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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in

error

but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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 *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

The information in this e-mail is intended only for the person to

whom it is

...

addressed. If you believe this e-mail was sent to you in error and

the e-mail

...

contains patient information, please contact the Partners Compliance

HelpLine at

...

http://www.partners.org/complianceline . If the e-mail was sent to

you in error

...

but does not contain patient information, please contact the sender

and properly

...

dispose of the e-mail.

---

---

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