TOPUP-eddy does not work

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!


Hi @Domenico ,

Welcome to Neurostars!

If eddy_openmp went through, it is already a good news! You didn’t get any error and got all the output files you wanted?
How did you determine that the output file is identical to the original? Could you give more details on the output you got? You may want to run eddyQC to get an easy way to assess the output of eddy.

Also, even if you may find several users of FSL on this forum, you may get better luck with the FSL forum where the FSL developers are present and pretty responsive: