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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