Dear FreeSurfer experts,
I’m running tracula on longitudinal data but I’ve encountered the following error at the “trac-all -prep” stage: ERROR: flag ; unrecognized (see below)
trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T1/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01_T1/scripts/trac-all.cmd ; trac-preproc -c /Documents/TRACULA/TEST/S0001.01_T2/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01_T2/scripts/trac-all.cmd ; trac-preproc -c /Documents/TRACULA/TEST/S0001.01/scripts/dmrirc.local -log /Documents/TRACULA/TEST/S0001.01/scripts/trac-all.log -cmd /Documents/TRACULA/TEST/S0001.01/scripts/trac-all.cmd ; ERROR: flag ; unrecognized
As an example, I defined the parameters in my dmrirc file as: set subjlist = ( S0001.01_T1 \ S0001.01_T2 \ S0004.00_T1 \ S0004.00_T2 )
set baselist = ( S0001.01 \ S0001.01 \ S0004.00 \ S0004.00 )
set dcmlist = ( S0001.01_T1/DTI.nii \ S0001.01_T2/DTI.nii \ S0004.00_T1/DTI.nii \ S0004.00_T2/DTI.nii )
From the mailing list, it seems a similar issue has been fixed in previous updates but I have tried both version 5.3 and 6.0 and still get this error...
My tracula directory contains 3 directories per participant: 2 with the *.long.* output for timepoint 1 and 2, and a directory with the base. Including the base gives the error above, but if I take it out, it asks for it: ERROR: cannot find /Documents/TRACULA/TEST/S0001.01
From what I understand, the base is not necessary to run any analysis, but it has to be there anyhow (?): https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg45332.html Maybe I am understanding this incorrectly?
Since the base is used to create the longitudinal output (*long*), including the aparc+aseg.mgz file, and those are then used in tracula, I thought I could run things without it. I decided to take out the “set baselist” part from the configuration file — this way it seems to run fine (so far). But I assume it’s there for a reason so I’m not sure this is a solution at all...
Any help would be much appreciated!
Details: 1) freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) platform: CentOS release 6.8 (Final) 3) Operating system details (kernel name, release, version, etc.): Linux 2.6.32-642.11.1.el6.x86_64 #1 SMP Fri Nov 18 19:25:05 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux