Honestly, this was just based on our instructor's suggestion, who used to work with you a few years back, so I just trusted his hunch. I will ask him to clarify why he prefers this method of registration over bbregisteration. Considering the hint you gave me in previous message, I changed the configuration file. I am attaching it here. With this configuration file, the trac-all -prep -c ran without any errors. However, it was all done in 40 minutes which keep me thinking if there is something wrong with it. (I set usethalnuc = 0 for now, but I plan to change it to 1 after I have done the thalamic sub segmentation step).

Can I ask you to check if my configuration file is correct? And if the attached trac-all.log file looks good (not alarming)?

Thank you for your time and constant help,

____________________________________________________________________________________________________________________________________________

From: Yendiki, Anastasia
Sent: Monday, January 3, 2022
To: elaheh.salardini@yale.edu
Subject: Trac-all -prep -c error

Hi Ela - Is there a specific reason why you are not using the default method 
for dMRI-to-T1 registration (bbregister, a.k.a. boundary-based registration in 
the config file)?

Anastasia.

From: Salar Dini, Elaheh
Sent: Monday, January 3, 2022 9:09 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Trac-all -prep -c error

Dear Freesurfer developers and Anastasia,

Happy new year. I am trying to run trac-all -pep -c dmriEla. dmriEla is my config file which is also attached to this message. I am also attaching the trac-all.log file to this email. I am getting the following error:

Segmentation fault (core dumped)

When I check the /home1/es2263/freesurfer_7.2.0/trctrain/hcp/mgh_1024/mni folder, there is a file named acomm.bbr.prep.trk, but no file with the name acomm.flt.prep.trk. I uninstall and reinstalled freesurfer 7.2.0, considering there might be a problem in installation and some files might be missed, but I still face the same error.

I'm running freesurfer on Linux Centos7, the version of freesurfer is 7.2.0 and the installed package is freesurfer-linux-centos7_x86_64-7.2.0.tar.gz. The installed fsl version is 6.0.5.1 .

Thank you for your help and best wishes in 2022,

Ela