacobian.nii --folding-constraint-weight 0 --smooth-sigma-max 16 --smooth-sigma-min 0 --smooth-sigma-diff 1 --iterations 5 --smoothness-constraint-weight 1e4 --phase-encode-ap dwi_fwd.nii dwi_rev.nii ${tmpdir}/c1.nii ${tmpdir}/c2.nii ${tmpdir}/df.nrrd
        unset CMTK_NUM_THREADS
	check_images c1.nii c2.nii jacobian.nii
	check_results df.nrrd
	;;
    fib2image)
        run_eval "${BINDIR}/fib2image -o ${tmpdir}/fibers.nii fiber_grid.hdr < fibers.fib"
	check_images fibers.nii
        ;;
    fibxform)
        run_eval "${BINDIR}/fibxform crop-x30.xform < fibers.fib > ${tmpdir}/output.fib"
	check_results output.fib
        ;;
    fibxformSourceTarget)
        run_eval "${BINDIR}/fibxform --source-image fiber_grid.hdr --target-image fiber_grid.hdr crop-x30.xform < fibers.fib > ${tmpdir}/output.fib"
	check_results output.fib
        ;;
    filterGaussian)
	run filter --gaussian 1 --radius 2 rat_fse_erly.hdr ${tmpdir}/filter.hdr
	check_results filter.img
	;;
    filterGaussianSmallKernel)
	run filter --gaussian 1 --radius 1.1 rat_fse_erly.hdr ${tmpdir}/filter.hdr
	check_results filter.img
	;;
    filterGaussianNoFilter)
	run filter --gaussian 1 --radius 0.5 rat_fse_erly.hdr ${tmpdir}/filter.hdr
	check_results filter.img
	;;
    filterRohlfing)
        run filter --rohlfing --intensity-gaussian 1 --gaussian 10 spgr_3t.hdr ${tmpdir}/filter.hdr spgr_3t_mask.hdr
	check_results filter.img
	;;
    filmFourthOrder)
	run film --coronal --nmi --fourth-order-error --passes 3 --num-iterations 3 --injection-kernel-radius 2 --injection-kernel-sigma 1 --write-injected-image ${tmpdir}/injected.hdr interleave_thnfse.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    filmCubic)
	run film --coronal --nmi --cubic --passes 3 --num-iterations 3 --injection-kernel-radius 2 --injection-kernel-sigma 1 --write-injected-image ${tmpdir}/injected.hdr interleave_thnfse.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    filmMSDLinearNoTrunc)
	run film --msd --coronal --linear --no-truncation --passes 3 --num-iterations 3 --injection-kernel-radius 2 --injection-kernel-sigma 1 interleave_thnfse.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    filmMISincRefSPGR)
	run film --mi --coronal --cubic --passes 3 --num-iterations 3 --injection-kernel-radius 2 --injection-kernel-sigma 1 --reference-image interleave_3dspgr.hdr interleave_thnfse.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    fit_affine_xform)
        run fit_affine_xform -o ${tmpdir}/affine.xform vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1.list
	check_results affine.xform
	;;
    fit_affine_xformRigid)
        run fit_affine_xform --rigid -o ${tmpdir}/rigid.xform vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1.list
	check_results rigid.xform
	;;
    fit_affine_xformReverse)
        run fit_affine_xform -o ${tmpdir}/affine.xform vol001_mr_t1.hdr --inverse vol001_mr_t0t1.list vol001_mr_t0t1_warp.xform
	check_results affine.xform
	;;
    fit_affine_xform_landmarksRigid)
        run fit_affine_xform_landmarks landmarksSource landmarksTargetRigid ${tmpdir}/affine.xform
	check_results affine.xform
	;;
    fit_affine_xform_landmarksScales)
        run fit_affine_xform_landmarks landmarksSource landmarksTargetScales ${tmpdir}/affine.xform
	check_results affine.xform
	;;
    fit_affine_xform_landmarksShear)
        run fit_affine_xform_landmarks landmarksSource landmarksTargetShear ${tmpdir}/affine.xform
	check_results affine.xform
	;;
    fit_affine_xform_landmarksRigidRigid)
        run fit_affine_xform_landmarks --rigid landmarksSource landmarksTargetRigid ${tmpdir}/affine.xform
	check_results affine.xform
	;;
    fit_affine_xform_landmarksRigidRigidFlip)
        run fit_affine_xform_landmarks --rigid landmarksSource2 landmarksTarget2 ${tmpdir}/rigid.xform
	check_results rigid.xform
	;;
    fit_affine_xform_landmarksRigidScales)
        run fit_affine_xform_landmarks --rigid landmarksSource landmarksTargetScales ${tmpdir}/affine.xform
	check_results affine.xform
	;;
    fit_affine_xform_landmarksRigidShear)
        run fit_affine_xform_landmarks --rigid landmarksSource landmarksTargetShear ${tmpdir}/affine.xform
	check_results affine.xform
	;;
    fit_affine_dfieldDField)
        run fit_affine_dfield vol001_mr_t0t1_dfield.nrrd ${tmpdir}/affine_fit.xform
	check_results affine_fit.xform
	;;
    fit_affine_dfieldFFD)
        run fit_affine_dfield vol001_mr_t0t1_warp.xform ${tmpdir}/affine_fit.xform
	check_results affine_fit.xform
	;;
    fit_spline_dfieldSpacing)
        run fit_spline_dfield --final-cp-spacing 40 vol001_mr_t0t1_dfield.nrrd ${tmpdir}/warp.xform
	check_results warp.xform
	;;
    fit_spline_dfieldSpacingMultiLevel)
        run fit_spline_dfield --final-cp-spacing 40 --levels 2 vol001_mr_t0t1_dfield.nrrd ${tmpdir}/warp.xform
	check_results warp.xform
	;;
    fit_spline_dfieldDims)
        run fit_spline_dfield --final-cp-dims 10,10,5 vol001_mr_t0t1_dfield.nrrd ${tmpdir}/warp.xform
	check_results warp.xform
	;;
    fit_spline_dfieldDimsRelative)
        run fit_spline_dfield --relative --final-cp-dims 10,10,5 vol001_mr_t0t1_dfield.nrrd ${tmpdir}/warp.xform
	check_results warp.xform
	;;
    fit_spline_dfieldDimsMultiLevel)
        run fit_spline_dfield --final-cp-dims 10,10,5 --levels 2 vol001_mr_t0t1_dfield.nrrd ${tmpdir}/warp.xform
	check_results warp.xform
	;;
    fit_spline_dfieldDimsMultiLevelSafe)
        run fit_spline_dfield --final-cp-dims 10,10,5 --levels 400 vol001_mr_t0t1_dfield.nrrd ${tmpdir}/warp.xform
	check_results warp.xform
	;;
    fit_spline_dfieldDimsWithAffine)
        run fit_spline_dfield --fit-affine-first --final-cp-dims 10,10,5 vol001_mr_t0t1_dfield.nrrd ${tmpdir}/warp.xform
	check_results warp.xform
	;;
    fit_spline_xformSpacing)
        run fit_spline_xform --final-cp-spacing 40 -o ${tmpdir}/warp.xform vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1.list
	check_results warp.xform
	;;
    fit_spline_xformSpacingReverse)
        run fit_spline_xform --final-cp-spacing 40 -o ${tmpdir}/warp.xform vol001_mr_t1.hdr --inverse vol001_mr_t0t1.list vol001_mr_t0t1_warp.xform
	check_results warp.xform
	;;
    fit_spline_xformSpacingMultiLevel)
        run fit_spline_xform --final-cp-spacing 40 --levels 2 -o ${tmpdir}/warp.xform vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1.list
	check_results warp.xform
	;;
    fit_spline_xformDims)
        run fit_spline_xform --final-cp-dims 10,10,5 -o ${tmpdir}/warp.xform vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1.list
	check_results warp.xform
	;;
    fit_spline_xformDimsMultiLevel)
        run fit_spline_xform --final-cp-dims 10,10,5 --levels 2 -o ${tmpdir}/warp.xform vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1.list
	check_results warp.xform
	;;
    geomatchAxSa)
	run_eval_expect_fail "${BINDIR}/geomatch -v phantom_ax.nii.gz phantom_sa.nii.gz >& ${tmpdir}/stderr"
	check_results stderr
	;;
    geomatchAxSaRAS)
	run_eval_expect_fail "${BINDIR}/geomatch -v --no-check-xforms --read-ras phantom_ax.nii.gz phantom_sa.nii.gz >& ${tmpdir}/stderr"
	check_results stderr
	;;
    geomatchAxSaNoXforms)
	run_eval "${BINDIR}/geomatch -v --no-check-xforms phantom_ax.nii.gz phantom_sa.nii.gz >& ${tmpdir}/stderr"
	check_results stderr
	;;
    glmDefault)
	run_eval "${BINDIR}/glm -v -O ${tmpdir}/model_%s_%02d_%s.hdr jacobian_glm.txt jacobian-%s.nii | fgrep -v ${tmpdir} > ${tmpdir}/model_stdout.txt"
	check_results model_stdout.txt model_fstat_00_model.img  model_tstat_00_age.img model_param_00_age.img
	check_results model_tstat_01_sex.img model_param_01_sex.img model_tstat_02_CONST.img model_param_02_CONST.img
	;;
    glmNormalize)
	run_eval "${BINDIR}/glm --normalize -v -O ${tmpdir}/model_%s_%02d_%s.hdr jacobian_glm.txt jacobian-%s.nii | fgrep -v ${tmpdir} > ${tmpdir}/model_stdout.txt"
	check_results model_stdout.txt model_fstat_00_model.img  model_tstat_00_age.img model_param_00_age.img
	check_results model_tstat_01_sex.img model_param_01_sex.img model_tstat_02_CONST.img model_param_02_CONST.img
	;;
    glmExp)
	run_eval "${BINDIR}/glm --exp -v -O ${tmpdir}/model_%s_%02d_%s.hdr jacobian_glm.txt jacobian-%s.nii | fgrep -v ${tmpdir} > ${tmpdir}/model_stdout.txt"
	check_results model_stdout.txt model_fstat_00_model.img  model_tstat_00_age.img model_param_00_age.img
	check_results model_tstat_01_sex.img model_param_01_sex.img model_tstat_02_CONST.img model_param_02_CONST.img
	;;
    glmNoConstant)
	run_eval "${BINDIR}/glm --exclude-constant -v -O ${tmpdir}/model_%s_%02d_%s.hdr jacobian_glm.txt jacobian-%s.nii | fgrep -v ${tmpdir} > ${tmpdir}/model_stdout.txt"
	check_results model_stdout.txt model_fstat_00_model.img  model_tstat_00_age.img model_param_00_age.img
	check_results model_tstat_01_sex.img model_param_01_sex.img
	;;
    glmIgnore)
	run_eval "${BINDIR}/glm --ignore-parameter 1 -v -O ${tmpdir}/model_%s_%02d_%s.hdr jacobian_glm.txt jacobian-%s.nii | fgrep -v ${tmpdir} > ${tmpdir}/model_stdout.txt"
	check_results model_stdout.txt model_fstat_00_model.img  model_tstat_00_age.img model_param_00_age.img
	check_results model_tstat_02_CONST.img model_param_02_CONST.img
	;;
    glmSelect)
	run_eval "${BINDIR}/glm --select-parameter age -v -O ${tmpdir}/model_%s_%02d_%s.hdr jacobian_glm.txt jacobian-%s.nii | fgrep -v ${tmpdir} > ${tmpdir}/model_stdout.txt"
	check_results model_stdout.txt model_fstat_00_model.img
	check_results model_tstat_00_age.img model_param_00_age.img model_tstat_02_CONST.img model_param_02_CONST.img
	;; 
    glmCrop)
	run_eval "${BINDIR}/glm --crop 10,10,0,20,20,2 -v -O ${tmpdir}/model_%s_%02d_%s.hdr jacobian_glm.txt jacobian-%s.nii | fgrep -v ${tmpdir} > ${tmpdir}/model_stdout.txt"
	check_results model_stdout.txt model_fstat_00_model.img  model_tstat_00_age.img model_param_00_age.img
	check_results model_tstat_01_sex.img model_param_01_sex.img model_tstat_02_CONST.img model_param_02_CONST.img
	;;
    gmmDefault)
        run gmm --mask gmm/mask.nii gmm/spgr.nii ${tmpdir}/gmm.nii gmm/prior1.nii gmm/prior2.nii gmm/prior3.nii
	check_results gmm.nii
	;;
    gmmAlternative)
        run gmm --classes 2 --iterations 5 --priors-init-only --prior-epsilon 0.05 --probability-maps gmm/spgr.nii ${tmpdir}/gmm.nii gmm/prior1.nii gmm/prior2.nii
	check_results gmm.nii
	check_images gmm_prob1.nii gmm_prob2.nii
	;;
    gregxformFordwardBackward)
	run_eval "cat vol001_t0_points.xyz | ${BINDIR}/gregxform -f vol001_mr_t0t1_warp.xform | ${BINDIR}/gregxform vol001_mr_t0t1_warp.xform > ${tmpdir}/vol001_t0_points.xyz"
	check_results vol001_t0_points.xyz
	;;
    gregxformAffine)
	run_eval "cat vol001_t0_points.xyz | ${BINDIR}/gregxform -f vol001_mr_t0t1.list > ${tmpdir}/vol001_t0_points.xyz"
	check_results vol001_t0_points.xyz
	;;
    gregxformAffineFromWarp)
	run_eval "cat vol001_t0_points.xyz | ${BINDIR}/gregxform --affine -f vol001_mr_t0t1_warp.xform > ${tmpdir}/vol001_t0_points.xyz"
	check_results vol001_t0_points.xyz
	;;
    gregxformAffineFromWarpFwdBwd)
	run_eval "cat vol001_t0_points.xyz | ${BINDIR}/gregxform --affine -f vol001_mr_t0t1_warp.xform | ${BINDIR}/gregxform --affine vol001_mr_t0t1_warp.xform > ${tmpdir}/vol001_t0_points.xyz"
	check_results vol001_t0_points.xyz
	;;
    groupwise_affineFromInit)
	run groupwise_affine -v --force-background 0 -O ${tmpdir} --dofs 6 --dofs 9 -e 4 -a 0.25 --downsample-from 2 --downsample-to 1 --sampling-density 1.0 --zero-sum groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_affineMatchHistograms)
        export CMTK_NUM_THREADS=1
	run groupwise_affine -v --match-histograms --force-background 0 -O ${tmpdir} --dofs 6 --dofs 9 -e 4 -a 0.25 --downsample-from 2 --downsample-to 1 --sampling-density 1.0 --zero-sum groupwise_init_brain123.xforms
	unset CMTK_NUM_THREADS
	check_results groupwise.xforms average.nii
	;;
    groupwise_affineFromInitSampling)
	run groupwise_affine -v --force-background 0 -O ${tmpdir} --dofs 6 --dofs 9 -e 4 -a 0.25 --downsample-to 1 --sampling-density 0.5 --zero-sum groupwise_init_brain123.xforms
	## no baseline; this mode uses probabilistic sampling
	;;
    groupwise_affineBackground)
	run groupwise_affine -v --force-background 0 -O ${tmpdir} --template spgr_brain_1.hdr --dofs 6 --dofs 9 -e 2 -a 0.25 --downsample-from 2 --downsample-to 1 --sampling-density 1.0 --zero-sum spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results groupwise.xforms average.nii
	;;
    groupwise_affineUseTemplate)
        export CMTK_NUM_THREADS=1
	run groupwise_affine -v --force-background 0 -O ${tmpdir} --template spgr_brain_1.hdr --dofs 6 --dofs 9 -e 2 -a 0.25 --downsample-from 2 --downsample-to 1 --sampling-density 1.0 --template-with-data spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
        unset CMTK_NUM_THREADS
	check_results groupwise.xforms average.nii
	;;
    groupwise_affineZeroSumSmooth)
        export CMTK_NUM_THREADS=1
	run groupwise_affine -v --smooth 0.5 --downsample-to 0 -O ${tmpdir} --template spgr_brain_1.hdr --dofs 6 --dofs 9 -e 2 -a 0.25 --downsample-from 2 --sampling-density 1.0 --zero-sum spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
        unset CMTK_NUM_THREADS
	check_results groupwise.xforms average.nii
	;;
    groupwise_affineRMIFromInit)
	run groupwise_affine --rmi --force-background 0 -O ${tmpdir} --dofs 6 --dofs 9 -e 4 -a 0.25 --downsample-from 2 --downsample-to 1 --sampling-density 1.0 --zero-sum groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_affineRMIFromInitDeltaF)
	run groupwise_affine --rmi --force-background 0 -O ${tmpdir} --dofs 6,9 -e 4 --delta-f-threshold 0.1 -a 0.25 --downsample-from 2 --downsample-to 1 --sampling-density 1.0 --zero-sum groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_affineRMIFromInitSampling)
	run groupwise_affine --rmi --force-background 0 -O ${tmpdir} --dofs 6 --dofs 9 -e 4 -a 0.25 --downsample-to 1 --sampling-density 0.5 --zero-sum groupwise_init_brain123.xforms
	## no baseline; this mode uses probabilistic sampling
	;;
    groupwise_affineRMIBackground)
	run groupwise_affine --rmi --force-background 0 -O ${tmpdir} --template spgr_brain_1.hdr --dofs 6 --dofs 9 -e 2 -a 0.25 --downsample-from 2 --downsample-to 1 --sampling-density 1.0 --zero-sum spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results groupwise.xforms average.nii
	;;
    groupwise_affineRMIZeroSumSmooth)
	run groupwise_affine --rmi --smooth 0.5  --downsample-to 0 -O ${tmpdir} --template spgr_brain_1.hdr --dofs 6 --dofs 9 -e 2 -a 0.25 --downsample-from 2 --sampling-density 1.0 --zero-sum spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpFromInit)
	run groupwise_warp -v --force-background 0 -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 1 groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpFromInitProtect)
	run groupwise_warp -v --force-background 0 -vv --disable-cp-mask box_corner.nii -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 1 groupwise_init_brain123.xforms
	check_results groupwise.xforms
	;;
    groupwise_warpFitFromInit)
	run groupwise_warp -v --force-background 0 -O ${tmpdir} --grid-spacing 200 --grid-spacing-fit --refine-grid 1 -e 4 -a 1 --downsample-from 2 --downsample-to 1 groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpUseTemplate)
	run groupwise_warp -v --force-background 0 -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 2 --template-with-data spgr_brain_1.hdr groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpUseTemplateMatchHistograms)
        export CMTK_NUM_THREADS=1
	run groupwise_warp -v --match-histograms --force-background 0 -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 2 --template-with-data spgr_brain_1.hdr groupwise_init_brain123.xforms
        unset CMTK_NUM_THREADS
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpMatchHistograms)
        export CMTK_NUM_THREADS=1
	run groupwise_warp -v --match-histograms --force-background 0 -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 2 --template spgr_brain_1.hdr groupwise_init_brain123.xforms
        unset CMTK_NUM_THREADS
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpFromInitZeroSum)
	run groupwise_warp -v --zero-sum --force-background 0 -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 1 groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpFromInitNoBG)
	run groupwise_warp -v -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 1 groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpUseTemplateNoBG)
	run groupwise_warp -v -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 2 --template-with-data spgr_brain_1.hdr groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpRMIFromInit)
	run groupwise_warp --rmi -v --force-background 0 -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 1 groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpRMIFitFromInit)
	run groupwise_warp --rmi -v --force-background 0 -O ${tmpdir} --grid-spacing 200 --grid-spacing-fit --refine-grid 1 -e 4 -a 1 --downsample-from 2 --downsample-to 1 groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_warpRMIFromInitZeroSum)
	run groupwise_warp --rmi -v --zero-sum --force-background 0 -O ${tmpdir} --grid-spacing 200 --refine-grid 1 -e 2 -a 1 --downsample-from 2 --downsample-to 1 groupwise_init_brain123.xforms
	check_results groupwise.xforms average.nii
	;;
    groupwise_initCentersOfMass)
	run groupwise_init -O ${tmpdir} --align-centers-of-mass spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results groupwise.xforms
	# cannot compare separate xforms due to local file system path in the file
	check_results average.nii
	;;
    groupwise_initCenterFOV)
	run groupwise_init -O ${tmpdir} --center-template spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results groupwise.xforms
	# cannot compare separate xforms due to local file system path in the file
	check_results average.nii
	;;
    groupwise_initCentersOfMassScale)
	run groupwise_init -O ${tmpdir} --align-centers-of-mass --init-scales spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results groupwise.xforms
	# cannot compare separate xforms due to local file system path in the file
	check_results average.nii
	;;
    groupwise_initCentersOfMassTemplate)
	run groupwise_init -O ${tmpdir} --template spgr_brain_1.hdr --align-centers-of-mass spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr
	check_results groupwise.xforms
	check_results pairs/target-000.list/registration pairs/target-001.list/registration pairs/target-002.list/registration
	check_results average.nii
	;;
    hausdorffBinary12)
        run_eval "${BINDIR}/hausdorff parc1_bin.hdr parc2_bin.hdr > ${tmpdir}/hd.txt"
	check_results hd.txt
	;;
    hausdorffBinary21)
        run_eval "${BINDIR}/hausdorff parc2_bin.hdr parc1_bin.hdr > ${tmpdir}/hd.txt"
	check_results hd.txt
	;;
    hausdorffBinaryForced)
        run_eval "${BINDIR}/hausdorff parc1.hdr parc2.hdr > ${tmpdir}/hd.txt"
	check_results hd.txt
	;;
    histogram)
	run histogram -o ${tmpdir}/histogram spgr_3t.hdr
	check_results histogram
	;;
    histogramNorm)
	run histogram --normalize -o ${tmpdir}/histogram spgr_3t.hdr
	check_results histogram
	;;
    histogramBinsMinMax)
	run histogram --min 300 --max 3000 --nbins 16 -o ${tmpdir}/histogram spgr_3t.hdr
	check_results histogram
	;;
    histogramBinsMinMaxTrunc)
	run histogram --truncate --min 300 --max 3000 --nbins 16 -o ${tmpdir}/histogram spgr_3t.hdr
	check_results histogram
	;;
    histogramMask)
	run histogram --mask spgr_3t_mask.hdr -o ${tmpdir}/histogram spgr_3t.hdr
	check_results histogram
	;;
    imagemathAbsPop)
        run imagemath --in pat001_pet.hdr pat001_mr_T1.hdr --pop --abs --out ${tmpdir}/abs.nii
	check_results abs.nii
	;;
    imagemathSqrSqrt)
        run imagemath --in pat001_pet.hdr --sqr --sqrt --out ${tmpdir}/abs.nii
	check_results abs.nii
	;;
    imagemathLogExp)
        run imagemath --in spgr_brain_1.hdr --log --exp --out ${tmpdir}/logexp.nii
	check_results logexp.nii
	;;
    imagemathDupAddMulDiv)
        run imagemath --in spgr_brain_1.hdr --dup --in spgr_brain_2.hdr spgr_brain_3.hdr --add --mul --div --out ${tmpdir}/damd.nii
	check_results damd.nii
	;;
    imagemathThreshAboveBelow)
        run imagemath --in pat001_pet.hdr --thresh-above 1000 --thresh-below 0 --out ${tmpdir}/thresh.nii
	check_results thresh.nii
	;;
    imagemathAverage)
	run imagemath --in parc1_bin.hdr parc2_bin.hdr parc3_bin.hdr --average --out ${tmpdir}/average.hdr
	check_results average.img
	;;
    imagemathVariance)
	run imagemath --in  spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr --variance --out ${tmpdir}/variance.nii
	check_results variance.nii
	;;
    imagemathMaskAverage)
        run imagemath --in spgr_3t.hdr spgr_3t_mask.hdr --mask-average --out ${tmpdir}/average.hdr
	check_results average.img
	;;
    imagemathXor)
	run imagemath --in parc1.hdr --scalar-xor 1 --out ${tmpdir}/xor.hdr
	check_results xor.img
	;;
    imagemathDupFillMaxValue)
	run imagemath --in parc1.hdr --dup --fill 1 --max-value --out ${tmpdir}/result.hdr
	check_results result.img
	;;
    imagemathAnd)
        run imagemath --in parc1.hdr --scalar-and 1 --out ${tmpdir}/and.hdr
	check_results and.img
	;;
    imagemathContractLabels)
	run imagemath --in parc1.hdr parc2.hdr parc3.hdr --contract-labels --out ${tmpdir}/contract.hdr
	check_results contract.img
	;;
    imagemathMaxIndex)
	run imagemath --in parc1.hdr parc2.hdr parc3.hdr --max-index --out ${tmpdir}/maxidx.nii
	check_results maxidx.nii
	;;
    imagemathMaxValue)
	run imagemath --in parc1.hdr parc2.hdr parc3.hdr --max-value --out ${tmpdir}/maxval.nii
	check_results maxval.nii
	;;
    imagemathVote)
	run imagemath --in parc1_bin.hdr parc2_bin.hdr parc3_bin.hdr --vote --out ${tmpdir}/vote.hdr
	check_results vote.img
	;;
    imagemathProduct)
	run imagemath --in parc1_bin.hdr parc2_bin.hdr parc3_bin.hdr --product --out ${tmpdir}/prod.nii
	check_results prod.nii
	;;
    imagemathStackEntropyLabels)
	run imagemath --in parc1_bin.hdr parc2_bin.hdr parc3_bin.hdr --stack-entropy-labels --out ${tmpdir}/entropy.hdr
	check_results entropy.img
	;;
    imagemathSTAPLE)
	run imagemath --in parc1_bin.hdr parc2_bin.hdr parc3_bin.hdr --staple 10 --out ${tmpdir}/staple.hdr
	check_results staple.img
	;;
    imagemathMultiClassSTAPLE)
	run imagemath --in parc1.hdr parc2.hdr parc3.hdr --mstaple 2 --out ${tmpdir}/mstaple.hdr
	check_results mstaple.img
	;;
    imagemathMultiClassDisputedSTAPLE)
	run imagemath --in parc1.hdr parc2.hdr parc3.hdr --mstaple-disputed 2 --out ${tmpdir}/mstaple.hdr
	check_results mstaple.img
	;;
    imagemathCombinePCA)
	run imagemath --in rat_fse_erly.hdr rat_fse_late.hdr --combine-pca --trunc --out ${tmpdir}/combine_pca.hdr
	check_results combine_pca.img
	;;
    imagemathT2)
	run imagemath --float --in rat_fse_erly.hdr --log --in rat_fse_late.hdr --log --scalar-mul -1 --add --one-over --out ${tmpdir}/t2.hdr
	check_results t2.img
	;;
    imagemathAtan2)
	run imagemath --float --in rat_fse_erly.hdr rat_fse_late.hdr --atan2 --out ${tmpdir}/atan.nii
	check_results atan.nii
	;;
    imagemathLogOddsAdd)
	run imagemath --float --in pbmap_wm_2.nii --logit --in pbmap_wm_1.nii --logit --average --logistic --out ${tmpdir}/logodds_add.hdr
	check_results logodds_add.img
	;;
    imagemathLogOddsAdd2)
	run imagemath --float --in pbmap_wm_2.nii pbmap_wm_1.nii --all --logit --average --all --logistic --out ${tmpdir}/logodds_add.hdr
	check_results logodds_add.img
	;;
    imagemathMatchMeanSDev)
        run imagemath --in spgr_brain_1.hdr spgr_brain_2.hdr --match-mean-sdev --out ${tmpdir}/match.nii
        check_results match.nii
        ;;
    imagemathMatchMeanSDev3)
        run imagemath --in spgr_brain_1.hdr spgr_brain_2.hdr spgr_brain_3.hdr --match-mean-sdev3 --out ${tmpdir}/match.nii
        check_results match.nii
        ;;
    imagemathMatchHistograms)
        run imagemath --in spgr_brain_1.hdr spgr_brain_2.hdr --match-histograms --out ${tmpdir}/match_histograms.hdr
        check_results match_histograms.img
        ;;
    imagemathMatchHistogramsPadding)
        run imagemath --set-padding-value 0 --in spgr_brain_1.hdr spgr_brain_2.hdr --match-histograms --out ${tmpdir}/match_histograms.hdr
        check_results match_histograms.img
        ;;
    imagemathMatchHistogramsPadding2)
        run imagemath --in spgr_brain_1.hdr spgr_brain_2.hdr --set-padding-value 0 --match-histograms --out ${tmpdir}/match_histograms.hdr
        check_results match_histograms.img
        ;;
    imagemathMatchHistogramsPaddingUnset)
        run imagemath --set-padding-value 0 --in spgr_brain_1.hdr --unset-padding --in spgr_brain_2.hdr --match-histograms --out ${tmpdir}/match_histograms.hdr
        check_results match_histograms.img
        ;;
    interleaved_bad_slicesDefault)
	run interleaved_bad_slices rsfMRI-motion/*.nii* > ${tmpdir}/badSlices.txt
	check_results badSlices.txt
	;;
    interleaved_bad_slicesStdDev1)
	run interleaved_bad_slices --stdev-thresh 1 rsfMRI-motion/*.nii* > ${tmpdir}/badSlices.txt
	check_results badSlices.txt
	;;
    interleaved_bad_slicesRMS)
	run interleaved_bad_slices --rms rsfMRI-motion/*.nii* > ${tmpdir}/badSlices.txt
	check_results badSlices.txt
	;;
    interleaved_bad_slicesBulk)
	run interleaved_bad_slices --bad-slices-thresh 1 rsfMRI-motion/*.nii* > ${tmpdir}/badSlices.txt
	check_results badSlices.txt
	;;
    jidbBoxFourthOrder)
        run jidb --coronal --nmi --psf box --fourth-order-error --passes 3 --num-iterations 3 --injection-kernel-radius 2 --injection-kernel-sigma 1 --write-injected-image ${tmpdir}/injected.hdr interleave_thnfse.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    jidbGaussian)
	run jidb --coronal --nmi --psf gaussian --passes 3 --num-iterations 3 --injection-kernel-radius 2 --injection-kernel-sigma 1 --write-injected-image ${tmpdir}/injected.hdr interleave_thnfse.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    jidbGaussianScale)
	run jidb --psf gaussian --nmi --psf-scale 0.5 --no-truncation --passes 3 --num-iterations 3 --injection-kernel-radius 2 --injection-kernel-sigma 1 interleave_thnfse.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    jidbMIRefSPGR)
	run jidb --mi --passes 3 --num-iterations 3 --injection-kernel-radius 2 --injection-kernel-sigma 1 --reference-image interleave_3dspgr.hdr interleave_thnfse.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    levelsetDefault)
	run levelset -v vol001_mr_t1.hdr ${tmpdir}/levelset.hdr
	check_results levelset.img
	;;
    levelsetScaleInitial)
        run levelset -v --scale-initial-sphere 0.5 vol001_mr_t1.hdr ${tmpdir}/levelset.hdr
	check_results levelset.img
	;;
    levelsetBinarizeFastWideBinary)
        run levelset -v --binarize --delta 1.0 --filter-sigma 4.0 vol001_mr_t1.hdr ${tmpdir}/levelset.hdr
	check_results levelset.img
	;;
    lvoteDefault)
        run lvote -v -o ${tmpdir}/lvote.nii lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lvote.nii
	;;
    lvoteGlobalWeights)
        run lvote -v -o ${tmpdir}/lvote.nii --use-global-weights lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lvote.nii
	;;
    lvoteRadius3)
        run lvote -v -o ${tmpdir}/lvote.nii --patch-radius 3 lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lvote.nii
	;;
    lvoteOutliersGlobal)
        run lvote -v -o ${tmpdir}/lvote.nii --patch-radius 3 --no-global-outliers lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lvote.nii
	;;
    lsbaRadius3)
        run lsba -v -o ${tmpdir}/lsba.nii --patch-radius 3 lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lsba.nii
	;;
    lsbaRadius3Outliers)
        run lsba -v -o ${tmpdir}/lsba.nii --patch-radius 3 --no-local-outliers lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lsba.nii
	;;
    lsbaRadius3OutliersGlobal)
        run lsba -v -o ${tmpdir}/lsba.nii --patch-radius 3 --no-global-outliers lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lsba.nii
	;;
    lsbaRadius3Search1)
        run lsba -v -o ${tmpdir}/lsba.nii --search-radius 1 --patch-radius 3 --no-local-outliers lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lsba.nii
	;;
    lmsbaRadius3)
        run lmsba -v -o ${tmpdir}/lmsba.nii --patch-radius 3 lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lmsba.nii
	;;
    lmsbaRadius3Outliers)
        run lmsba -v -o ${tmpdir}/lmsba.nii --patch-radius 3 --no-local-outliers lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lmsba.nii
	;;
    lmsbaRadius3OutliersGlobal)
        run lmsba -v -o ${tmpdir}/lmsba.nii --patch-radius 3 --no-global-outliers lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lmsba.nii
	;;
    lmsbaRadius3Search1)
        run lmsba -v -o ${tmpdir}/lmsba.nii --search-radius 1 --patch-radius 3 --no-local-outliers lvote_target.nii lvote_atlas_i0.nii lvote_atlas_l0.nii lvote_atlas_i1.nii lvote_atlas_l1.nii lvote_atlas_i2.nii lvote_atlas_l2.nii
	check_results lmsba.nii
	;;
    make_initial_affineCenterOfMass)
	run make_initial_affine --mode centers-of-mass box1.hdr box3.hdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affinePrincipalAxes1)
	run make_initial_affine --mode principal-axes box1.hdr box2.hdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affinePrincipalAxes2)
	run make_initial_affine --mode principal-axes box1.hdr box3.hdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affinePrincipalAxes3)
	run make_initial_affine --mode principal-axes box2.hdr box3.hdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affinePrincipalAxes4)
	run make_initial_affine --mode principal-axes box1.hdr box4.hdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affinePrincipalAxes5)
	run make_initial_affine --mode principal-axes box2.hdr box4.hdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affinePrincipalAxes6)
	run make_initial_affine --mode principal-axes box3.hdr box4.hdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affineDirectionVectorsNrrdAxSa)
	run make_initial_affine phantom_ax.nhdr phantom_sa.nhdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affineDirectionVectorsNrrdAxCo)
	run make_initial_affine phantom_ax.nhdr phantom_co.nhdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affineDirectionVectorsNrrdSaCo)
	run make_initial_affine phantom_sa.nhdr phantom_co.nhdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affineDirectionVectorsNrrdAxSaNative)
	run make_initial_affine --native-space phantom_ax.nhdr phantom_sa.nhdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affineDirectionVectorsNrrdAxCoNative)
	run make_initial_affine --native-space phantom_ax.nhdr phantom_co.nhdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affineDirectionVectorsNrrdSaCoNative)
	run make_initial_affine --native-space phantom_sa.nhdr phantom_co.nhdr ${tmpdir}/xform
	check_results xform
	;;
    make_initial_affineDB)
	run make_initial_affine --db ${tmpdir}/db.sqlite box1.hdr box3.hdr ${tmpdir}/xform
	# only test for crash; local xform path in database is not portable for comparison
	;;
    mat2dof1)
        run_eval "${BINDIR}/mat2dof --transpose --center -28,-48,-28 --offset 28,48,28 --pixel-size 1.06667,0.5,1.06667 --list ${tmpdir} < rigid-air.mat"
	check_results registration
	;;
    mat2dof2)
        run_eval "${BINDIR}/mat2dof --transpose --center -28,-48,-28 --offset 28,48,28 --pixel-size 1.06667,0.5,1.06667 --inverse --list ${tmpdir} < rigid-air.mat"
	check_results registration
	;;
    mat2dofFile)
        run_eval "${BINDIR}/mat2dof --transpose --center -28,-48,-28 --offset 28,48,28 --pixel-size 1.06667,0.5,1.06667 --list ${tmpdir} rigid-air.mat"
	check_results registration
	;;    
    mat2dofToFile)
        run_eval "${BINDIR}/mat2dof -o ${tmpdir}/xform rigid-air.mat"
	check_results xform
	;;    
    mat2dofToFileAppend)
	echo "WILL THIS STILL BE HERE?" > ${tmpdir}/xform
        run_eval "${BINDIR}/mat2dof --append -o ${tmpdir}/xform rigid-air.mat"
	check_results xform
	;;    
    mcaffine1)
	export CMTK_NUM_THREADS=1
	run mcaffine --downsample-from 4 --downsample-to 1 --initial-step-size 1 --final-step-size 0.5 --dofs 6 --covariance -o ${tmpdir}/xform pat001_mr_T1.hdr -- pat001_pet.hdr
	unset CMTK_NUM_THREADS
	check_results xform
	;;
    mcaffine2)
	run mcaffine --initial-xform mcaffine2_initial.xform --downsample-from 4 --downsample-to 1 --initial-step-size 1 --final-step-size 0.5 --dofs 6 --histograms -o ${tmpdir}/xform pat001_mr_T1.hdr -- pat001_pet.hdr
	check_results xform
	;;
    mcaffine3)
	run mcaffine --downsample-from 4 --downsample-to 1 --initial-step-size 1 --final-step-size 0.5 --dofs 6 --dofs 9 --covariance -o ${tmpdir}/xform rat_fse_erly.hdr rat_fse_late.hdr -- rat2_fse_erly.hdr rat2_fse_late.hdr
	check_results xform
	;;
    mcaffine4)
	run mcaffine --downsample-from 4 --downsample-to 1 --delta-f-threshold 0.1 --initial-step-size 1 --final-step-size 0.5 --dofs 6,9 --covariance -o ${tmpdir}/xform rat_fse_erly.hdr rat_fse_late.hdr -- rat2_fse_erly.hdr rat2_fse_late.hdr
	check_results xform
	;;
    mcwarp1)
	# Test breaks when using multiple threads due to floating point effects
	export CMTK_NUM_THREADS=1
	run mcwarp --downsample-from 2 --downsample-to 1 --initial-step-size 1 --final-step-size 0.5 --grid-spacing 14 --refine-grid 2 --covariance -o ${tmpdir}/xform mcaffine_rat_rat2.xform
	unset CMTK_NUM_THREADS
	check_results xform
	;;
    mcwarp2)
	# Test breaks when using multiple threads due to floating point effects
	export CMTK_NUM_THREADS=1
	run mcwarp --downsample-from 2 --downsample-to 1 --initial-step-size 1 --final-step-size 0.5 --grid-spacing 14 --refine-grid 2 --histograms -o ${tmpdir}/xform mcaffine_rat_rat2.xform
	unset CMTK_NUM_THREADS
	check_results xform
	;;
    mcwarp3)
	# Test breaks when using multiple threads due to floating point effects
	export CMTK_NUM_THREADS=1
	run mcwarp --downsample-from 2 --downsample-to 1 --delta-f-threshold 0.1 --initial-step-size 1 --final-step-size 0.5 --grid-spacing 14 --refine-grid 2 --covariance -o ${tmpdir}/xform mcaffine_rat_rat2.xform
	unset CMTK_NUM_THREADS
	check_results xform
	;;
    mcwarp4)
	# Test breaks when using multiple threads due to floating point effects
	export CMTK_NUM_THREADS=1
	run mcwarp --downsample-from 2 --downsample-to 1 --delta-f-threshold 0.1 --initial-step-size 1 --final-step-size 0.5 --grid-spacing 14 --refine-grid 2 --covariance --intensity-correction -o ${tmpdir}/xform mcaffine_rat_rat2.xform
	unset CMTK_NUM_THREADS
	check_results xform
	;;
    mcwarp5)
	# Test breaks when using multiple threads due to floating point effects
	export CMTK_NUM_THREADS=1
	run mcwarp --downsample-from 2 --downsample-to 1 --delta-f-threshold 0.1 --initial-step-size 1 --final-step-size 0.5 --grid-spacing 14 --adaptive-fix-thresh-factor 0.5 -o ${tmpdir}/xform mcaffine_rat_rat2.xform
	unset CMTK_NUM_THREADS
	check_results xform
	;;
    mcwarp6)
	# Test breaks when using multiple threads due to floating point effects
	export CMTK_NUM_THREADS=1
	run mcwarp --downsample-from 2 --downsample-to 1 --delta-f-threshold 0.1 --initial-step-size 1 --final-step-size 0.5 --grid-spacing 14 --adaptive-fix-thresh-factor-entropy 0.5 -o ${tmpdir}/xform mcaffine_rat_rat2.xform
	unset CMTK_NUM_THREADS
	check_results xform
	;;
    mk_adni_phantom2mm)
        run mk_adni_phantom --resolution 2 ${tmpdir}/phantom.nii
        check_results phantom.nii
        ;;
    mk_adni_phantom2mmLabels)
        run mk_adni_phantom --resolution 2 --write-labels ${tmpdir}/phantom.lbl --write-landmarks ${tmpdir}/phantom.xyz --labels ${tmpdir}/phantom.nii
        check_results phantom.nii phantom.lbl phantom.xyz
        ;;
    mk_analyze_hdrDefault)
        run mk_analyze_hdr ${tmpdir}/analyze.hdr
	run_eval "${BINDIR}/describe -m ${tmpdir}/analyze.hdr | fgrep --invert-match FNAME > ${tmpdir}/analyze.txt"
	check_results analyze.hdr analyze.txt
	;;
    mk_analyze_hdrImport)
        run mk_analyze_hdr --import spgr_3t.hdr ${tmpdir}/analyze.hdr
	run_eval "${BINDIR}/describe -m ${tmpdir}/analyze.hdr | fgrep --invert-match FNAME > ${tmpdir}/analyze.txt"
	check_results analyze.hdr analyze.txt
	;;
    mk_analyze_hdrLittleEndian)
        run mk_analyze_hdr --description LittleEndian --little-endian --float --dims 100,200,300 --voxel 0.3,0.2,0.1 --offset 1024 ${tmpdir}/analyze.hdr
	run_eval "${BINDIR}/describe -m ${tmpdir}/analyze.hdr | fgrep --invert-match FNAME > ${tmpdir}/analyze.txt"
	check_results analyze.hdr analyze.txt
	;;
    mk_analyze_hdrBigEndian)
        run mk_analyze_hdr --description BigEndian  --big-endian --ushort --dims 100,200,300 --voxel 0.3,0.2,0.1 --offset 1024 ${tmpdir}/analyze.hdr
	run_eval "${BINDIR}/describe -m ${tmpdir}/analyze.hdr | fgrep --invert-match FNAME > ${tmpdir}/analyze.txt"
	check_results analyze.hdr analyze.txt
	;;
    mk_nifti_hdrDefault)
        run mk_nifti_hdr ${tmpdir}/nifti.hdr
	run_eval "${BINDIR}/describe -m ${tmpdir}/nifti.hdr | fgrep --invert-match FNAME > ${tmpdir}/nifti.txt"
	check_results nifti.hdr nifti.txt
	;;
    mk_nifti_hdrDescription)
        run_eval "${BINDIR}/mk_nifti_hdr --description \"This is a description text\" ${tmpdir}/nifti.hdr"
	check_results nifti.hdr
	;;
    mk_nifti_hdrImport)
        run mk_nifti_hdr --import phantom_ax.nii ${tmpdir}/nifti.hdr
	run_eval "${BINDIR}/describe -m ${tmpdir}/nifti.hdr | fgrep --invert-match FNAME > ${tmpdir}/nifti.txt"
	check_results nifti.hdr nifti.txt
	;;
    mk_nifti_hdrDefaultAttached)
        run mk_nifti_hdr --attached ${tmpdir}/nifti.nii
	run_eval "${BINDIR}/describe -m ${tmpdir}/nifti.nii | fgrep --invert-match FNAME > ${tmpdir}/nifti.txt"
	check_results nifti.nii nifti.txt
	;;
    mk_nifti_hdrDescriptionAttached)
        run_eval "${BINDIR}/mk_nifti_hdr --attached --description \"This is a description text\" ${tmpdir}/nifti.nii"
	check_results nifti.nii
	;;
    mk_nifti_hdrImportAttached)
        run mk_nifti_hdr --attached --import phantom_ax.nii ${tmpdir}/nifti.nii
	run_eval "${BINDIR}/describe -m ${tmpdir}/nifti.nii | fgrep --invert-match FNAME > ${tmpdir}/nifti.txt"
	check_results nifti.nii nifti.txt
	;;
    mk_phantom_3dBoxIndexed)
	run mk_phantom_3d -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 2,2,2 box 2,2,2 5,5,5 10
	check_results phantom.nii
	;;
    mk_phantom_3dBoxIndexedRange)
        run mk_phantom_3d -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 2,2,2 box 11,11,11 5,5,5 10
	check_results phantom.nii
	;;
    mk_phantom_3dBoxAbsolute)
	run mk_phantom_3d --absolute -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 1,1,1 box 2,2,2 5,5,5 10
	check_results phantom.nii
	;;
    mk_phantom_3dBoxRelative)
    run mk_phantom_3d --relative -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 1,1,1 box 0.1,0.2,0.3 0.5,0.5,0.5 10
	check_results phantom.nii
	;;
    mk_phantom_3dSphereIndexed)
	run mk_phantom_3d --coordinates indexed -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 1,1,1 sphere 7,7,7 5 20
	check_results phantom.nii
	;;
    mk_phantom_3dSphereAbsolute)
        run mk_phantom_3d --coordinates absolute -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 1,1,1 sphere 7,7,7 5 20
	check_results phantom.nii
	;;
    mk_phantom_3dSphereAbsolute2)
        run mk_phantom_3d --coordinates absolute -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 1,1,2 sphere 7,7,7 5 20
	check_results phantom.nii
	;;
    mk_phantom_3dSphereRelative)
        run mk_phantom_3d --coordinates relative -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 1,1,1 sphere 0.5,0.4,0.3 0.4 20
	check_results phantom.nii
	;;
    mk_phantom_3dSphereRelative2)
        run mk_phantom_3d --coordinates relative -o ${tmpdir}/phantom.nii --dims 10,10,10 --voxel 1,1,2 sphere 0.5,0.4,0.3 0.4 20
	check_results phantom.nii
	;;
    mk_phantom_3dBoxSphere)
	run mk_phantom_3d -o ${tmpdir}/phantom.nii --char --bg 50 --dims 10,10,10 --voxel 1,1,1 sphere 7,7,7 5 20 box 2,2,2 5,5,5 10
	check_results phantom.nii
	;;
    mk_phantom_3dImport)
	run mk_phantom_3d -o ${tmpdir}/phantom.nii --import spgr_3t_mask.hdr sphere 30,40,30 20 0
	check_results phantom.nii
	;;
    mk_phantom_3dImportGrid)
	run mk_phantom_3d -o ${tmpdir}/phantom.nii --import-grid spgr_3t_mask.hdr sphere 30,40,30 20 10
	check_results phantom.nii
	;;
    mk_phantom_3dMRSVoxel)
	run mk_phantom_3d --echo -v --bg 0 -o ${tmpdir}/voxel.nii --import-grid ge-mrs/lfse.nii mrs-voxel ge-mrs/spectro.dcm 100
	check_results voxel.nii
	;;
    mrbiasMulIncremental)
	run mrbias --incremental -M 2 --write-bias-mul ${tmpdir}/bias_mul.hdr --thresh-min 100 spgr_3t.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img bias_mul.img
	;;
    mrbiasMulAutoThresh)
        run mrbias -v -M 2 --set-padding-value 0 --thresh-auto spgr_3t.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    mrbiasMulOtsuThresh)
        run mrbias -v -M 2 --set-padding-value 0 --thresh-otsu-nbins 256 spgr_3t.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img
	;;
    mrbiasMulLogIntensity)
	run mrbias --log-intensities -M 2 --write-bias-mul ${tmpdir}/bias_mul.hdr --thresh-min 100 spgr_3t.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img bias_mul.img
	;;
    mrbiasAddMulMask)
	export CMTK_NUM_THREADS=1
	run mrbias -A 1 -M 2 --mask spgr_3t_mask.hdr --write-bias-add ${tmpdir}/bias_add.hdr --write-bias-mul ${tmpdir}/bias_mul.hdr spgr_3t.hdr ${tmpdir}/corrected.hdr
	unset CMTK_NUM_THREADS
	check_results corrected.img bias_mul.img bias_add.img
	;;
    mrbiasMulIncrementalCUDA)
	run mrbias_cuda --incremental -M 2 --write-bias-mul ${tmpdir}/bias_mul.hdr --thresh-min 100 spgr_3t.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img bias_mul.img
	;;
    mrbiasMulLogIntensityCUDA)
	run mrbias_cuda --log-intensities -M 2 --write-bias-mul ${tmpdir}/bias_mul.hdr --thresh-min 100 spgr_3t.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img bias_mul.img
	;;
    mrbiasAddMulMaskCUDA)
	run mrbias_cuda -A 1 -M 2 --mask spgr_3t_mask.hdr --write-bias-add ${tmpdir}/bias_add.hdr --write-bias-mul ${tmpdir}/bias_mul.hdr spgr_3t.hdr ${tmpdir}/corrected.hdr
	check_results corrected.img bias_mul.img bias_add.img
	;;
    overlap)
	run_eval "${BINDIR}/overlap parc1.hdr parc2.hdr parc3.hdr > ${tmpdir}/overlap.txt"
	check_results overlap.txt
	;;
    overlapNumLabels)
	run_eval "${BINDIR}/overlap -N 2 parc1.hdr parc2.hdr parc3.hdr > ${tmpdir}/overlap.txt"
	check_results overlap.txt
	;;
    overlapByLabel)
	run_eval "${BINDIR}/overlap --by-label parc1.hdr parc2.hdr parc3.hdr > ${tmpdir}/overlap.txt"
	check_results overlap.txt
	;;
    overlapFirst)
	run_eval "${BINDIR}/overlap --first-label 10 parc1.hdr parc2.hdr parc3.hdr > ${tmpdir}/overlap.txt"
	check_results overlap.txt
	;;
    overlapFirstByLabel)
	run_eval "${BINDIR}/overlap --by-label --first-label 10 parc1.hdr parc2.hdr parc3.hdr > ${tmpdir}/overlap.txt"
	check_results overlap.txt
	;;
    overlapFirstByLabelNumLabels)
	run_eval "${BINDIR}/overlap --by-label --first-label 10 --num-labels 10 parc1.hdr parc2.hdr parc3.hdr > ${tmpdir}/overlap.txt"
	check_results overlap.txt
	;;
    probeIndexed)
        run_eval "echo 98 154 1 |${BINDIR}/probe --indexed phantom_ax.nii.gz > ${tmpdir}/probe.txt"
	check_results probe.txt
	;;
    probeAbsolute)
        run_eval "echo 91.875 144.375 3 |${BINDIR}/probe --absolute phantom_ax.nii.gz > ${tmpdir}/probe.txt"
	check_results probe.txt
	;;
    probeRelative)
        run_eval "echo 0.384313725 0.603921569 0.5 |${BINDIR}/probe --relative phantom_ax.nii.gz > ${tmpdir}/probe.txt"
	check_results probe.txt
	;;
    probePhysical)
        run_eval "echo -27.656 24.844 0 |${BINDIR}/probe --physical phantom_ax.nii.gz > ${tmpdir}/probe.txt"
	check_results probe.txt
	;;
    probeIndexedLinear)
        run_eval "echo 98.5 154.5 1 |${BINDIR}/probe --linear --indexed phantom_ax.nii.gz > ${tmpdir}/probe.txt"
	check_results probe.txt
	;;
    probeIndexedCubic)
        run_eval "echo 98.5 154.5 1 |${BINDIR}/probe --cubic --indexed phantom_ax.nii.gz > ${tmpdir}/probe.txt"
	check_results probe.txt
	;;
    probeIndexedSinc)
        run_eval "echo 98.5 154.5 1 |${BINDIR}/probe --sinc-cosine --indexed phantom_ax.nii.gz > ${tmpdir}/probe.txt"
	check_results probe.txt
	;;
    pxsearchIndexed)
        run_eval "echo 98 154 1 |${BINDIR}/pxsearch --input-coordinates indexed --output-coordinates indexed phantom_ax.nii.gz > ${tmpdir}/pxsearch.txt"
	check_results pxsearch.txt
	;;
    pxsearchIndexedRadius3)
        run_eval "echo 98 154 1 |${BINDIR}/pxsearch --radius 3 --input-coordinates indexed --output-coordinates indexed phantom_ax.nii.gz > ${tmpdir}/pxsearch.txt"
	check_results pxsearch.txt
	;;
    pxsearchIndexedRadius311)
        run_eval "echo 98 154 1 |${BINDIR}/pxsearch --radius 3,1,1 --input-coordinates indexed --output-coordinates indexed phantom_ax.nii.gz > ${tmpdir}/pxsearch.txt"
	check_results pxsearch.txt
	;;
    pxsearchAbsolute)
        run_eval "echo 91.875 144.375 3 |${BINDIR}/pxsearch --input-coordinates absolute --output-coordinates absolute phantom_ax.nii.gz > ${tmpdir}/pxsearch.txt"
	check_results pxsearch.txt
	;;
    pxsearchRelative)
        run_eval "echo 0.384313725 0.603921569 0.5 |${BINDIR}/pxsearch --input-coordinates relative --output-coordinates relative phantom_ax.nii.gz > ${tmpdir}/pxsearch.txt"
	check_results pxsearch.txt
	;;
    pxsearchPhysical)
        run_eval "echo -27.656 24.844 0 |${BINDIR}/pxsearch --input-coordinates physical --output-coordinates physical phantom_ax.nii.gz > ${tmpdir}/pxsearch.txt"
	check_results pxsearch.txt
	;;
    reformatxNoXform)
	run reformatx --linear -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr
	check_results reformat.img
	;;
    reformatxLinear)
	run reformatx --linear -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr vol001_mr_t0t1.list
	check_results reformat.img
	;;
    reformatxNearestNeighbor)
	run reformatx --nn -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr vol001_mr_t0t1.list
	check_results reformat.img
	;;
    reformatxPartialVolume)
	run reformatx --pv -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr vol001_mr_t0t1.list
	check_results reformat.img
	;;
    reformatxLinearFwdBwd)
	run reformatx --linear --short -o ${tmpdir}/reformat.hdr --floating vol001_mr_t0.hdr vol001_mr_t0.hdr vol001_mr_t0t1.list --inverse vol001_mr_t0t1.list
	check_results vol001_mr_t0.img
	;;
    reformatxCubic)
	run reformatx --cubic -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr vol001_mr_t0t1.list
	check_results reformat.img
	;;
    reformatxCubicInverse)
	run reformatx --cubic -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr --inverse vol001_mr_t0t1.list
	check_results reformat.img
	;;
    reformatxSincCosine)
	run reformatx --sinc-cosine -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr vol001_mr_t0t1.list
	check_results reformat.img
	;;
    reformatxSincHamming)
	run reformatx --sinc-hamming -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr vol001_mr_t0t1.list
	check_results reformat.img
	;;
    reformatxSincCosine5)
	run reformatx --sinc-cosine --sinc-window-radius 5 -o ${tmpdir}/reformat.hdr --floating vol001_mr_t1.hdr vol001_mr_t0_crop.hdr vol001_mr_t0t1.list
	check_results reformat.img
	;;
    reformatxMassPreserving)
        run reformatx --preserve-mass -o ${tmpdir}/reformat.hdr  --floating vol001_mr_t1.hdr vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform
	check_results reformat.img
	;;
    reformatxJacobian)
	run reformatx --jacobian-correct-global -o ${tmpdir}/jacobian.hdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform --jacobian vol001_mr_t0t1_warp.xform
	check_results jacobian.img
	;;
    reformatxJacobianDefault)
	run reformatx -o ${tmpdir}/jacobian.hdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform --jacobian vol001_mr_t0t1_warp.xform
	check_results jacobian.img
	;;
    reformatxInverseJacobian)
	run reformatx --jacobian-correct-global -o ${tmpdir}/jacobian.hdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform --jacobian --inverse vol001_mr_t0t1_warp.xform
	check_results jacobian.img
	;;
    reformatxInverseJacobianDefault)
	run reformatx -o ${tmpdir}/jacobian.hdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform --jacobian --inverse vol001_mr_t0t1_warp.xform
	check_results jacobian.img
	;;
    reformatxDfieldNrrd)
	run reformatx -o ${tmpdir}/reformat.hdr --floating parc2.hdr parc1.hdr parc1_parc2_dfield.nrrd
	check_results reformat.img
	;;
    reformatxDfieldNrrdJacobian)
	run reformatx -o ${tmpdir}/jacobian.hdr vol001_mr_t0.hdr --jacobian vol001_mr_t0t1_dfield.nrrd
	check_results jacobian.img
	;;
    reformatxTargetGrid)
        run reformatx -o ${tmpdir}/reformat.nii --target-grid 32,43,21:5.625,5.625,7.5 --floating spgr_brain_1.hdr
	check_results reformat.nii
	;;
    reformatxTargetGridAnalyze)
        run reformatx -o ${tmpdir}/reformat.hdr --target-grid 32,43,21:5.625,5.625,7.5 --floating spgr_brain_1.hdr
	check_results reformat.hdr reformat.img
	;;
    reformatxTargetGridOffset)
        run reformatx -o ${tmpdir}/reformat.nii --target-grid 32,43,21:5.625,5.625,7.5:5.625,0,0 --floating spgr_brain_1.hdr
	check_results reformat.nii
	;;
    registrationAffineMrMrMSD)
	run registration -i --dofs 6,9 --msd --match-histograms -o ${tmpdir} pat001_mr_T1.hdr pat002_mr_T2.hdr
	check_results registration
	;;
    registrationFromList)
	run registration -v --dofs 0 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    registrationWithInitial)
	run registration -v --dofs 0 -o ${tmpdir} --initial vol001_mr_t0t1.list vol001_mr_t0.hdr vol001_mr_t1.hdr
	check_results registration
	;;
    registrationWithInitialInverse)
	run registration -v --dofs 0 -o ${tmpdir} --initial vol001_mr_t0t1.list --initial-is-inverse vol001_mr_t0t1.list
	check_results registration
	;;
    registrationAutoLevelsRat4)
	run registration -v -i --auto-multi-levels 4 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationAutoLevelsRat2)
	run registration -v -i --auto-multi-levels 2 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationAutoLevelsRatToRat)
	run registration -v -i --auto-multi-levels 2 --dofs 6,9 --msd --match-histograms -o ${tmpdir} rat_fse_erly.hdr rat2_fse_erly.hdr
	check_results registration
	;;
    registrationAutoLevelsRatToRatDeltaFThreshold)
	run registration -v -i --auto-multi-levels 2 --dofs 6,9 --msd --match-histograms --delta-f-threshold 0.01 -o ${tmpdir} rat_fse_erly.hdr rat2_fse_erly.hdr
	check_results registration
	;;
    registrationAutoLevelsCt3)
	run registration --msd --auto-multi-levels 3 --dofs 6 -o ${tmpdir} pat002_ct.hdr pat002_ct.hdr
	check_results registration
	;;
    registrationxAffineMrMrMSD)
	run registrationx --init fov --dofs 6,9 --msd --match-histograms -o ${tmpdir} pat001_mr_T1.hdr pat002_mr_T2.hdr
	check_results registration
	;;
    registrationxShearNoScaleMrMrMSD)
	run registrationx --auto-multi-levels 4 --init fov --dofs 603 --msd --match-histograms -o ${tmpdir} pat001_mr_T1.hdr pat002_mr_T2.hdr
	check_results registration
	;;
    registrationxFromList)
	run registrationx -v --dofs 0 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    registrationxWithInitial)
	run registrationx -v --dofs 0 -o ${tmpdir} --initial vol001_mr_t0t1.list vol001_mr_t0.hdr vol001_mr_t1.hdr
	check_results registration
	;;
    registrationxWithInitialInverse)
	run registrationx -v --dofs 0 -o ${tmpdir} --initial vol001_mr_t0t1.list --initial-is-inverse vol001_mr_t0t1.list
	check_results registration
	;;
    registrationxFromListDB)
	run registrationx --db ${tmpdir}/db.sqlite -v --dofs 0 -o ${tmpdir} vol001_mr_t0t1.list
	;;
    registrationxWithInitialDB)
	run registrationx --db ${tmpdir}/db.sqlite -v --dofs 0 -o ${tmpdir} --initial vol001_mr_t0t1.list vol001_mr_t0.hdr vol001_mr_t1.hdr
	;;
    registrationxWithInitialInverseDB)
	run registrationx --db ${tmpdir}/db.sqlite -v --dofs 0 -o ${tmpdir} --initial vol001_mr_t0t1.list --initial-is-inverse vol001_mr_t0t1.list
	;;
    registrationxAutoLevelsRat4)
	run registrationx -v --auto-multi-levels 4 --dofs 6 -o ${tmpdir} --write-itk ${tmpdir}/xform.tfm rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration xform.tfm
	;;
    registrationxAutoLevelsRat4XY)
        run registrationx -v --restrict-in-plane xy --auto-multi-levels 4 --dofs 6,9,12 -o ${tmpdir} rat_fse_erly.hdr rat2_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat4XZ)
        run registrationx -v --restrict-in-plane xz --auto-multi-levels 4 --dofs 6,9,12 -o ${tmpdir} rat_fse_erly.hdr rat2_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat4YZ)
        run registrationx -v --restrict-in-plane yz --auto-multi-levels 4 --dofs 6,9,12 -o ${tmpdir} rat_fse_erly.hdr rat2_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat4Symmetric)
	run registrationx -v --symmetric --auto-multi-levels 4 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat4NONE)
	run registrationx -v --init none --auto-multi-levels 4 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat4FOV)
	run registrationx -v --init fov --auto-multi-levels 4 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat4COM)
	run registrationx -v --init com --auto-multi-levels 4 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat4PAX)
	run registrationx -v --init pax --auto-multi-levels 4 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat2)
	run registrationx -v --init fov --auto-multi-levels 2 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat2Cubic)
	run registrationx -v --cubic --init fov --auto-multi-levels 2 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat2Sinc)
	run registrationx -v --cosine-sinc --init fov --auto-multi-levels 2 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRat2NN)
	run registrationx -v --nearest-neighbor --init fov --auto-multi-levels 2 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    registrationxAutoLevelsRatToRat)
        export CMTK_NUM_THREADS=1
        run registrationx -v --init fov --auto-multi-levels 2 --dofs 6,9 --msd --match-histograms -o ${tmpdir} rat_fse_erly.hdr rat2_fse_erly.hdr
        unset CMTK_NUM_THREADS
	check_results registration
	;;
    registrationxAutoLevelsRatToRatNCC)
        run registrationx -v --init fov --auto-multi-levels 2 --ncc -o ${tmpdir} rat_fse_erly.hdr rat2_fse_erly.hdr
	check_results registration
	;;
    registrationxAutoLevelsRatToRatRMS)
        run registrationx -v --init fov --auto-multi-levels 2 --rms -o ${tmpdir} rat_fse_erly.hdr rat2_fse_erly.hdr
	check_results registration
	;;
    registrationxAutoLevelsRatToRatCR)
        run registrationx -v --init fov --auto-multi-levels 2 --cr -o ${tmpdir} rat_fse_erly.hdr rat2_fse_erly.hdr
	check_results registration
	;;
    registrationxAutoLevelsRatToRatMI)
        run registrationx -v --init fov --auto-multi-levels 2 --mi -o ${tmpdir} rat_fse_erly.hdr rat2_fse_erly.hdr
	check_results registration
	;;
    registrationxAutoLevelsRatToRatDeltaFThreshold)
        export CMTK_NUM_THREADS=1
	run registrationx -v --init fov --auto-multi-levels 2 --dofs 6,9 --msd --match-histograms --delta-f-threshold 0.01 -o ${tmpdir} rat_fse_erly.hdr rat2_fse_erly.hdr
        unset CMTK_NUM_THREADS
	check_results registration
	;;
    registrationxAutoLevelsCt3)
	run registrationx --pad-flt -10000 --write-reformatted ${tmpdir}/reformat.nii --msd --auto-multi-levels 3 --dofs 6 -o ${tmpdir} pat002_ct.hdr pat002_ct.hdr
	check_results registration reformat.nii
	;;
    registrationxAutoLevelsLabelsNN)
        run registrationx -v --interpolation nearest-neighbor --class-ref label --class-flt label --auto-multi-levels 4 --dofs 6,9 --nmi -o ${tmpdir} parc1.hdr parc2.hdr
	check_results registration
	;;
    registrationxAutoLevelsLabelsPV)
        run registrationx -v --interpolation partial-volume --class-ref label --class-flt label --auto-multi-levels 4 --dofs 6,9 --nmi -o ${tmpdir} parc1.hdr parc2.hdr
	check_results registration
	;;
    reorientHdrSaToAx)
	run reorient -o RAS phantom_sa.hdr ${tmpdir}/reorient.hdr
	check_results reorient.hdr reorient.img
	;;
    reorientHdrSaToAxNifti)
	run reorient -i RAS -o RAS phantom_sa.hdr ${tmpdir}/reorient.nii
	check_results reorient.nii
	;;
    reorientHdrCoToAx)
	run reorient -o RAS phantom_co.hdr ${tmpdir}/reorient.hdr
	check_results reorient.hdr reorient.img
	;;
    reorientHdrAxToSa)
	run reorient -o ASL phantom_ax.hdr ${tmpdir}/reorient.hdr
	check_results reorient.hdr reorient.img
	;;
    reorientHdrCoToSa)
	run reorient -o ASL phantom_co.hdr ${tmpdir}/reorient.hdr
	check_results reorient.hdr reorient.img
	;;
    reorientHdrAxToCo)
	run reorient -o LSA phantom_ax.hdr ${tmpdir}/reorient.hdr
	check_results reorient.hdr reorient.img
	;;
    reorientHdrSaToCo)
	run reorient -o LSA phantom_sa.hdr ${tmpdir}/reorient.hdr
	check_results reorient.hdr reorient.img
	;;
    reorientNrrdToNrrd)
        run reorient vol001_mr_t0_crop.nrrd ${tmpdir}/vol001_mr_t0_crop.nhdr
        check_results vol001_mr_t0_crop.nhdr vol001_mr_t0_crop.raw
	;;
    reorientNrrdToNrrdRAS)
        run reorient --output-orientation RAS vol001_mr_t0_crop.nrrd ${tmpdir}/vol001_mr_t0_crop.nhdr
        check_results vol001_mr_t0_crop.nhdr vol001_mr_t0_crop.raw
	;;
    reorientNrrdToNrrdSpaceLPS)
        run reorient --output-space LPS vol001_mr_t0_crop.nrrd ${tmpdir}/vol001_mr_t0_crop.nhdr
        check_results vol001_mr_t0_crop.nhdr vol001_mr_t0_crop.raw
	;;
    registrationRigidMrPet)
	run registration -i --dofs 6 -o ${tmpdir} pat001_mr_T1.hdr pat001_pet.hdr
	check_results registration
	;;
    registrationRigidMrCt)
	run registration -i --dofs 6 -o ${tmpdir} pat002_mr_T2.hdr pat002_ct.hdr
	check_results registration
	;;
    registrationRigidCt)
	run registration --msd -i --dofs 6 -o ${tmpdir} pat002_ct.hdr pat002_ct.hdr
	check_results registration
	;;
    registrationRigidPetMr)
	run registration -i --dofs 6 -o ${tmpdir} pat001_pet.hdr pat001_mr_T1.hdr
	check_results registration
	;;
    registrationRigidCtMr)
	run registration -i --dofs 6 -o ${tmpdir} pat002_ct.hdr pat002_mr_T2.hdr
	check_results registration
	;;
    registrationRigidMrPetNoSwap)
	run registration --no-switch -i --dofs 6 -o ${tmpdir} pat001_mr_T1.hdr pat001_pet.hdr
	check_results registration
	;;
    registrationRigidMrCtNoSwap)
	run registration --no-switch -i --dofs 6 -o ${tmpdir} pat002_mr_T2.hdr pat002_ct.hdr
	check_results registration
	;;
    registrationRigidPetMrDOF9)
	run registration -i --dofs 9 -o ${tmpdir} pat001_pet.hdr pat001_mr_T1.hdr
	check_results registration
	;;
    registrationRigidCtMrDOF7)
	run registration -i --dofs 7 -o ${tmpdir} pat002_ct.hdr pat002_mr_T2.hdr
	check_results registration
	;;
    registrationRigidLabelsDOF69)
	run registration --dofs 6 --dofs 9 --class-ref label --class-flt label -o ${tmpdir} parc1.hdr parc2.hdr
	check_results registration
	;;
    registrationRigidCrop)
	run registration -v -i -e 2.0 -a 0.125 --sampling 0.25 --crop-index-ref 17,20,0,47,49,12 --crop-index-flt 12,15,0,52,54,12 --dofs 6 -o ${tmpdir} rat_fse_erly.hdr rat_fse_late.hdr
	check_results registration
	;;
    sbaDefault)
	run sba -o ${tmpdir}/sba.nii -n 255 parc1.hdr parc2.hdr parc3.hdr
	check_results sba.nii
	;;
    sbaOutliers)
	run sba --exclude-outliers -o ${tmpdir}/sba.nii -n 255 parc1.hdr parc1.hdr parc1.hdr parc1.hdr parc1.hdr parc2.hdr
	check_results sba.nii
	;;
    sbaOutliers2)
	run sba --exclude-outliers -o ${tmpdir}/sba.nii -n 255 parc1.hdr parc2.hdr parc3.hdr
	check_results sba.nii
	;;
    sbaiDefault)
	run sbai -o ${tmpdir}/sbai.nii -n 255 parc12_warp.xform parc13_warp.xform
	check_results sbai.nii
	;;
    sequenceDefault)
	run_eval "cat numbers.txt | ${BINDIR}/sequence > ${tmpdir}/sequence.txt"
	check_results sequence.txt
	;;
    sequenceFormat)
	run_eval "cat numbers.txt | ${BINDIR}/sequence --format %g > ${tmpdir}/sequence.txt"
	check_results sequence.txt
	;;
    sequenceThresh)
	run_eval "cat numbers.txt | ${BINDIR}/sequence --thresh 1e4 > ${tmpdir}/sequence.txt"	
	check_results sequence.txt
	;;
    sequenceAbs)
	run_eval "cat numbers.txt | ${BINDIR}/sequence --abs > ${tmpdir}/sequence.txt"
	check_results sequence.txt
	;;
    sequenceAbsThresh)
	run_eval "cat numbers.txt | ${BINDIR}/sequence --thresh 1000 --abs > ${tmpdir}/sequence.txt"
	check_results sequence.txt
	;;
    sequenceHistogramDefault)
	run_eval "cat numbers.txt | ${BINDIR}/sequence --write-histogram ${tmpdir}/histogram.csv > ${tmpdir}/sequence.txt"
	check_results sequence.txt histogram.csv
	;;
    sequenceHistogramExplicit)
	run_eval "cat numbers.txt | ${BINDIR}/sequence --histogram-bins 10 --histogram-min 0 --histogram-max 1000 --write-histogram ${tmpdir}/histogram.csv > ${tmpdir}/sequence.txt"
	check_results sequence.txt histogram.csv
	;;
    similarityGrey)
	run_eval "${BINDIR}/similarity --histogram-text-file ${tmpdir}/histogram.txt rat_fse_erly.hdr rat_fse_late.hdr > ${tmpdir}/similarity.txt"
	check_results histogram.txt similarity.txt
	;;
    similarityWithInf)
	run_eval "${BINDIR}/similarity float_with_inf.nii.gz float_with_inf.nii.gz > ${tmpdir}/similarity.txt"
	check_results similarity.txt
	;;
    similarityLabels)
	run_eval "${BINDIR}/similarity --labels --histogram-text-file ${tmpdir}/histogram.txt parc1.hdr parc2.hdr > ${tmpdir}/similarity.txt"
	check_results histogram.txt similarity.txt
	;;
    similarityGreyMask)
	run_eval "${BINDIR}/similarity --mask rat_fse_erly.hdr --histogram-text-file ${tmpdir}/histogram.txt rat_fse_erly.hdr rat_fse_late.hdr > ${tmpdir}/similarity.txt"
	check_results histogram.txt similarity.txt
	;;
    similarityLabelsMask)
	run_eval "${BINDIR}/similarity --mask parc3_bin.hdr --labels --histogram-text-file ${tmpdir}/histogram.txt parc1.hdr parc2.hdr > ${tmpdir}/similarity.txt"
	check_results histogram.txt similarity.txt
	;;
    splitAxial)
	run split --output-xform-path ${tmpdir}/split_ax_%1d.xform --axial spgr_3t.hdr ${tmpdir}/split_ax_%1d.hdr
	check_results split_ax_0.img split_ax_1.img split_ax_0.xform split_ax_1.xform
	;;
    splitAxialSlices)
	run split --factor 0 --axial phantom_ax_downsampled.nii ${tmpdir}/slice_%1d.nii
	check_results slice_0.nii slice_1.nii slice_2.nii
	;;
    splitAxialNrrd)
	run split --axial --factor 3 spgr_3t.hdr ${tmpdir}/split_ax_%1d.nhdr
	check_results split_ax_0.nhdr split_ax_0.raw split_ax_1.nhdr split_ax_1.raw split_ax_2.nhdr split_ax_2.raw
	;;
    splitSagittal2)
	run split --output-xform-path ${tmpdir}/split_sa_%1d.xform --factor 2 --sagittal spgr_3t.hdr ${tmpdir}/split_sa_%1d.hdr
	check_results split_sa_0.img split_sa_1.img split_sa_0.xform split_sa_1.xform
	;;
    splitCoronal3)
	run split --output-xform-path ${tmpdir}/split_co_%1d.xform --factor 3 --coronal spgr_3t.hdr ${tmpdir}/split_co_%1d.hdr
	check_results split_co_0.img split_co_1.img split_co_2.img split_co_0.xform split_co_1.xform split_co_2.xform
	;;
    statisticsGrey)
	run_eval "${BINDIR}/statistics spgr_3t.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsPercentiles)
	run_eval "${BINDIR}/statistics -p 0.1 --percentile 0.5 -p 0.75 spgr_3t.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsGreyColumn)
	run_eval "${BINDIR}/statistics -C spgr_3t.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsGreyExpNotation)
	run_eval "${BINDIR}/statistics -E spgr_3t.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsGreyMask)
	run_eval "${BINDIR}/statistics -m spgr_3t_mask.hdr spgr_3t.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsGreyMultiMask)
	run_eval "${BINDIR}/statistics -M spgr_3t_mask.hdr spgr_3t.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsMaskMismatch)
	run_eval "${BINDIR}/statistics -M parc1.hdr spgr_3t.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsLabels)
	run_eval "${BINDIR}/statistics -l parc1.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsLabelsAllUpToHi)
	run_eval "${BINDIR}/statistics --mask-output-all-up-to 256 -l parc1.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    statisticsLabelsAllUpToLo)
	run_eval "${BINDIR}/statistics --mask-output-all-up-to 2 -l parc1.hdr > ${tmpdir}/statistics.txt"
	check_results statistics.txt
	;;
    streamxformFordwardBackward)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1_warp.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformBackwardForward)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform -- --inverse vol001_mr_t0t1_warp.xform vol001_mr_t0t1_warp.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformFordwardBackwardPoly0)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform poly0.xform --inverse poly0.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformFordwardBackwardPoly1)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform poly1.xform --inverse poly1.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformFordwardBackwardPoly2)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform poly2.xform --inverse poly2.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformFordwardBackwardPoly3)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform poly3.xform --inverse poly3.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformFordwardBackwardPoly4)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform poly4.xform --inverse poly4.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformAffinePoly4)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform --affine-only poly4.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformAffineForward)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform --affine-only vol001_mr_t0t1_warp.xform > ${tmpdir}/vol001_t1_points.xyzl"
	check_results vol001_t1_points.xyzl
	;;
    streamxformAffineForwardBackward)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform --affine-only vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1_warp.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformFordwardBackwardTolerance)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform --inversion-tolerance 0.1 vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1_warp.xform > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformAffine)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform vol001_mr_t0t1.list > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    streamxformAffineFromTo)
	run_eval "cat vol001_t0_points.xyzl | ${BINDIR}/streamxform --source-image vol001_mr_t0.hdr --target-image vol001_mr_t1.hdr vol001_mr_t0t1.list > ${tmpdir}/vol001_t0_points.xyzl"
	check_results vol001_t0_points.xyzl
	;;
    symmetry_plane)
	run sympl --sampling 1 --levels 4 --accuracy 0.1 --write-xform ${tmpdir}/xform --sinc --write-subtract ${tmpdir}/subtract.hdr --write-marked ${tmpdir}/marked.nii --write-mirror ${tmpdir}/mirror.nii -o ${tmpdir}/parameters cad001_ct.hdr
	check_results parameters xform subtract.img marked.nii mirror.nii
	;;
    symmetry_planeThresh)
	run sympl --sampling 1 --levels 4 --accuracy 0.1 --min-value -224 --max-value 176 --cubic --write-aligned ${tmpdir}/aligned.hdr -o ${tmpdir}/parameters cad001_ct.hdr
	check_results parameters aligned.img
	;;
    symplx_Default)
	run symplx --sampling 1 --levels 4 --accuracy 0.1 --write-xform ${tmpdir}/xform --sinc --write-subtract ${tmpdir}/subtract.hdr --write-marked ${tmpdir}/marked.nii --write-mirror ${tmpdir}/mirror.nii -o ${tmpdir}/parameters cad001_ct.hdr
	check_results parameters xform subtract.img marked.nii mirror.nii
	;;
    symplx_Thresh)
	run symplx --sampling 1 --levels 4 --accuracy 0.1 --min-value -224 --max-value 176 --cubic --write-aligned ${tmpdir}/aligned.hdr -o ${tmpdir}/parameters cad001_ct.hdr
	check_results parameters aligned.img
	;;
    symplx_FixOffset)
	run symplx --sampling 1 --levels 4 --accuracy 0.1 --fix-offset --cubic --write-aligned ${tmpdir}/aligned.hdr -o ${tmpdir}/parameters cad001_ct.hdr
	check_results parameters aligned.img
	;;
    symplx_DefaultCUDA)
	run symplx_cuda --sampling 1 --levels 4 --accuracy 0.1 --write-xform ${tmpdir}/xform --sinc --write-subtract ${tmpdir}/subtract.hdr -o ${tmpdir}/parameters cad001_ct.hdr
	check_results parameters xform subtract.img
	;;
    symplx_ThreshCUDA)
	run symplx_cuda --sampling 1 --levels 4 --accuracy 0.1 --min-value -224 --max-value 176 --cubic --write-aligned ${tmpdir}/aligned.hdr -o ${tmpdir}/parameters cad001_ct.hdr
	check_results parameters aligned.img
	;;
    symplx_FixOffsetCUDA)
	run symplx_cuda --sampling 1 --levels 4 --accuracy 0.1 --fix-offset --cubic --write-aligned ${tmpdir}/aligned.hdr -o ${tmpdir}/parameters cad001_ct.hdr
	check_results parameters aligned.img
	;;
    ttestDefault)
	run ttest -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/tstats.hdr jacobian-01.nii jacobian-02.nii -- jacobian-03.nii jacobian-04.nii
	check_results ttest.img tstats.img
	;;
    ttestOneSided)
	run ttest -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/tstats.hdr jacobian-01.nii jacobian-02.nii jacobian-03.nii jacobian-04.nii
	check_results ttest.img tstats.img
	;;
    ttestSymmetric)
	run ttest -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/tstats.hdr --symmetric jacobian-01.nii jacobian-02.nii jacobian-03.nii jacobian-04.nii
	check_results ttest.img tstats.img
	;;
    ttestLog)
	run ttest --log -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/tstats.hdr jacobian-01.nii jacobian-02.nii -- jacobian-03.nii jacobian-04.nii
	check_results ttest.img tstats.img
	;;
    ttestAbsLog)
	run ttest --abs --log -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/tstats.hdr jacobian-01.nii jacobian-02.nii -- jacobian-03.nii jacobian-04.nii
	check_results ttest.img tstats.img
	;;
    ttestInvert)
	run ttest --invert -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/tstats.hdr jacobian-01.nii jacobian-02.nii -- jacobian-03.nii jacobian-04.nii
	check_results ttest.img tstats.img
	;;
    ttestPaired)
	run ttest --paired -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/tstats.hdr jacobian-01.nii jacobian-02.nii -- jacobian-03.nii jacobian-04.nii
	check_results ttest.img tstats.img
	;;
    ttestCrossCorrelation)
	run ttest --cross-correlation -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/pvals.hdr jacobian-01.nii jacobian-02.nii jacobian-03.nii -- jacobian-04.nii jacobian-03.nii jacobian-02.nii 
	check_results ttest.img pvals.img
	;;
    ttestZScores)
	run ttest --zscores -o ${tmpdir}/zscores.hdr jacobian-01.nii jacobian-02.nii -- jacobian-03.nii jacobian-04.nii
	check_results zscores.img
	;;
    ttestMask)
	run ttest --mask jacobian-mask.nii -o ${tmpdir}/ttest.hdr --tstats-file ${tmpdir}/tstats.hdr jacobian-01.nii jacobian-02.nii -- jacobian-03.nii jacobian-04.nii
	check_results ttest.img tstats.img
	;;
    unsplitHdrAx)
	run unsplit --axial -o ${tmpdir}/unsplit.hdr split_ax_0.hdr split_ax_1.hdr
	check_results unsplit.hdr unsplit.img
	;;
    unsplitHdrSa)
	run unsplit --sagittal -o ${tmpdir}/unsplit.hdr split_sa_0.hdr split_sa_1.hdr
	check_results unsplit.hdr unsplit.img
	;;
    unsplitHdrCo)
	run unsplit --coronal -o ${tmpdir}/unsplit.hdr split_co_0.hdr split_co_1.hdr split_co_2.hdr
	check_results unsplit.hdr unsplit.img
	;;
    unsplitHdrNrrdAx)
	run unsplit --axial -o ${tmpdir}/unsplit.nhdr split_ax_0.hdr split_ax_1.hdr
	check_results unsplit.nhdr unsplit.raw
	;;
    unsplitHdrNrrdSa)
	run unsplit --sagittal -o ${tmpdir}/unsplit.nhdr split_sa_0.hdr split_sa_1.hdr
	check_results unsplit.nhdr unsplit.raw
	;;
    unsplitHdrNrrdCo)
	run unsplit --coronal -o ${tmpdir}/unsplit.nhdr split_co_0.hdr split_co_1.hdr split_co_2.hdr
	check_results unsplit.nhdr unsplit.raw
	;;
    unsplitNrrdNrrd)
	run unsplit --axial -o ${tmpdir}/unsplit.nhdr split_ax_0.nhdr split_ax_1.nhdr split_ax_2.nhdr
	check_results unsplit.nhdr unsplit.raw
	;;
    unsplitSlices)
        run unsplit --axial -o ${tmpdir}/unsplit.nii phantom_ax_downsampled_slice_0.nii phantom_ax_downsampled_slice_1.nii phantom_ax_downsampled_slice_2.nii
	check_results unsplit.nii
	;;
    unwarp_image_phantomDefault)
        run unwarp_image_phantom magphan.xml spgr_magphan.nii ${tmpdir}/poly.xform
	check_results poly.xform
	;;
    unwarp_image_phantomPoly)
        run unwarp_image_phantom --poly magphan.xml spgr_magphan.nii ${tmpdir}/poly.xform
	check_results poly.xform
	;;
    unwarp_image_phantomPolyDegree2)
        run unwarp_image_phantom --poly --degree 2 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomSpacing)
        run unwarp_image_phantom --spline --iterations-per-level 1 --final-cp-spacing 80 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomSpacingInverse)
        run unwarp_image_phantom --spline --iterations-per-level 1 --final-cp-spacing 80 --fit-inverse magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomSpacingLevels)
        run unwarp_image_phantom --spline --iterations-per-level 1 --final-cp-spacing 80 --levels 3 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomSpacingDirect)
        run unwarp_image_phantom --spline --iterations-per-level 1 --no-fit-affine --final-cp-spacing 80 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomDims)
        run unwarp_image_phantom --spline --iterations-per-level 1 --final-cp-dims 5,5,5 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomDimsLevels)
        run unwarp_image_phantom --spline --iterations-per-level 1 --final-cp-dims 5,5,5 --levels 3 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomDimsLevelsIterations)
        run unwarp_image_phantom --spline --iterations-per-level 10 --final-cp-dims 5,5,5 --levels 3 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomDimsLevelsThreshold)
        run unwarp_image_phantom --spline --iterations-per-level 1 --rms-threshold 0.1 --final-cp-dims 5,5,5 --levels 3 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomDimsLevelsIterationsThreshold)
        run unwarp_image_phantom --spline --iterations-per-level 10 --rms-threshold 0.1 --final-cp-dims 5,5,5 --levels 3 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    unwarp_image_phantomDimsDefault)
        run unwarp_image_phantom --spline --final-cp-dims 5,5,5 magphan.xml spgr_magphan.nii ${tmpdir}/ffd.xform
	check_results ffd.xform
	;;
    volume_injection)
	run volume_injection --recon-grid-path spgr_3t.hdr -o ${tmpdir}/injection.hdr --injection-kernel-sigma 0.5 --injection-kernel-radius 2 split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.img
	;;
    volume_injectionReconGrid)
	run volume_injection --recon-grid 49,65,35:3.75,3.75,3.75 -o ${tmpdir}/injection.nii --injection-kernel-sigma 0.5 --injection-kernel-radius 2 split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.nii
	;;
    volume_injectionReconGridOffset)
	run volume_injection --recon-grid 48,64,34:3.75,3.75,3.75:1.875,1.875,1.875 -o ${tmpdir}/injection.nii --injection-kernel-sigma 0.5 --injection-kernel-radius 2 split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.nii
	;;
    volume_injectionIsotropic)
	run volume_injection --recon-grid-path spgr_3t.hdr -o ${tmpdir}/injection.hdr --injection-kernel-sigma 0.5 --injection-kernel-radius 2 --isotropic-injection split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.img
	;;
    volume_injectionNoXform)
	run volume_injection -o ${tmpdir}/injection.hdr --injection-kernel-sigma 0.5 --injection-kernel-radius 2 --exclude-first-image spgr_3t.hdr -- split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.img
	;;
    volume_injectionNoXformIsotropic)
	run volume_injection -o ${tmpdir}/injection.hdr --injection-kernel-sigma 0.5 --injection-kernel-radius 2 --isotropic-injection --exclude-first-image spgr_3t.hdr -- split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.img
	;;
    volume_reconstructionFourthOrder)
	run volume_reconstruction --recon-grid-path spgr_3t.hdr -o ${tmpdir}/reconstruction.hdr --linear --fourth-order-error --num-iterations 2 --injection-kernel-sigma 0.5 --injection-kernel-radius 2 --isotropic-injection --write-injected-image ${tmpdir}/injection.hdr split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.img reconstruction.img
	;;
    volume_reconstructionCubic)
	run volume_reconstruction --recon-grid-path spgr_3t.hdr -o ${tmpdir}/reconstruction.hdr --cubic --num-iterations 2 --injection-kernel-sigma 0.5 --injection-kernel-radius 2 --isotropic-injection --write-injected-image ${tmpdir}/injection.hdr split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.img reconstruction.img
	;;
    volume_reconstructionNoXform)
	run volume_reconstruction -o ${tmpdir}/reconstruction.hdr --linear --num-iterations 2 --injection-kernel-sigma 0.5 --injection-kernel-radius 2 --isotropic-injection --write-injected-image ${tmpdir}/injection.hdr --exclude-first-image spgr_3t.hdr -- split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results injection.img reconstruction.img
	;;
    volume_reconstructionBoxPSF)
	run volume_reconstruction --recon-grid-path spgr_3t.hdr -o ${tmpdir}/reconstruction.hdr --deblurring box --psf 0.9375,0.9375,1.25 --num-iterations 2 --injection-kernel-sigma 0.5 --injection-kernel-radius 2 split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results reconstruction.img
	;;
    volume_reconstructionGaussianPSF)
	run volume_reconstruction --recon-grid-path spgr_3t.hdr -o ${tmpdir}/reconstruction.hdr --deblurring gaussian --psf 0.9375,0.9375,1.25 --num-iterations 2 --injection-kernel-sigma 0.5 --injection-kernel-radius 2 split_ax_0.hdr split_ax_01.xform split_ax_1.hdr
	check_results reconstruction.img
	;;
    warpSingleLevel)
	run warp --fast --exploration 8 --grid-spacing 160 --accuracy 1 --no-adaptive-fix -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpSingleLevelExact)
	run warp --fast --exploration 8 --grid-spacing 180 --exact-spacing --accuracy 1 --sampling 3 --no-adaptive-fix -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpInverseConsistentCC)
	run warp --fast --exploration 8 --grid-spacing 80 --accuracy 1 --ncc --ic-weight 1e-2 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpMultiLevel)
	run warp --fast --exploration 8 --grid-spacing 160 --accuracy 1 --refine 1 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpMultiLevelMatchHistograms)
	run warp --fast --exploration 8 --match-histograms --msd --grid-spacing 160 --accuracy 1 --refine 1 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpMultiLevelDeltaFThreshold)
	run warp --fast --exploration 8 --delta-f-threshold 0.01 --msd --grid-spacing 160 --accuracy 1 --refine 1 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpMultiLevelExact)
	run warp --fast --exploration 8 --grid-spacing 160 --exact-spacing --accuracy 1 --refine 1 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpDelayRefine)
	run warp --fast --exploration 12 --grid-spacing 160 --accuracy 2 --refine 1 --delay-refine --sampling 6 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpEnergy)
	run warp --fast --exploration 8 --grid-spacing 160 --accuracy 1 --refine 1 --energy-weight 1e-1 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpEnergyRelax)
	run warp --fast --exploration 8 --grid-spacing 160 --accuracy 1 --refine 1 --energy-weight 1e-1 --relax 1e-2 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpJacobian)
	export CMTK_NUM_THREADS=1
	run warp --fast --exploration 12 --grid-spacing 160 --accuracy 2 --refine 1 --jacobian-weight 1e-1 --sampling 12 --omit-original-data -o ${tmpdir} vol001_mr_t0t1.list
	unset CMTK_NUM_THREADS
	check_results registration
	;;
    warpRigidity)
	run warp --fast --exploration 12 --grid-spacing 160 --accuracy 2 --refine 1 --rigidity-weight 1e-1 --sampling 12 --omit-original-data -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpLabels)
	run warp --fast --exploration 8 --grid-spacing 90 --accuracy 1 --refine 1 --class-ref label --class-flt label -o ${tmpdir} --initial parc1_parc2_9dof.xform parc1.hdr parc2.hdr
	check_results registration
	;;
    warpxSingleLevel)
	run warpx --fast --max-stepsize 8 --grid-spacing 160 --min-stepsize 1 --no-adaptive-fix -o ${tmpdir} --write-itk-xform ${tmpdir}/xform.tfm vol001_mr_t0t1.list
	check_results registration xform.tfm
	;;
    warpxSingleLevelExact)
	run warpx --fast --max-stepsize 8 --grid-spacing 180 --exact-spacing --min-stepsize 1 --sampling 3 --no-adaptive-fix -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpxInverseConsistentCC)
        export CMTK_NUM_THREADS=1
	run warpx --fast --max-stepsize 8 --grid-spacing 80 --min-stepsize 1 --ncc --inverse-consistency-weight 1e-2 -o ${tmpdir} vol001_mr_t0t1.list
        unset CMTK_NUM_THREADS
	check_results registration
	;;
    warpxMultiLevel)
	run warpx --pad-flt -10000 --write-reformatted ${tmpdir}/reformat.nii --fast --max-stepsize 8 --grid-spacing 160 --min-stepsize 1 --grid-refine 1 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration reformat.nii
	;;
    warpxMultiLevelMatchHistograms)
        export CMTK_NUM_THREADS=1
	run warpx --fast --max-stepsize 8 --match-histograms --msd --grid-spacing 160 --min-stepsize 1 --grid-refine 1 -o ${tmpdir} vol001_mr_t0t1.list
	unset CMTK_NUM_THREADS
	check_results registration
	;;
    warpxMultiLevelDeltaFThreshold)
        export CMTK_NUM_THREADS=1
	run warpx --fast --max-stepsize 8 --delta-f-threshold 0.01 --msd --grid-spacing 160 --min-stepsize 1 --grid-refine 1 -o ${tmpdir} vol001_mr_t0t1.list
	unset CMTK_NUM_THREADS
	check_results registration
	;;
    warpxMultiLevelExact)
	run warpx --fast --max-stepsize 8 --grid-spacing 160 --exact-spacing --min-stepsize 1 --grid-refine 1 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpxDelayRefine)
	run warpx --fast --max-stepsize 12 --grid-spacing 160 --min-stepsize 2 --grid-refine 1 --delay-refine --sampling 6 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpxEnergy)
	run warpx --fast --max-stepsize 8 --grid-spacing 160 --min-stepsize 1 --grid-refine 1 --smoothness-constraint-weight 1e-1 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpxEnergyRelax)
	run warpx --fast --max-stepsize 8 --grid-spacing 160 --min-stepsize 1 --grid-refine 1 --smoothness-constraint-weight 1e-1 --constraint-relaxation-factor 1e-2 -o ${tmpdir} vol001_mr_t0t1.list
	check_results registration
	;;
    warpxJacobian)
	export CMTK_NUM_THREADS=1
	run warpx --fast --max-stepsize 12 --grid-spacing 160 --min-stepsize 2 --grid-refine 1 --jacobian-constraint-weight 1e-1 --sampling 12 --omit-original-data -o ${tmpdir} vol001_mr_t0t1.list
	unset CMTK_NUM_THREADS
	check_results registration
	;;
    warpxJacobianUnfold)
	export CMTK_NUM_THREADS=1
	run warpx --fast --relax-to-unfold --max-stepsize 12 --grid-spacing 160 --min-stepsize 2 --grid-refine 1 --jacobian-constraint-weight 1e-1 --sampling 12 --omit-original-data -o ${tmpdir} vol001_mr_t0t1.list
	unset CMTK_NUM_THREADS
	check_results registration
	;;
    warpxLabels)
	run warpx --fast --max-stepsize 8 --grid-spacing 90 --min-stepsize 1 --grid-refine 1 --class-ref label --class-flt label -o ${tmpdir} --initial parc1_parc2_9dof.xform parc1.hdr parc2.hdr
	check_results registration
	;;
    vtkxform)
        run_eval "${BINDIR}/vtkxform vol001_mr_t0t1.list < polydata_ascii.vtk > ${tmpdir}/output.vtk"
	check_results output.vtk
	;;
    vtkxformInverse)
        run_eval "${BINDIR}/vtkxform -- --inverse vol001_mr_t0t1.list < polydata_ascii.vtk > ${tmpdir}/output.vtk"
	check_results output.vtk
	;;
    xform2dfieldWarpNrrd)
	run xform2dfield -v ${tmpdir}/dfield.nhdr vol001_mr_t0_crop.hdr vol001_mr_t0t1_warp.xform
	check_results dfield.nhdr dfield.raw
	;;
    xform2dfieldWarpNifti)
	run xform2dfield -v ${tmpdir}/dfield.nii vol001_mr_t0_crop.hdr vol001_mr_t0t1_warp.xform
	check_results dfield.nii
	;;
    xform2dfieldWarpNiftiFSL)
	run xform2dfield --target-image-fsl ncanda_t1_jacobian.nii.gz --output-absolute ${tmpdir}/dfield.nii vol001_mr_t0_crop.hdr vol001_mr_t0t1_warp.xform
	check_results dfield.nii
	;;
    xform2dfieldWarpNiftiHdr)
	run xform2dfield -v ${tmpdir}/dfield.img vol001_mr_t0_crop.hdr vol001_mr_t0t1_warp.xform
	check_results dfield.hdr dfield.img
	;;
    xform2dfieldAffineNrrd)
	run xform2dfield -v ${tmpdir}/dfield.nhdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform
	check_results dfield.nhdr dfield.raw
	;;
    xform2dfieldDownsampleXYZNrrd)
	run xform2dfield -v --downsample 4,4,2 ${tmpdir}/dfield.nhdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform
	check_results dfield.nhdr dfield.raw
	;;
    xform2dfieldDownsampleXNrrd)
	run xform2dfield -v --downsample 4 ${tmpdir}/dfield.nhdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform
	check_results dfield.nhdr dfield.raw
	;;
    xform2dfieldConcatNrrd)
	run xform2dfield -v ${tmpdir}/dfield.nhdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform vol001_mr_t0t1_warp.xform
	check_results dfield.nhdr dfield.raw
	;;
    xform2dfieldInverseNrrd)
	run xform2dfield -v ${tmpdir}/dfield.nhdr vol001_mr_t0_crop.hdr vol001_mr_t0_crop.xform --inverse vol001_mr_t0t1_warp.xform
	check_results dfield.nhdr dfield.raw
	;;
    xform2scalarAffine)
	run xform2scalar --float --output ${tmpdir}/magnitude.nii vol001_mr_t0.hdr vol001_mr_t0t1.list
	check_results magnitude.nii
	;;
    xform2scalarAffineDoubleY)
	run xform2scalar --mode x-component --output ${tmpdir}/xcomponent.nii vol001_mr_t0.hdr vol001_mr_t0t1.list
	check_results xcomponent.nii
	;;
    xform2scalarWarp)
	run xform2scalar --float --output ${tmpdir}/magnitude.nii vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform
	check_results magnitude.nii
	;;
    xform2scalarWarpInverseError)
	run xform2scalar --float --output ${tmpdir}/magnitude.nii vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform --inverse vol001_mr_t0t1_warp.xform
	check_results magnitude.nii
	;;
    xform2scalarWarpOnly)
	run xform2scalar --warp-only --float --output ${tmpdir}/magnitude.nii vol001_mr_t0.hdr vol001_mr_t0t1_warp.xform
	check_results magnitude.nii
	;;
    xform2scalarDfield)
	run xform2scalar --float --output ${tmpdir}/magnitude.nii parc1.hdr parc1_parc2_dfield.nrrd
	check_results magnitude.nii
	;;
    vol2csvLabels)
	run vol2csv -o ${tmpdir}/volumes.csv --labels-file sri24_ventricles.txt ncanda_t1_ventricles.nii ncanda_t1_pve_0.nii ncanda_t1_pve_1.nii ncanda_t1_pve_2.nii
	check_results volumes.csv
	;;
    vol2csvLabelsNoBackground)
	run vol2csv -o ${tmpdir}/volumes.csv --labels-file sri24_ventricles_noBG.txt ncanda_t1_ventricles.nii ncanda_t1_pve_0.nii ncanda_t1_pve_1.nii ncanda_t1_pve_2.nii
	check_results volumes.csv
	;;
    vol2csvDensityLabels)
	run vol2csv -o ${tmpdir}/volumes.csv --density-labels CSF,GM,WM ncanda_t1_ventricles.nii ncanda_t1_pve_0.nii ncanda_t1_pve_1.nii ncanda_t1_pve_2.nii
	check_results volumes.csv
	;;
    vol2csvScale)
	run vol2csv -o ${tmpdir}/volumes.csv --pixel-scale-image ncanda_t1_jacobian.nii ncanda_t1_ventricles.nii ncanda_t1_pve_0.nii ncanda_t1_pve_1.nii ncanda_t1_pve_2.nii
	check_results volumes.csv
	;;
    vol2csvScaleGlobal)
	run vol2csv -o ${tmpdir}/volumes.csv --pixel-scale-factor 2 ncanda_t1_ventricles.nii ncanda_t1_pve_0.nii ncanda_t1_pve_1.nii ncanda_t1_pve_2.nii
	check_results volumes.csv
	;;
    help_film)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/film --help > ${tmpdir}/film.help"
	check_results film.help
	;;
    help_all_film)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/film --help-all > ${tmpdir}/film.help"
	check_results film.help
	;;
    xml_film)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/film --xml | ${sed} '/<version>/{ N; s/^.*$/<version>/ }' > ${tmpdir}/film.xml"
	check_results film.xml
	;;
    xml_gmm)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/gmm --xml | ${sed} '/<version>/{ N; s/^.*$/<version>/ }' > ${tmpdir}/gmm.xml"
	check_results gmm.xml
	;;
    xml_levelset)
        run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/levelset --xml | ${sed} '/<version>/{ N; s/^.*$/<version>/ }' > ${tmpdir}/levelset.xml"
	check_results levelset.xml
	;;
    xml_mrbias)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/mrbias --xml | ${sed} '/<version>/{ N; s/^.*$/<version>/ }' > ${tmpdir}/mrbias.xml"
	check_results mrbias.xml
	;;
    xml_registration)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/registration --xml | ${sed} '/<version>/{ N; s/^.*$/<version>/ }' > ${tmpdir}/registration.xml"
	check_results registration.xml
	;;
    wiki_film)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/film --wiki > ${tmpdir}/film.wiki"
	check_results film.wiki
	;;
    wiki_levelset)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/levelset --wiki > ${tmpdir}/levelset.wiki"
	check_results levelset.wiki
	;;
    wiki_mrbias)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/mrbias --wiki > ${tmpdir}/mrbias.wiki"
	check_results mrbias.wiki
	;;
    wiki_registration)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/registration --wiki > ${tmpdir}/registration.wiki"
	check_results registration.wiki
	;;
    man_film)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/film --man | fgrep -v .TH > ${tmpdir}/film.man"
	check_results film.man
	;;
    man_levelset)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/levelset --man | fgrep -v .TH > ${tmpdir}/levelset.man"
	check_results levelset.man
	;;
    man_mrbias)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/mrbias --man | fgrep -v .TH > ${tmpdir}/mrbias.man"
	check_results mrbias.man
	;;
    man_registration)
	run_eval "CMTK_CONSOLE_LINE_WIDTH=100 ${BINDIR}/registration --man | fgrep -v .TH > ${tmpdir}/registration.man"
	check_results registration.man
	;;
    *)
	exit 2
	;;
esac

if [ "${tmpdir}" != "" ]; then
    rm -rf ${tmpdir}
fi