I tried running eddy in the latest FSL version with this command line:
eddy --imain=allRawData.nii.gz --mask=nodif_brain_mask.nii --acqp=my_acq_param_allData.txt --index=allData_index.txt --bvecs=bvecs_allData --bvals=bvals_allData --topup=my_topup_results --out=eddy_wTopup_out
and got this error message.
terminate called after throwing an instance of 'NEWMAT::IndexException'
Abort
I was able to use all these same files to run eddy and then applytopup consecutively. So, I think the files are fine.
The results from performing the corrections in two steps look quite good.
Am I doing something wrong in the first command I used?
Thanks, Stefano Marenco
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