Hi Ela - From the log file it looks like it fails when it tries to do the eddy-current correction, because it can't find this file:

/pet/apps/fsl6.0/fslpython/envs/fslpython/lib/python3.7/site-packages/mkl/../../../libmkl_core.so

I'd check with your sysadmin to see if FSL was installed properly and if it needs to be updated.

Hope this helps,
Anastasia.
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Salar Dini, Elaheh <elaheh.salardini@yale.edu>
Sent: Friday, December 3, 2021 5:56 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] follow-up on trac-all -prep -c error
 

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Sorry, I just realized that I sent a wrong trac-all.log and trac-all.error file. 

From: Salar Dini, Elaheh
Sent: Friday, December 3, 2021 5:11 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: follow-up on trac-all -prep -c error
 
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