Hi Joelle - See my previous email, you should download the 6.0 version. In this version TRACULA will attempt to detect which tracts require reinitialization, so hopefully you'll see an improvement in this.
a.y
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Joëlle Ismay Rosanne Van Der Molen [Joelle.Vandermolen@etu.unige.ch] Sent: Thursday, May 04, 2017 8:20 AM To: Freesurfer support list Subject: [Freesurfer] TRACULA tracts corrections
Hi Anastasia & Freesurfer experts,
I've been going through the different processing steps of the longitudinal TRACULA stream and as some tracts needed to be rerun, I set up my dmrirc file as recommended (subjlist limited to the subject to correct; pathlist limited to the path(s) to rerun; npcts corresponding to the tract to rerun; set reinit = 1) and then ran this file with the -prior flag, followed by the -path flag.
However, surprisingly, it looks as if all the tracts are being reconstructed again, not only the one that is specified under pathlist... At least, that is the impression I get when looking at the new merged_avg33_mni_bbr.mgz file, and at the trac-all.log file.
This brings me to my 2 questions:
1) Is there a way to check that TRACULA reinitializes and reconstructs only the desired tracts?
2) If indeed all tracts were reinitialized and rerun, how can I fix that? I suspect I'm then doing something wrong in the configuration of the dmrirc file, but I cannot seem to find out what.
I added the dmrirc file and the trac-all.log file; I would greatly appreciate it if you could help me out.
Additional info: freesurfer version is 6.0, operating system is OS X Yosemite 10.10.5. Let me know if you need any other information or files.
Best,
Joëlle