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 To: Shahin shahin@nmr.mgh.harvard.edu Cc: Freesurfer 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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