Merge pull request #116 from oesteban/enh/prepare-topup

MAINT: Add FLIRT config files to prepare for TOPUP integration

Author: oesteban

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

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

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

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

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

setup.cfg

@@ -68,6 +68,7 @@ sdcflows =
     data/*.json
     data/*.nii.gz
     data/*.mat
+    data/flirtsch/*.cnf
     VERSION
 
 [options.entry_points]