Hi Ela - The example config file that you used is from the old version, not the new version. That's why the old version doesn't give you an error and the new one does. Take the example config file from the new version (in $FREESURFER_HOME/bin/), then adapt it accordingly for your data.

This wiki page explains which example file to use, depending on your study design: https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc

And the TRACULA tutorial on the wiki is also updated for the new version.

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 12:41 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] trac-all -prep -c error

External Email - Use Caution

Hi all,

I am trying to run trac-all -prep -c dmrirc1.txt, with dmrirc1.txt being the configuration file. As soon as I attempt, I get the following 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 am attaching the dmrirc1.txt to this message.

The FreeSurfer segmentations of T1, produced by running Freesurfer recon-all, was done using freesurfer version 6. We try to run trac-all using freesurfer version 7.2.0.

Interestingly, we don’t face the same error when we tried running trac-all using version 6 of freesurfer.

Lastly, it is worth mentioning that no dmri folder has been made after running trac-all, and there is no trac-all log file in the script folder.

1) FreeSurfer version: freesurfer-CentOS7-7.2.0-1.x86_64.rpm. (Build-stamp text: freesurfer-linux-centos7_x86_64-7.2.0-20210720-aa8f76b)

2) Platform: CentOS7

Thank you and Kind regards,

Ela Salardini