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