Hi all,
I’m trying to use topup and eddy on a multi shell sequence with many bvals (from 10 to 3000).
I run the following commands:
topup -v --imain=b0APPA --datain=acqp --out=*name*_topup --iout=*name*_topup --warpres=3 --config=b02b0.cnf
where b0APPA is the file composed by the merging of b0 AP and PA volumes and where acqp is:
0 -1 0 0.01
0 1 0 0.01
and name is the base name of the file to be read and to be produced.
Then I use:
eddy_openmp -v --imain=*name* --mask=*name*_deskulled_mask --index=index --acqp=acqp --topup=*name*_topup --bvecs= *name*.bvec --bvals=*name*.bval --data_is_shelled=true -v --out=*name*_eddy
where index is a file composed by N one values (N=number of volumes).
The processing works but in the output file I don’t see any deformation correction, i.e. is identical to the original.
Which could be the problem?
Thank you!
Domenico