It is needed in make_average_surface. I've created a new version that does not use the aparc (thought I have not tested it). You can get it from here:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface.no-aparc Make a backup of your current version of make_average_surface and then copy this one over it douig Shahin wrote: > Yes, I have made a template on the basis of many monkeys > (mris_make_template) and then I have done spherical registeration for > each individual monkey (to this template) by using mris_register. Now > it is the final step and I have to run the make_average_subject but it > generates an error saying that I don't have a lh and rh.aparc.annot files. > > Apparently very old versions of freesurfer (version 3) didnt need > these files. Am I right? Do you suggest to use old versions? > > Shahin Nasr > > PhD in Cognitive Neuroscience > Martinos Imaging Center, MGH > Harvard Medical School > > > ------------------------------------------------------------------------ > *From:* Bruce Fischl <fis...@nmr.mgh.harvard.edu> > *To:* Shahin <sha...@nmr.mgh.harvard.edu> > *Cc:* Freesurfer <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Mon, November 8, 2010 12:33:03 PM > *Subject:* Re: [Freesurfer] how to generate aparc.annotion files? > > Hi Shahin > > have you run spherical registration? If so, to what target? I don't think > the monkey-to-human atlas aligment is that robust, so you would need a > monkey geometry atlas (which is a lot easier to build as you don't > need to > do manual labeling for it). Probably someone on list has one? > > Bruce > > On Mon, 8 Nov 2010, Shahin wrote: > > > Thanks Bruce, > > > > To avoid this problem, is there anyway to run > make_average_subject without > > having lh and rh.aparc.annot files? > > Shahin Nasr > > > > > > PhD in Cognitive Neuroscience > > Martinos Imaging Center, MGH > > Harvard Medical School > > > > > > > > > > ________________________________ > > From: Bruce Fischl <fis...@nmr.mgh.harvard.edu > <mailto:fis...@nmr.mgh.harvard.edu>> > > To: Shahin <sha...@nmr.mgh.harvard.edu > <mailto:sha...@nmr.mgh.harvard.edu>> > > Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>> > > Sent: Mon, November 8, 2010 12:10:38 PM > > Subject: Re: [Freesurfer] how to generate aparc.annotion files? > > > > Hi Shahin > > > > you'll need a monkey atlas based on manually labeled monkey folding > > patterns. we don't have one, but it's possible that someone else on the > > list does (it would be a lot easier to do for monkey than it was for > human > > as the folds are so much simpler) > > > > cheers > > Bruce > > > > On Mon, 8 Nov 2010, Shahin wrote: > > > >> Hi Freesurfers, > >> > >> Anybody knows how can I make lh and rh.annotation.aparc files > for a monkey? > >> I > >> need them initiate an brain averaging process. > >> Shahin Nasr > >> > >> > >> PhD in Cognitive Neuroscience > >> Martinos Imaging Center, MGH > >> Harvard Medical School > >> > >> > >> > > > > > > The information in this e-mail is intended only for the person to > whom it is > > addressed. If you believe this e-mail was sent to you in error and > the e-mail > > contains patient information, please contact the Partners Compliance > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to > you in error > > but does not contain patient information, please contact the sender > and properly > > dispose of the e-mail. > > > > > > > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
