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ENH: Add option for SyN gradient step in scripts #1129

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Jan 14, 2021
Merged

ENH: Add option for SyN gradient step in scripts #1129

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17 changes: 13 additions & 4 deletions Scripts/antsRegistrationSyN.sh
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,8 @@ Optional arguments:

-s: spline distance for deformable B-spline SyN transform (default = 26)

-g: gradient step size for SyN and B-spline SyN (default = 0.1)

-x: mask(s) for the fixed image space. Should specify either a single image to be used for
all stages or one should specify a mask image for each "stage" (cf -t option). If
no mask is to be used for a particular stage, the keyword 'NULL' should be used
Expand Down Expand Up @@ -160,6 +162,8 @@ Optional arguments:

-s: spline distance for deformable B-spline SyN transform (default = 26)

-g: gradient step size for SyN and B-spline SyN (default = 0.1)

-x: mask(s) for the fixed image space. Should specify either a single image to be used for
all stages or one should specify a mask image for each "stage" (cf -t option). If
no mask is to be used for a particular stage, the keyword 'NULL' should be used
Expand All @@ -186,7 +190,7 @@ Optional arguments:
--------------------------------------------------------------------------------------
Get the latest ANTs version at:
--------------------------------------------------------------------------------------
https://github.com/stnava/ANTs/
https://github.com/ANTsX/ANTs/

--------------------------------------------------------------------------------------
Read the ANTS documentation at:
Expand Down Expand Up @@ -227,6 +231,7 @@ function reportMappingParameters {
Initial transforms: ${INITIALTRANSFORMS[@]}
Number of threads: $NUMBEROFTHREADS
Spline distance: $SPLINEDISTANCE
SyN gradient step: $SYNGRADIENTSTEP
Transform type: $TRANSFORMTYPE
CC radius: $CCRADIUS
Precision: $PRECISIONTYPE
Expand Down Expand Up @@ -278,6 +283,7 @@ INITIALTRANSFORMS=()
OUTPUTNAME=output
NUMBEROFTHREADS=0
SPLINEDISTANCE=26
SYNGRADIENTSTEP=0.1
TRANSFORMTYPE='s'
PRECISIONTYPE='d'
CCRADIUS=4
Expand All @@ -287,7 +293,7 @@ COLLAPSEOUTPUTTRANSFORMS=1
RANDOMSEED=0

# reading command line arguments
while getopts "d:e:f:h:i:m:j:n:o:p:r:s:t:x:z:" OPT
while getopts "d:e:f:g:h:i:m:j:n:o:p:r:s:t:x:z:" OPT
do
case $OPT in
h) #help
Expand All @@ -305,6 +311,9 @@ while getopts "d:e:f:h:i:m:j:n:o:p:r:s:t:x:z:" OPT
;;
f) # fixed image
FIXEDIMAGES[${#FIXEDIMAGES[@]}]=$OPTARG
;;
g) # SyN gradient step
SYNGRADIENTSTEP=$OPTARG
;;
j) # histogram matching
USEHISTOGRAMMATCHING=$OPTARG
Expand Down Expand Up @@ -523,13 +532,13 @@ if [[ $TRANSFORMTYPE == 'sr' ]] || [[ $TRANSFORMTYPE == 'br' ]];

if [[ $TRANSFORMTYPE == 'b' ]] || [[ $TRANSFORMTYPE == 'br' ]] || [[ $TRANSFORMTYPE == 'bo' ]];
then
SYNSTAGE="--transform BSplineSyN[ 0.1,${SPLINEDISTANCE},0,3 ] \
SYNSTAGE="--transform BSplineSyN[ ${SYNGRADIENTSTEP},${SPLINEDISTANCE},0,3 ] \
$SYNSTAGE"
fi

if [[ $TRANSFORMTYPE == 's' ]] || [[ $TRANSFORMTYPE == 'sr' ]] || [[ $TRANSFORMTYPE == 'so' ]];
then
SYNSTAGE="--transform SyN[ 0.1,3,0 ] \
SYNSTAGE="--transform SyN[ ${SYNGRADIENTSTEP},3,0 ] \
$SYNSTAGE"
fi

Expand Down
17 changes: 13 additions & 4 deletions Scripts/antsRegistrationSyNQuick.sh
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,8 @@ Optional arguments:

-s: spline distance for deformable B-spline SyN transform (default = 26)

-g: gradient step size for SyN and B-spline SyN (default = 0.1)

-x: mask(s) for the fixed image space. Should specify either a single image to be used for
all stages or one should specify a mask image for each "stage" (cf -t option). If
no mask is to be used for a particular stage, the keyword 'NULL' should be used
Expand Down Expand Up @@ -160,6 +162,8 @@ Optional arguments:

-s: spline distance for deformable B-spline SyN transform (default = 26)

-g: gradient step size for SyN and B-spline SyN (default = 0.1)

-x: mask(s) for the fixed image space. Should specify either a single image to be used for
all stages or one should specify a mask image for each "stage" (cf -t option). If
no mask is to be used for a particular stage, the keyword 'NULL' should be used
Expand All @@ -186,7 +190,7 @@ Optional arguments:
--------------------------------------------------------------------------------------
Get the latest ANTs version at:
--------------------------------------------------------------------------------------
https://github.com/stnava/ANTs/
https://github.com/ANTsX/ANTs/

--------------------------------------------------------------------------------------
Read the ANTS documentation at:
Expand Down Expand Up @@ -227,6 +231,7 @@ function reportMappingParameters {
Initial transforms: ${INITIALTRANSFORMS[@]}
Number of threads: $NUMBEROFTHREADS
Spline distance: $SPLINEDISTANCE
SyN gradient step: $SYNGRADIENTSTEP
Transform type: $TRANSFORMTYPE
MI histogram bins: $NUMBEROFBINS
Precision: $PRECISIONTYPE
Expand Down Expand Up @@ -278,6 +283,7 @@ INITIALTRANSFORMS=()
OUTPUTNAME=output
NUMBEROFTHREADS=0
SPLINEDISTANCE=26
SYNGRADIENTSTEP=0.1
TRANSFORMTYPE='s'
PRECISIONTYPE='d'
NUMBEROFBINS=32
Expand All @@ -287,7 +293,7 @@ COLLAPSEOUTPUTTRANSFORMS=1
RANDOMSEED=0

# reading command line arguments
while getopts "d:e:f:h:i:m:j:n:o:p:r:s:t:x:z:" OPT
while getopts "d:e:f:g:h:i:m:j:n:o:p:r:s:t:x:z:" OPT
do
case $OPT in
h) #help
Expand All @@ -305,6 +311,9 @@ while getopts "d:e:f:h:i:m:j:n:o:p:r:s:t:x:z:" OPT
;;
f) # fixed image
FIXEDIMAGES[${#FIXEDIMAGES[@]}]=$OPTARG
;;
g) # SyN gradient step
SYNGRADIENTSTEP=$OPTARG
;;
j) # histogram matching
USEHISTOGRAMMATCHING=$OPTARG
Expand Down Expand Up @@ -523,13 +532,13 @@ if [[ $TRANSFORMTYPE == 'sr' ]] || [[ $TRANSFORMTYPE == 'br' ]];

if [[ $TRANSFORMTYPE == 'b' ]] || [[ $TRANSFORMTYPE == 'br' ]] || [[ $TRANSFORMTYPE == 'bo' ]];
then
SYNSTAGE="--transform BSplineSyN[ 0.1,${SPLINEDISTANCE},0,3 ] \
SYNSTAGE="--transform BSplineSyN[ ${SYNGRADIENTSTEP},${SPLINEDISTANCE},0,3 ] \
$SYNSTAGE"
fi

if [[ $TRANSFORMTYPE == 's' ]] || [[ $TRANSFORMTYPE == 'sr' ]] || [[ $TRANSFORMTYPE == 'so' ]];
then
SYNSTAGE="--transform SyN[ 0.1,3,0 ] \
SYNSTAGE="--transform SyN[ ${SYNGRADIENTSTEP},3,0 ] \
$SYNSTAGE"
fi

Expand Down