Hello FreeSurfer devs,

 

I am attempting to run a Longitudinal TRACULA analysis on 3 timepoints per subject using an HCP server. I have used the example dmrirc page (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/dmrirc#Example2.3ALongitudinalstudy.2Conediffusionscanpersession) to create a configuration file to be fed into the trac-all command, but I am running into issues with the naming of folders containing each subject and their respective FS timepoints.

 

I have attached my configuration file, as well as a log output from one subject run for reference, but the issues I am running into pertain to the directory names of each subject and the FS timepoint needed for the longitudinal analysis. When I follow the example configuration file, it notes that each subject should be listed for each number of timepoints that are being included (in this case, we have 3 timepoints for each subject, and they are stored as {subjID}_Y{0,2,4}). When running trac-all -prep while the FS directory is called 100_Y0, for example, this error appears: ERROR: cannot find /ifs/loni/faculty/thompson/four_d/bangelo/FS_DTI_longitudinal/100_Y0.long.100_Y0, where the FS_DTI_longitudinal directory contains all the completed FS recon-all runs for each subject and timepoint.

 

However, after changing the FS directory name to match the name it is searching for, I am met with an additional error after mri_convert is called: ERROR: cannot find /ifs/loni/faculty/thompson/four_d/bangelo/FS_DTI_longitudinal/100_Y0

 

I am extremely confused by this, as the configuration file example does not reference having an additional directory for each time point, that isn’t the directory that contains the FS output from that timepoint.

 

Is there a way to force the scripting to only look for 100_Y0, instead of 100_Y0.long.100_Y0? And what is this additional directory it is looking for? I know it is trying to find a folder of the same name that I have set in the baselist, but I am still confused why the baselist folder and the subject folder are different to the script. Any help with sorting this out and any additional information that can be provided about what directories the script is looking for and what they should contain would be extremely helpful.

 

1. FreeSurfer Version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

2. Platform: CentOS version 6 or 7 (I’ve been told both versions when I asked)

3. uname -a: Linux c2002 2.6.32-696.23.1.el6.x86_64 #1 SMP Tue Mar 13 22:44:18 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux

4. Tracula log file is attached

 

Thank you!

 

Sincerely,

Brendan Angelo

 

Brendan Angelo, MS

BRANCH Lab

USC