glad it worked, thanks for letting us know Bruce
On Mon, 28 Dec 2009, Matt Glasser wrote:
Well, I ended up using the -notal-check and -notalairach, flags along with increasing the voxel size from 0.8 to 1mm in the header. Aseg didn't work, but otherwise the surfaces were pretty good, aside from some issues in the medial temporal lobe. This was on chimpanzees by the way, not monkeys.
Peace,
Matt.
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, December 25, 2009 10:20 AM To: Bruce Fischl Cc: Matt Glasser; freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach on Non-human Primates
i'm not familiar with the monkey switch. there is this page: http://surfer.nmr.mgh.harvard.edu/fswiki/MonkeyData
which points to some scripts used by Sebastian Moeller to process monkey data. i'm hoping to expand this page with more info on this process, so Matt, if you want to pass along any notes, please do.
n.
On Fri, 2009-12-25 at 09:13 -0500, Bruce Fischl wrote:
actually, I can't find it anymore. It used to turn off all the things that weren't appropriate for non-humans (e.g. talairach, aseg, etc...). Not sure when it was deprecated. Nick: do you know?
merry christmas! Bruce On Thu, 24 Dec 2009, Matt Glasser wrote:
Hi Bruce,
Thanks for the help. What does the -monkey switch do? Does it remove
the
requirement to change the image header to 1mm from acquired resolution?
Thanks,
Matt.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, December 24, 2009 6:49 PM To: Matt Glasser Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Talairach on Non-human Primates
Hi Matt,
it shouldn't be needed for non-human primates, and in fact will probably mess things up. I thought the -monkey switch disabled it, but I could be wrong.
cheers Bruce On Thu, 24 Dec 2009, Matt Glasser wrote:
I am wondering if it is necessary to perform the taltransform (or care
about
the results when it fails) to get good surfaces of non-human primate
brains?
I know I can go in and manually edit it to get it right, but I would
rather
not do this if it isn't critical for surface generation. Is it okay to
just
use -notalcheck and ignore any errors? My brains are already AC/PC
aligned
in a non-human primate specific standard space.
Thanks,
Matt.
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