Dear Jesper,
Thanks for your help. I agree on that total readout time (0.043). I run Eddy with that value and it worked for many subjects, but not for all. It's strange because the acquisition parameters were the same. These are the steps I followed to get the field map and correct the images:
1. Transform the phase to T1 space
flirt -in phase -ref wT1_brain_spm.nii.gz -dof 6 -omat phase_to_T1 -applyxfm -usesqform -out phase_to_T1
2. Matrix Inversion
convert_xfm -omat inv_phase_to_T1 -inverse phase_to_T1
3. Transform T1 brain mask to phase space
flirt -in wT1_brain_spm_mask.nii.gz -ref phase.nii -applyxfm -init inv_phase_to_T1 -o wT1_brain_spm_mask_PHASEspace
4. Prepare fieldmap
fsl_prepare_fieldmap SIEMENS phase.nii wT1_brain_spm_mask_PHASEspace field_map_rad_s 2.46
5. Transform rad/s to Hz
fslmaths field_map_rad_s -div 6.2831853072 field_map_Hz
6. Transform the field_map to DWI space
flirt -in field_map_Hz -ref b0_brain.nii.gz -dof 6 -omat field_map_Hz_to_b0_mat -applyxfm -usesqform -out field_map_Hz_to_b0
7. Eddy corrections
eddy_openmp --imain=data.nii --acqp=acqparams_004386.txt --index=index.txt --bvecs=bvecs --bvals=bvals --mask=b0_brain_mask.nii.gz --field=field_map_Hz_to_b0 --repol --cnr_maps --very_verbose --out=myeddy
I uploaded here https://drive.google.com/file/d/1MB5IT5Q-7ae0lOpQxJHL8U_HRCePz0cK/view two examples of "good" and "bad" Eddy performance (as well as the intermediate steps). I would really appreciate if you can take a look at them to find out what I should correct.
Best regards,
Aldana
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