Dear Experts,
I have successfully managed to use topup followed by applytopup on my diffusion-weighted images. I have 61 images acquired in one phase-encoding direction and 61 images acquired in the opposite phase encoding direction (the first 6 of each are B0). However, I am now attempting to use eddy after topup, rather than applytopup (am I correct in thinking that I will not/should not then need to use applytopup after this?) and am running into problems.
Currently the two acquisitions are in separate datafiles, but I could of course merge them into one file with 122 images. My acqparams.txt file has two rows:
0 1 0 1
0 -1 0 1
and this works well in applytopup, where I use the following command:
applytopup --imain=DTI1.nii.gz,DTI2.nii.gz --datain=acqparams.txt --inindex=1,2 --topup=topup_results --out=corrected_DTI
When I similarly put in both acquisitions, separated by a comma, into the --imain of eddy, using the same acqparams.txt but now using an index.txt file which has 61 *1's and 61*2's I get the following error:
Image Exception : #22 :: ERROR: Could not open image DTI1.nii.gz,DTI2
libc++abi.dylib: terminate called throwing an exception
Abort trap: 6
I assume then that eddy does not like me to input both acquisitions. I then tried merging the two acquisitions in time, such that I now have one file with 122 images. My acqparams.txt remains as above and my index.txt file again has 61 *1's followed by 61*2's. I also merged my two bvecs and bvals files such that each row now has 122 values. I get the following error:
eddy: msg=AcqPara::AcqPara: Unrealistic read-out time
libc++abi.dylib: terminate called throwing an exception
Abort trap: 6
I also get the same error if I try to eddy correct just the first acquisition, where the index.txt file includes only 61* 1's.
Does anyone know what I might be doing wrong?
Many thanks,
Antoinette
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