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Hello FSL Community,
I am currently trying to process some multishell diffusion data using topup and eddy, however, when I try to run eddy, I receive the following error:
eddy: msg=--bvecs should contain a 3xN or Nx3 matrix where N is the number of volumes in --imain
eddy: msg=Error when attempting to read --bvecs file
libc++abi.dylib: terminating with uncaught exception of type EDDY::EddyException: eddy: msg=Error when attempting to read --bvecs file
Abort trap: 6
In case it is needed, here is what I did leading up to eddy:
1. Extracted 4 B0s from my first 4 diffusion scans and created my acqparam.txt file to match
2. Ran the following command: topup --imain=allb0_1432.nii.gz --datain=parameters.txt --config=b02b0.cnf --out=my_topup_results --fout=my_field --iout=my_unwarped_images
This seemed to have worked well after visual inspection.
3. Created a mask using: fslmaths my_unwarped_images.nii.gz -Tmean my_unwarped_images.nii.gz THEN bet my_unwarped_images.nii.gz my_unwarped_images_brain -m
4. Combined my 6 diffusion runs (in the order they were collected) using fslmerge
5. Created concatenated bvec and bval text files (attached)
6. Ran eddy using the following command:
eddy --imain=full_dwi_pilotd.nii.gz --mask=my_unwarped_images_brain_mask.nii.gz --acqp=parameters.txt --index=index.txt --bvecs=bvec.txt --bvals=bval.txt --topup=my_topup_results_fieldcoef.nii.gz --out=eddy_corrected_data
Thank you for your help!
Cristina
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