Hi Greg,
Nick programmed all the makefile stuff, so we'll have to wait until his
return next week to get this resolved. Can you use the traditional flags?
doug
Greg Harris wrote:
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
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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Phone Number: 617-724-2358
Fax: 617-726-7422
In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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