Greg, Yes, your suggested fix to recon-all.makefile for the brain.mgz target is correct, and the fix will appear in the next stable release.
Note that the recon-all makefile feature has a big shortcoming that has kept me from announcing its usage publicly, and that is that it doesn't account for manually created control points or manually specified seed points (the macros CP, SEED_PONS, SEED_CC, SEED_LH and SEED_RH in the recon-all.makefile). If someone were to create control points (for instance to fix a white-matter problem), then 'recon-all -make all' will not detect this. I haven't figured-out a clever (non-hacky) way to account for these, since the default stream is not dependent on control or seed points. Nick On Wed, 2007-08-29 at 12:45 -0500, Greg Harris wrote: > Hi, Doug, > > Thank you; I guess we'll wait a week. > > Greg > > > On 8/29/07 12:38 PM, "Doug Greve" <[EMAIL PROTECTED]> wrote: > > > 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 > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> > >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
