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Merge pull request #1255 from ANTsX/antsInitAffine
ENH: Allow users to specify an initial transform
2 parents 31f7a61 + 05813f8 commit 1023a76

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‎Scripts/antsBrainExtraction.sh

+51-38
Original file line numberDiff line numberDiff line change
@@ -54,24 +54,27 @@ Required arguments:
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Optional arguments:
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57-
-c: Tissue classification A k-means segmentation is run to find gray or white matter around
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-c: Tissue classification A k-means segmentation is run to find gray or white matter around
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the edge of the initial brain mask warped from the template.
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This produces a segmentation image with K classes, ordered by mean
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intensity in increasing order. With this option, you can control
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K and tell the script which classes represent CSF, gray and white matter.
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K and tell the script which classes represent CSF, gray and white matter.
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Format (\"KxcsfLabelxgmLabelxwmLabel\")
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Examples:
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Examples:
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-c 3x1x2x3 for T1 with K=3, CSF=1, GM=2, WM=3 (default)
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-c 3x3x2x1 for T2 with K=3, CSF=3, GM=2, WM=1
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-c 3x1x3x2 for FLAIR with K=3, CSF=1 GM=3, WM=2
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-c 4x4x2x3 uses K=4, CSF=4, GM=2, WM=3
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-f: Brain extraction registration mask Mask used for registration to limit the metric computation to
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a specific region.
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-s: image file suffix Any of the standard ITK IO formats e.g. nrrd, nii.gz (default), mhd
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-u: use random seeding Use random number generated from system clock in Atropos (default = 1)
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-k: keep temporary files Keep brain extraction/segmentation warps, etc (default = false).
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-q: use floating point precision Use antsRegistration with floating point precision.
71+
-r: Initial moving transform An ITK affine transform (eg, from antsAI or ITK-SNAP) for the moving image.
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Without this option, this script calls antsAI to search for a good initial moving
73+
transform.
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-s: Image file suffix Any of the standard ITK IO formats e.g. nrrd, nii.gz (default), mhd
75+
-u: Use random seeding Use random number generated from system clock in Atropos (default = 1)
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-k: Keep temporary files Keep brain extraction/segmentation warps, etc (default = false).
77+
-q: Use floating point precision Use antsRegistration with floating point precision.
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-z: Test / debug mode If > 0, runs a faster version of the script. Only for debugging, results will not be good.
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@@ -201,11 +204,14 @@ N4_BSPLINE_PARAMS="[ 200 ]"
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USE_FLOAT_PRECISION=0
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207+
# Intial affine supplied on command line
208+
USER_INITIAL_AFFINE=""
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if [[ $# -lt 3 ]] ; then
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Usage >&2
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exit 1
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else
208-
while getopts "a:c:d:e:f:h:k:m:o:q:s:u:z:" OPT
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while getopts "a:c:d:e:f:h:k:m:o:q:r:s:u:z:" OPT
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do
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case $OPT in
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d) #dimensions
@@ -225,11 +231,11 @@ else
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;;
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c) #k-means segmentation params
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# Check conventional ANTs vector designation (i.e., 'x')
228-
kmeansParamsArr=(${OPTARG//x/ })
234+
kmeansParamsArr=(${OPTARG//x/ })
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if [[ ${#kmeansParamsArr[@]} -ne 4 ]];
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then
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# Check alternative form
232-
kmeansParamsArr=(${OPTARG//,/ })
238+
kmeansParamsArr=(${OPTARG//,/ })
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if [[ ${#kmeansParamsArr[@]} -ne 4 ]];
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then
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echo "ERROR: unrecognized kmeans option (-c)."
@@ -239,7 +245,7 @@ else
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ATROPOS_NUM_CLASSES=${kmeansParamsArr[0]}
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ATROPOS_BRAIN_EXTRACTION_INITIALIZATION="kmeans[ ${ATROPOS_NUM_CLASSES} ]"
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ATROPOS_CSF_CLASS_LABEL=${kmeansParamsArr[1]}
242-
ATROPOS_GM_CLASS_LABEL=${kmeansParamsArr[2]}
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ATROPOS_GM_CLASS_LABEL=${kmeansParamsArr[2]}
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ATROPOS_WM_CLASS_LABEL=${kmeansParamsArr[3]}
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;;
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k) #keep tmp images
@@ -259,6 +265,9 @@ else
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;;
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q)
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USE_FLOAT_PRECISION=$OPTARG
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;;
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r)
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USER_INITIAL_AFFINE=$OPTARG
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;;
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s) #output suffix
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OUTPUT_SUFFIX=$OPTARG
@@ -292,7 +301,7 @@ if [[ -z "$ATROPOS_SEGMENTATION_MRF" ]];
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fi
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fi
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echo "
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echo "
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Will run Atropos segmentation with K=${ATROPOS_NUM_CLASSES}. Classes labeled in order of mean intensity. Assuming CSF=${ATROPOS_CSF_CLASS_LABEL}, GM=${ATROPOS_GM_CLASS_LABEL}, WM=${ATROPOS_WM_CLASS_LABEL}
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"
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@@ -423,7 +432,7 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
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## check if output was produced
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if [[ ! -f ${N4_CORRECTED_IMAGES[0]} ]];
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then
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echo "Expected output was not produce. The N4 corrected image doesn't exist:"
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echo "Expected output was not produced. The N4 corrected image doesn't exist:"
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echo " ${N4_CORRECTED_IMAGES[0]}"
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exit 1
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fi
@@ -454,29 +463,33 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
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echo
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## Step 1 ##
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logCmd ${ANTSPATH}/ResampleImageBySpacing ${DIMENSION} ${EXTRACTION_TEMPLATE} ${EXTRACTION_INITIAL_AFFINE_FIXED} 4 4 4 1
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logCmd ${ANTSPATH}/ResampleImageBySpacing ${DIMENSION} ${N4_CORRECTED_IMAGES[0]} ${EXTRACTION_INITIAL_AFFINE_MOVING} 4 4 4 1
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logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${EXTRACTION_LAPLACIAN} Laplacian ${N4_CORRECTED_IMAGES[0]} 1.5 1
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logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${EXTRACTION_TEMPLATE_LAPLACIAN} Laplacian ${EXTRACTION_TEMPLATE} 1.5 1
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# exe_initial_align="${ANTSPATH}/antsAffineInitializer ${DIMENSION} ${EXTRACTION_INITIAL_AFFINE_FIXED} ${EXTRACTION_INITIAL_AFFINE_MOVING} ${EXTRACTION_INITIAL_AFFINE} 15 0.1 0 10"
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exe_initial_align="${ANTSPATH}/antsAI -d ${DIMENSION} -v 1"
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exe_initial_align="${exe_initial_align} -m Mattes[ ${EXTRACTION_INITIAL_AFFINE_FIXED},${EXTRACTION_INITIAL_AFFINE_MOVING},32,Regular,0.2 ]"
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exe_initial_align="${exe_initial_align} -t Affine[ 0.1 ]"
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exe_initial_align="${exe_initial_align} -s [ 20,0.12 ]"
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exe_initial_align="${exe_initial_align} -g [ 40,0x40x40 ]"
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exe_initial_align="${exe_initial_align} -p 0"
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exe_initial_align="${exe_initial_align} -c 10"
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exe_initial_align="${exe_initial_align} -o ${EXTRACTION_INITIAL_AFFINE}"
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473-
if [[ -f ${EXTRACTION_REGISTRATION_MASK} ]];
469+
if [[ ! -f "${USER_INITIAL_AFFINE}" ]]
474470
then
475-
# exe_initial_align="${exe_initial_align} ${EXTRACTION_REGISTRATION_MASK}"
476-
exe_initial_align="${exe_initial_align} -x ${EXTRACTION_REGISTRATION_MASK}"
477-
fi
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479-
logCmd $exe_initial_align
472+
logCmd ${ANTSPATH}/ResampleImageBySpacing ${DIMENSION} ${EXTRACTION_TEMPLATE} ${EXTRACTION_INITIAL_AFFINE_FIXED} 4 4 4 1
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logCmd ${ANTSPATH}/ResampleImageBySpacing ${DIMENSION} ${N4_CORRECTED_IMAGES[0]} ${EXTRACTION_INITIAL_AFFINE_MOVING} 4 4 4 1
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475+
exe_initial_align="${ANTSPATH}/antsAI -d ${DIMENSION} -v 1"
476+
exe_initial_align="${exe_initial_align} -m Mattes[ ${EXTRACTION_INITIAL_AFFINE_FIXED},${EXTRACTION_INITIAL_AFFINE_MOVING},32,Regular,0.2 ]"
477+
exe_initial_align="${exe_initial_align} -t Affine[ 0.1 ]"
478+
exe_initial_align="${exe_initial_align} -s [ 20,0.12 ]"
479+
exe_initial_align="${exe_initial_align} -g [ 40,0x40x40 ]"
480+
exe_initial_align="${exe_initial_align} -p 0"
481+
exe_initial_align="${exe_initial_align} -c 10"
482+
exe_initial_align="${exe_initial_align} -o ${EXTRACTION_INITIAL_AFFINE}"
483+
484+
if [[ -f ${EXTRACTION_REGISTRATION_MASK} ]];
485+
then
486+
exe_initial_align="${exe_initial_align} -x ${EXTRACTION_REGISTRATION_MASK}"
487+
fi
488+
489+
logCmd $exe_initial_align
490+
else
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${ANTSPATH}/antsApplyTransforms -d ${DIMENSION} -t ${USER_INITIAL_AFFINE} -o Linear[ ${EXTRACTION_INITIAL_AFFINE}, 0 ]
492+
fi
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basecall="${ANTS} -d ${DIMENSION} -u 1 -w [ 0.025,0.975 ] -o ${EXTRACTION_WARP_OUTPUT_PREFIX} -r ${EXTRACTION_INITIAL_AFFINE} -z 1 --float ${USE_FLOAT_PRECISION} --verbose 1"
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if [[ -f ${EXTRACTION_REGISTRATION_MASK} ]];
@@ -507,8 +520,8 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
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fi
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fi
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511-
if [[ ! -f ${EXTRACTION_SEGMENTATION} ]];
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524+
if [[ ! -f ${EXTRACTION_SEGMENTATION} ]];
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then
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## Step 2 ##
@@ -530,8 +543,8 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
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exe_brain_extraction_3="${ATROPOS} -d ${DIMENSION} -o ${EXTRACTION_SEGMENTATION} ${ATROPOS_ANATOMICAL_IMAGES_COMMAND_LINE} -x ${EXTRACTION_MASK} -i ${ATROPOS_BRAIN_EXTRACTION_INITIALIZATION} -c ${ATROPOS_BRAIN_EXTRACTION_CONVERGENCE} -m ${ATROPOS_BRAIN_EXTRACTION_MRF} -k ${ATROPOS_BRAIN_EXTRACTION_LIKELIHOOD} -r ${USE_RANDOM_SEEDING} --verbose 1"
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logCmd $exe_brain_extraction_3
533-
fi
534-
546+
fi
547+
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# Pad image here to avoid errors from dilating into the edge of the image
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padVoxels=10
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@@ -541,7 +554,7 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
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logCmd ${ANTSPATH}/ThresholdImage ${DIMENSION} ${EXTRACTION_SEGMENTATION} ${EXTRACTION_WM} ${ATROPOS_WM_CLASS_LABEL} ${ATROPOS_WM_CLASS_LABEL} 1 0
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logCmd ${ANTSPATH}/ThresholdImage ${DIMENSION} ${EXTRACTION_SEGMENTATION} ${EXTRACTION_GM} ${ATROPOS_GM_CLASS_LABEL} ${ATROPOS_GM_CLASS_LABEL} 1 0
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logCmd ${ANTSPATH}/ThresholdImage ${DIMENSION} ${EXTRACTION_SEGMENTATION} ${EXTRACTION_CSF} ${ATROPOS_CSF_CLASS_LABEL} ${ATROPOS_CSF_CLASS_LABEL} 1 0
544-
557+
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logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${EXTRACTION_WM} GetLargestComponent ${EXTRACTION_WM}
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logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${EXTRACTION_GM} GetLargestComponent ${EXTRACTION_GM}
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@@ -573,13 +586,13 @@ if [[ ! -f ${EXTRACTION_MASK} || ! -f ${EXTRACTION_WM} ]];
573586
logCmd ${ANTSPATH}/ImageMath ${DIMENSION} ${img} PadImage ${img} -$padVoxels
574587
done
575588

576-
589+
577590
logCmd ${ANTSPATH}/MultiplyImages ${DIMENSION} ${N4_CORRECTED_IMAGES[0]} ${EXTRACTION_MASK} ${EXTRACTION_BRAIN}
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579592
# Copy header information from original image into output
580593
logCmd ${ANTSPATH}/CopyImageHeaderInformation ${ANATOMICAL_IMAGES[0]} ${EXTRACTION_BRAIN} ${EXTRACTION_BRAIN} 1 1 1 0
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logCmd ${ANTSPATH}/CopyImageHeaderInformation ${ANATOMICAL_IMAGES[0]} ${EXTRACTION_MASK} ${EXTRACTION_MASK} 1 1 1 0
582-
595+
583596

584597
if [[ ! -f ${EXTRACTION_MASK} ]];
585598
then

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