Hello,
I am working through fieldmap correction pipelines using topup and applytopup. When I run the topup command, the resulting fieldcoef file I get has a different voxel size and number than the b0 files I entered. I used the default b02b0.cnf config file. Can someone explain why this happened and how to fix it? I'm assuming the fieldcoef file I feed into applytopup should have the same voxel size and number as the EPI volumes I would like to correct.
Thank you in advance for any recommendations.
Dr. Helen Weng
University of California, San Francisco
Topup command:
topup --imain=both_b0_z60 --datain=my_acq_param.txt --config=b02b0.cnf --out=topup_rpi
both_b0_z60 data structure:
Data Axes Orientation:
first (x) = Right-to-Left
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient RPI]
R-to-L extent: -111.925 [R] -to- 105.684 [L] -step- 2.391 mm [ 92 voxels]
A-to-P extent: -107.918 [A] -to- 109.691 [P] -step- 2.391 mm [ 92 voxels]
I-to-S extent: -67.549 [I] -to- 73.538 [S] -step- 2.391 mm [ 60 voxels]
output file topup_rpi data structure:
Data Axes Orientation:
first (x) = Left-to-Right
second (y) = Posterior-to-Anterior
third (z) = Inferior-to-Superior [-orient LPI]
R-to-L extent: -140.000 [R] -to- -92.000 [R] -step- 1.000 mm [ 49 voxels]
A-to-P extent: -140.000 [A] -to- -92.000 [A] -step- 1.000 mm [ 49 voxels]
I-to-S extent: 60.000 [S] -to- 92.000 [S] -step- 1.000 mm [ 33 voxels]
b02b0.cnf config file:
# 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
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