Hi,
I have a few very basic clarification questions regarding the recon-all processing pipeline. I am currently following the instructions here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Near the end of the page, it instructs me to rerun the whole process using my new talairach, using the command: recon-all -all -subjid [subjid]
Questions: (1) Since the talairach file is created during recon-all, wouldn't rerunning the whole process overwrite my freshly edited file with whatever it came up with the first time? (2) Assuming the answer to question 1 is 'no', can i rerun the process in steps (-autorecon1, then -autorecons 2 and 3) without overwriting my freshly edited file? (3) Are there any files that are unusual in their likelihood of being overwritten? (e.g. running recon-all -all will overwrite aseg.stats but not talairach.xfm)
Thank you for your help, -Eric