Hi all,
Hit a snag with this error when trying to execute eddy_openmp. I've previously gone through this pipeline on another project's dataset without error, so I'm wondering if there's something different with the images going on (this is for the record using UK Biobank DTI data).
So far:
I've got DTI data of 50 directions (b1000) accompanied by 5 b0s (the raw data is multishell which I've stripped down to a single shell version). I've also got some reverse blip b0s.
I ran topup on a pair of b0s (the first from each respective set) -
topup
--imain=P01_topup_input.nii.gz
--datain=topup_acq_pars.txt
--config=b02b0.cnf
--out=my_topup_results
--iout=unwarped_images.
(written on multiple lines here for ease of reading - executed as a single line)
topup appeared to complete successfully. I created a binary brain mask from skull stripping the mean of the "unwarped" images. I can open the main output image ("my_topup_results_fieldcoef.nii.gz") in fsleyes and it looks sensible with areas of high signal around the ear canals / sinuses (as per the example images in the FSL guide). The accompanying movepar text file reads the following:
0 0 0 0 0 0
0.07034051596 0 -0.2176524195 2.252529773e-05 0.002028570614 0.0006216554997
I've then tried to feed this data into the main eddy call, which otherwise refers to the main 4D DTI set (5 b0s, none of the reverse blip stuff) and the accompanying bval and bvec files. The index file is the number 1 repeated 55 times with spaces inbetween, matching the number of volumes in the DTI set -
eddy_openmp
--imain=P01_mainvol_singleshell.nii.gz
--mask=P01_DTI_mask_mask.nii.gz
--acqp=topup_acq_pars.txt
--index=eddy_pars.txt
--bvecs=P01_mainvol_singleshell.bvec
--bvals=P01_mainvol_singleshell.bval
--topup=my_topup_results_fieldcoef.nii.gz
--out=test
And it hits this error pretty much immediately:
eddy: msg=Error when attempting to read --topup files
terminate called after throwing an instance of 'EDDY::EddyException'
what(): eddy: msg=Error when attempting to read --topup files
Aborted (core dumped)
Any help would be greatly appreciated.
Many thanks in advance,
Iain
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