You'll probably have to do it by hand with tkregister2. Someone on the list may have solved this problem before.
doug
Shahin wrote:
Ok now I faced another problem saying that I dont have talairach.xfm for monkeys. Would you tell me how can I generate it for monkeys?
Shahin Nasr
PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School
*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
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 12:33:03 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
<mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>
To: Shahin <shahin@nmr.mgh.harvard.edu
mailto:shahin@nmr.mgh.harvard.edu
<mailto:shahin@nmr.mgh.harvard.edu mailto:shahin@nmr.mgh.harvard.edu>>
Cc: Freesurfer <freesurfer@nmr.mgh.harvard.edu
mailto:freesurfer@nmr.mgh.harvard.edu
<mailto: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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