I am trying something a little unorthodox. I am attempting to use topup and applytopup to correct distortions in T1 structural images. For that, I have a pair of images, scanned in sequence. But they have opposite readout directions.
topup runs smoothly and produces a fieldcoef file that I can look at with fslview. However, when running applytopup I receive these error messages:
libc++abi.dylib: terminate called throwing an exception
Abort trap: 6
The sequence of commands that I used are:
topup --imain=LR_RL.nii.gz --datain=acqparams.txt --config=topup_b02b0.cnf --out=topup.LR_RL -v
applytopup --imain=struct.LR.nii.gz,struct.RL.nii.gz --inindex=1,2 --datain=acqparams.txt --topup=topup.LR_RL --out=struct.applytopup --method=jac
Using the following input:
struct.LR – Structural image with one readout direction.
struct.RL – Structural image with the opposite readout direction.
LR_RL – 4D volume. struct.RL appended after struct.LR, in time.
acqparams.txt – 0 -1 0 1 <newline> 0 1 0 1
topup_b02b0.cnf – A custom config file that is normally used for diffusion weighted data.
Your command above looks kosher so I would need to have a closer look to figure out what is going on.
Can you please upload all the data referred to on your applytopup command line (so that I can run the exact same command here) using the following link
? And please send me an email with the name of the tarball when the data is uploaded.
Also, I don't think Karla is reading the FSL mail base so can you please CC her on mails regarding these issues?
Jesper
Am I suffering from a simple syntactic error, or something more problematic? Note that the labels LR and RL do not refer to the readout directions.
Kind regards,
Jackson Smith