First of all, thank you for the wonderful codes, it really helps the research community when dealing with old, large-scale databases without reverse phase-encoding or good quality T2 images.
I have a similar issue with Topup failed following the generation of undistorted b0 through the synb0 docker #11 , where my b0_all_images are stretched along the anterior-posterior direction, starting from the plane of cerebellum, and continue till the bottom few slices. This carries over to FSL eddy current correction, producing very elongated slices of image at the inferior part of the brain. I wonder if anything went wrong before running topup (which I ran it outside of Docker in terminal, but following the topup settings as used in the script), but results seemed to look normal.
b0 all distorted (original)
b0 all undistorted
b0 raw
b0 all topup distorted
b0 all topup undistorted
My acqparams.txt looks like this:
0 1 0 0.07
0 1 0 0.000000
Hello,
First of all, thank you for the wonderful codes, it really helps the research community when dealing with old, large-scale databases without reverse phase-encoding or good quality T2 images.
I have a similar issue with Topup failed following the generation of undistorted b0 through the synb0 docker #11 , where my b0_all_images are stretched along the anterior-posterior direction, starting from the plane of cerebellum, and continue till the bottom few slices. This carries over to FSL eddy current correction, producing very elongated slices of image at the inferior part of the brain. I wonder if anything went wrong before running topup (which I ran it outside of Docker in terminal, but following the topup settings as used in the script), but results seemed to look normal.
My acqparams.txt looks like this: 0 1 0 0.07 0 1 0 0.000000
topup command: topup --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
Any ideas what caused the issue? Thank you in advance!
Best regards, Vincent