Dear Martin,
> I'm trying to use topup for phase distortion correction of the EPI scans
> from the Human Connectome Project. However, for some reason topup gives
> a segmentation fault. Here is what I tried:
>
> 1) Combine LR and RL field map files
>
> fslmerge -t 100307_3T_SpinEchoFieldMap_LRRL.nii.gz \
> 100307_3T_SpinEchoFieldMap_LR.nii.gz \
> 100307_3T_SpinEchoFieldMap_RL.nii.gz
topup takes (differently distorted) EPI images as input. Not field maps.
>
> this results in 100307_3T_SpinEchoFieldMap_LRRL.nii.gz with a total of 6
> volumes. The first three have L->R phase encoding, the last three R->L.
>
> 2) Run topup:
>
> topup --imain=100307_3T_SpinEchoFieldMap_LRRL.nii \ --datain=topup_lrrl.txt
You need to use a configuration file for running topup. There should be a file b02b0.cnf with the FSL distribution.
Hence, swap your field maps for regular b=0 EPI images, and add --config=b02b0.cnf to the command line.
Good luck Jesper
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