Hi Eric,

the talairach.xfm will not be overwritten. When run recon-all the first time, it creates two files: talairach.auto.xfm and talairach.xfm, which have the same contents. When you edit the registration, it changes the talairach.xfm. When recon-all is run again, it sees that the talairach.auto.xfm is different than talairach.xfm and does not change the talairach.xfm. It will behave this way for all invokations of recon-all (unless you use the "clean" options). This same principle is applied to all other manual interventions (ie, it should detect that the automatic is different than the manual and not overwrite the manual).

doug

On 10/3/12 10:58 PM, Eric Cunningham wrote:

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer