Dear all,
Thank you very much for sharing such useful processing tools, it is of a great help!
However, I am having trouble running topup on an axial diffusion dataset although I think I respected all necessary input parameters. My gut feeling is that the large gap (20mm) between the 3 axial slices making up the dataset is causing trouble to the script. However topup should be able to correct EPI readout-related distortions on such a dataset, either slice-by-slice or interpolating in-between slices.
I am ready to share the data, I think it might be the easiest and most efficient way of fixing this issue, as the error message is not very specific.
Here is the command line used:
topup --imain=dwi_rl_lr.nii.gz --datain=acqparams.txt --out=topup_results --fout=field_estimate --iout=dwi_topup_corrected
And here is the output:
Segmentation fault: 11
Many thanks for your help.
Best regards,
Simon Levy
|