Hi Anastasia,

Looking through the trac-preproc and trac-paths scripts, it is now clear to me that all the time points for a given subject have to be contained/specified within the same dmrirc configuration file in order to implement a longitudinal TRACULA analysis. So, I've answered my previous question in that regard.

The challenge in our case is that we have separately pre-processed the dMRI data for each subject and time point, removing bad frames/volumes (using the DTIPrep QA tool). Thus, the bvecs/bvals are not identical for all the time points of a given subject. We can specify the bvec file for each subject/time point using the bveclist configuration parameter. But there is no analog available for bvals, since only a single bvalfile can be specified.

I see that this issue has been raised in a couple other posts relatively recently (2015):

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg41737.html

https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40007.html

but no working solution was provided at that time.

I’m wondering if there is perhaps now a development version of TRACULA that supports a “bvallist” capability? If not, it doesn’t look like it would be too difficult to modify trac-all to include that capability (modeling after what is already in trac-all for the bveclist/bvecfile stuff). But, in that case, it isn’t immediately clear to me if there are other downstream “gotchas” in the preproc, paths, or stats stage specific scripts/binaries that would need modifications as well. [I don’t see anything in the sections related to the BASE-specific processing in trac-preproc involving bvals/bvecs, so think we are fine there. But it is harder for me to tell what is going on in trac-paths].

thanks,

-MH

Michael Harms, Ph.D.

-----------------------------------------------------------

Conte Center for the Neuroscience of Mental Disorders

Washington University School of Medicine

Department of Psychiatry, Box 8134

660 South Euclid Ave. Tel: 314-747-6173

St. Louis, MO 63110 Email: mharms@wustl.edu

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Harms, Michael" <mharms@wustl.edu>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, June 29, 2016 at 5:00 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] longitudinal tracula

Hi,

When running TRACULA with longitudinal data, is it necessary for all scan waves of a given subject to be included in a single dmrirc file? My initial thought was “no”, that it would be fine to run one scan wave per subject per dmrirc file (as long as the “baselist” variable is set appropriately for each scan wave and subject).

But looking at the ‘trac-all’ script, I see

if ($#baselist == 0) then#--->>> A single time point for each subject

…

else#--->>> Multiple time points for each subject

…

So, I’m wondering why different sections in the code would be necessary if in fact it is ok to process a single scan wave per dmrirc file.