From 0df9ff1e972014e41ce71601b0912aa81c1b0a0e Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Sun, 1 Nov 2020 15:11:41 +0100 Subject: [PATCH] MAINT: Add FLIRT config files to prepare for TOPUP integration --- sdcflows/data/flirtsch/b02b0.cnf | 26 ++++++++++++++++++++++++++ sdcflows/data/flirtsch/b02b0_1.cnf | 26 ++++++++++++++++++++++++++ sdcflows/data/flirtsch/b02b0_2.cnf | 26 ++++++++++++++++++++++++++ sdcflows/data/flirtsch/b02b0_4.cnf | 26 ++++++++++++++++++++++++++ sdcflows/data/flirtsch/b02b0_quick.cnf | 26 ++++++++++++++++++++++++++ setup.cfg | 1 + 6 files changed, 131 insertions(+) create mode 100644 sdcflows/data/flirtsch/b02b0.cnf create mode 100644 sdcflows/data/flirtsch/b02b0_1.cnf create mode 100644 sdcflows/data/flirtsch/b02b0_2.cnf create mode 100644 sdcflows/data/flirtsch/b02b0_4.cnf create mode 100644 sdcflows/data/flirtsch/b02b0_quick.cnf diff --git a/sdcflows/data/flirtsch/b02b0.cnf b/sdcflows/data/flirtsch/b02b0.cnf new file mode 100644 index 0000000000..77c4cd5901 --- /dev/null +++ b/sdcflows/data/flirtsch/b02b0.cnf @@ -0,0 +1,26 @@ +# Resolution (knot-spacing) of warps in mm +--warpres=20,16,14,12,10,6,4,4,4 +# Subsampling level (a value of 2 indicates that a 2x2x2 neighbourhood is collapsed to 1 voxel) +--subsamp=2,2,2,2,2,1,1,1,1 +# FWHM of gaussian smoothing +--fwhm=8,6,4,3,3,2,1,0,0 +# Maximum number of iterations +--miter=5,5,5,5,5,10,10,20,20 +# Relative weight of regularisation +--lambda=0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001 +# If set to 1 lambda is multiplied by the current average squared difference +--ssqlambda=1 +# Regularisation model +--regmod=bending_energy +# If set to 1 movements are estimated along with the field +--estmov=1,1,1,1,1,0,0,0,0 +# 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient +--minmet=0,0,0,0,0,1,1,1,1 +# Quadratic or cubic splines +--splineorder=3 +# Precision for calculation and storage of Hessian +--numprec=double +# Linear or spline interpolation +--interp=spline +# If set to 1 the images are individually scaled to a common mean intensity +--scale=1 \ No newline at end of file diff --git a/sdcflows/data/flirtsch/b02b0_1.cnf b/sdcflows/data/flirtsch/b02b0_1.cnf new file mode 100644 index 0000000000..07924b4157 --- /dev/null +++ b/sdcflows/data/flirtsch/b02b0_1.cnf @@ -0,0 +1,26 @@ +# Resolution (knot-spacing) of warps in mm +--warpres=20,16,14,12,10,6,4,4,4 +# Subsampling level (a value of 2 indicates that a 2x2x2 neighbourhood is collapsed to 1 voxel) +--subsamp=1,1,1,1,1,1,1,1,1 +# FWHM of gaussian smoothing +--fwhm=8,6,4,3,3,2,1,0,0 +# Maximum number of iterations +--miter=5,5,5,5,5,10,10,20,20 +# Relative weight of regularisation +--lambda=0.0005,0.0001,0.00001,0.0000015,0.0000005,0.0000005,0.00000005,0.0000000005,0.00000000001 +# If set to 1 lambda is multiplied by the current average squared difference +--ssqlambda=1 +# Regularisation model +--regmod=bending_energy +# If set to 1 movements are estimated along with the field +--estmov=1,1,1,1,1,0,0,0,0 +# 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient +--minmet=0,0,0,0,0,1,1,1,1 +# Quadratic or cubic splines +--splineorder=3 +# Precision for calculation and storage of Hessian +--numprec=double +# Linear or spline interpolation +--interp=spline +# If set to 1 the images are individually scaled to a common mean intensity +--scale=1 \ No newline at end of file diff --git a/sdcflows/data/flirtsch/b02b0_2.cnf b/sdcflows/data/flirtsch/b02b0_2.cnf new file mode 100644 index 0000000000..77c4cd5901 --- /dev/null +++ b/sdcflows/data/flirtsch/b02b0_2.cnf @@ -0,0 +1,26 @@ +# Resolution (knot-spacing) of warps in mm +--warpres=20,16,14,12,10,6,4,4,4 +# Subsampling level (a value of 2 indicates that a 2x2x2 neighbourhood is collapsed to 1 voxel) +--subsamp=2,2,2,2,2,1,1,1,1 +# FWHM of gaussian smoothing +--fwhm=8,6,4,3,3,2,1,0,0 +# Maximum number of iterations +--miter=5,5,5,5,5,10,10,20,20 +# Relative weight of regularisation +--lambda=0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001 +# If set to 1 lambda is multiplied by the current average squared difference +--ssqlambda=1 +# Regularisation model +--regmod=bending_energy +# If set to 1 movements are estimated along with the field +--estmov=1,1,1,1,1,0,0,0,0 +# 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient +--minmet=0,0,0,0,0,1,1,1,1 +# Quadratic or cubic splines +--splineorder=3 +# Precision for calculation and storage of Hessian +--numprec=double +# Linear or spline interpolation +--interp=spline +# If set to 1 the images are individually scaled to a common mean intensity +--scale=1 \ No newline at end of file diff --git a/sdcflows/data/flirtsch/b02b0_4.cnf b/sdcflows/data/flirtsch/b02b0_4.cnf new file mode 100644 index 0000000000..4e6f426676 --- /dev/null +++ b/sdcflows/data/flirtsch/b02b0_4.cnf @@ -0,0 +1,26 @@ +# Resolution (knot-spacing) of warps in mm +--warpres=20,16,14,12,10,6,4,4,4 +# Subsampling level (a value of 2 indicates that a 2x2x2 neighbourhood is collapsed to 1 voxel) +--subsamp=4,4,2,2,2,1,1,1,1 +# FWHM of gaussian smoothing +--fwhm=8,6,4,3,3,2,1,0,0 +# Maximum number of iterations +--miter=5,5,5,5,5,10,10,20,20 +# Relative weight of regularisation +--lambda=0.035,0.006,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001 +# If set to 1 lambda is multiplied by the current average squared difference +--ssqlambda=1 +# Regularisation model +--regmod=bending_energy +# If set to 1 movements are estimated along with the field +--estmov=1,1,1,1,1,0,0,0,0 +# 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient +--minmet=0,0,0,0,0,1,1,1,1 +# Quadratic or cubic splines +--splineorder=3 +# Precision for calculation and storage of Hessian +--numprec=double +# Linear or spline interpolation +--interp=spline +# If set to 1 the images are individually scaled to a common mean intensity +--scale=1 \ No newline at end of file diff --git a/sdcflows/data/flirtsch/b02b0_quick.cnf b/sdcflows/data/flirtsch/b02b0_quick.cnf new file mode 100644 index 0000000000..5eef46f811 --- /dev/null +++ b/sdcflows/data/flirtsch/b02b0_quick.cnf @@ -0,0 +1,26 @@ +# Resolution (knot-spacing) of warps in mm +--warpres=20,14,10 +# Subsampling level (a value of 2 indicates that a 2x2x2 neighbourhood is collapsed to 1 voxel) +--subsamp=2,2,2 +# FWHM of gaussian smoothing +--fwhm=8,2,1 +# Maximum number of iterations +--miter=5,5,5 +# Relative weight of regularisation +--lambda=0.005,0.000005,0.0000005 +# If set to 1 lambda is multiplied by the current average squared difference +--ssqlambda=1 +# Regularisation model +--regmod=bending_energy +# If set to 1 movements are estimated along with the field +--estmov=0,0,0 +# 0=Levenberg-Marquardt, 1=Scaled Conjugate Gradient +--minmet=0,0,1 +# Quadratic or cubic splines +--splineorder=3 +# Precision for calculation and storage of Hessian +--numprec=double +# Linear or spline interpolation +--interp=spline +# If set to 1 the images are individually scaled to a common mean intensity +--scale=1 \ No newline at end of file diff --git a/setup.cfg b/setup.cfg index 0d00445227..f7ea5a792e 100644 --- a/setup.cfg +++ b/setup.cfg @@ -68,6 +68,7 @@ sdcflows = data/*.json data/*.nii.gz data/*.mat + data/flirtsch/*.cnf VERSION [options.entry_points]