On 20 Jan 2017, at 23:52, Yendiki, Anastasia <AYENDIKI@mgh.harvard.edu> wrote:

Hi Barbara - If you take out the "set baselist" part, you'll run the cross-sectional TRACULA stream, i.e., analyze each time point independently. So you want to leave that in to use the longitudinal TRACULA stream.

The base template itself (i.e., the median of the T1s of the time-points) may not be used, but the files under the base template's directory are used. Longitudinal TRACULA maps between the base space to the space of each DWI time point, as described in the paper.

Can you please attach the file scripts/trac-all.local-copy? Since there's no official 6.0 version yet but multiple beta versions of it, it's hard to know which one you used.

Thanks,

a.y

---

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bárbara Avelar Pereira [barbara.avelar.pereira@ki.se]
Sent: Friday, January 20, 2017 9:01 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] longitudinal tracula error

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

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