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Hello Anastasia, Thank you so much for your response. It was very useful. I have changed the config file to the one I'm attaching to this message, but I'm still getting the same error:
ERROR: for B0 distortion correction with reverse-polarity DWIs ERROR: or for model-based eddy-current distortion correction, ERROR: must specify PE direction
I don't get any log for error file in this instance too. However, if I change the doeddy from default=2 to 1, it starts to work with an error later on. I'm attaching the log file, and error file for tra-all with doeddy=1 to this message too. Lastly, I wanted to ask if the fact that we ran recon-all with freesurfer version 6 and do the TRACULA with version 7.2.0 is problematic here? In other words, should the segmentation of T1 be done by same version of freesurfer as the one that trac-all is used from?
Thanks again very much for your help. Ela