Dear FreeSurfers,
I am trying to be a user of 'recon-all -make all'. The method stops when it attempts the step 'recon-all -s $(subj) -hemi lh -finalsurfs'. The problem at that point is that the file mri/brain.finalsurfs.mgz does not exist. The command to create this file, the only possible command if we go through rec on-all, is 'recon-all -s $(subj) -maskbfs'. Doing this command by hand after the error permits a repeated 'recon-all -make all' command to continue happily. One plausible place to fix this is in bin/recon-all.makefile, at or about line 83-84:
$(BRAIN): $(BRAINMASK) $(NORM) recon-all -s $(subj) -normalization2 recon-all -s $(subj) -maskbfs
i.e. add the step for making the brain masked brain.finalsurfs.mgz file after the -normalization2 step. Would this be correct, and should I do this or something like it?
Sincerely, Greg