Re: [Freesurfer] running longitudinal TRACULA on a subset of already processed baseline DTI scans?

Hi Fred - The longitudinal stream processes the diffusion data from all time points jointly, which, for most of the processing steps, will not be the same as processing each time point independently. It also uses the aparc+aseg from the longitudinal recon-all stream, which will not be the same as the one from the cross-sectional recon-all stream, either. If you want to overwrite the output of the cross-sectional TRACULA stream with that of the longitudinal, you can rename the TRACULA subject directories, e.g, from $subj1time1/ to $subj1time1.long.$subj1base/ (so that they match the names of the corresponding longitudinal recon-all subject directories). Set your config file following the example in $FREESURFER_HOME/bin/dmrirc.long.example. Then you can try skipping some of the steps by running "trac-all -prep -nocorr -noqa" and then "trac-all -path".

Hope this helps!

a.y

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fred Sampedro fredsampedro@gmail.com Sent: Monday, December 18, 2017 5:51:42 AM To: Freesurfer support list Subject: [Freesurfer] running longitudinal TRACULA on a subset of already processed baseline DTI scans?

Dear TRACULA users,

I ran near 100 subjects through the standard (cross-sectional) TRACULA pipeline. Some of them (about 70) have also a longitudinal DTI scan 1-year after the already processed scans. I would like to run longitudinal TRACULA to obtain for those 70 subjects longitudinal changes in FA/MD in the major white matter tracts.

My question is: should I specify in the longitudinal dmrirc file that the 80 baseline subjects have already been processed? Will tracula already know it and not re-compute? Could you please provide a fully-working sample dmrirc file for this scenario so I could see the format?

I’ve found this pdf https://ftp.nmr.mgh.harvard.edu/pub/docs/TraculaNov2013/tracula.workshop.v.p... only but didn’t manage to solve my questions.

Thanks a lot in advance,

Fred Sampedro, PhD

Hospital de Sant Pau (Barcelona)