hi all,
i noticed this bug in the recon-all script. according to the reconAllDevTable, if recon-all is called with just the -normalization2 flag it should call both mri_normalize and mri_mask. however, in looking at the script it seems to only call mri_normalize. so, if using that flag you should be aware that it will not call both processes and brain.finalsurfs.mgz will not be produced.
this issue came up as i was working on parallelizing; but it was pointed out to me that this info would be useful to others as well, so i'm starting a new thread.
the solution i used was to change the recon-all script so that it calls both processes with that flag...or you could just explicitly call mri_mask on the commandline after you've run recon-all with the -normalization2 flag.
sarah