Hi Ela - It ran fast because it's a relatively small data set (2mm resolution and 25 directions based on the log file). So that's not a problem. No errors in the log file as far as I can see.

I'd recommend using the default settings for both the intra- and inter-subject registration. The new version of TRACULA is using a whole new (and improved) atlas, so even if you use the same registration settings as someone did many versions ago, you're not really replicating what they did (nor would it be desirable to).

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: Tuesday, January 4, 2022 3:40 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Trac-all -prep -c error
 

        External Email - Use Caution        

Dear Anastasia,

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,
Ela
____________________________________________________________________________________________________________________________________________

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