new topup config

Author: leonyichencai

src/pipeline.sh

@@ -61,7 +61,7 @@ if [[ $TOPUP -eq 1 ]]; then
     # Merge results and run through topup
     echo Running topup
     fslmerge -t /OUTPUTS/b0_all.nii.gz /OUTPUTS/b0_d_smooth.nii.gz /OUTPUTS/b0_u.nii.gz
-    topup -v --imain=/OUTPUTS/b0_all.nii.gz --datain=/INPUTS/acqparams.txt --config=b02b0.cnf --iout=/OUTPUTS/b0_all_topup.nii.gz --out=/OUTPUTS/topup --subsamp=1,1,1,1,1,1,1,1,1 --miter=10,10,10,10,10,20,20,30,30 --lambda=0.00033,0.000067,0.0000067,0.000001,0.00000033,0.000000033,0.0000000033,0.000000000033,0.00000000000067 --scale=0
+    topup -v --imain=/OUTPUTS/b0_all.nii.gz --datain=/INPUTS/acqparams.txt --config=/extra/synb0.cnf --iout=/OUTPUTS/b0_all_topup.nii.gz --out=/OUTPUTS/topup
 fi
 
 

src/synb0.cnf

@@ -0,0 +1,26 @@
+# Resolution (knot-spacing) of warps in mm
+--warpres=20,16,14,12,10,6,4
+# Subsampling level (a value of 2 indicates that a 2x2x2 neighbourhood is collapsed to 1 voxel)
+--subsamp=2,2,2,2,2,1,1
+# FWHM of gaussian smoothing
+--fwhm=8,6,4,3,3,2,1
+# Maximum number of iterations
+--miter=5,5,5,5,5,15,15
+# Relative weight of regularisation
+--lambda=0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005
+# 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=Levenberg-Marquardt, 1=Scaled Conjugate Gradient
+--minmet=0,0,0,0,0,1,1
+# 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