---

From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
To: Shahin <shahin@nmr.mgh.harvard.edu>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu>
Sent: Mon, November 8, 2010 12:55:37 PM
Subject: Re: [Freesurfer] how to generate aparc.annotion files?

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 <fischl@nmr.mgh.harvard.edu>
> *To:* Shahin <shahin@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 <fischl@nmr.mgh.harvard.edu
> <mailto:fischl@nmr.mgh.harvard.edu>>
> > To: Shahin <shahin@nmr.mgh.harvard.edu
> <mailto:shahin@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
> >>
> >>
> >>
> >
> >
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>
> ------------------------------------------------------------------------
>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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

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