I had no idea they had added the FreeSurfer thalamic nuclei; thanks a lot for the pointer!

Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Zeng, Victor (BIDMC - Keshavan - Psychiatry)" vzeng@bidmc.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Thursday, July 9, 2020 at 10:07 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] [External] The thalamic atlas in MNI space

You may be interested in https://www.oxcns.org/aal3.html%E2%80%8B AAL3, which has the estimations of the thalamus nucleis from fs6

Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab -- ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of 邹广源 zouguangyuan@pku.edu.cn Sent: Wednesday, July 8, 2020 8:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [External] [Freesurfer] The thalamic atlas in MNI space

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Dear experts

I am performing a fMRI analysis about the thalamus. I would like to see the overlap of my thalamic ROI with the atlas derived in 'A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology' (Iglesias, NeuroImage, 2018). Is there a version of this atlas in the MNI space? I found the 'ThalamicNuclei' folder in FreeSurfer but it seems not an atlas in the MNI space. I am new in FreeSurfer. Could you please give me some suggestions?

Thanks for your time.

Best,

Guangyuan Zou

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You can run the mni152 through recon-all, then run the thalamic seg on it. I'm sure that it will give you something that looks reasonable, but it is probably a bogus way to analyze your data because the mni is so blurry and the structures are so small that a small misregistration would cause major misseggmentations.

On 7/9/2020 12:44 PM, Iglesias Gonzalez, Juan E. wrote:

Dear GZ,

The atlas lives in its own space, and it is hard to register to MNI because it only describes probabilities, and not image intensities. But you could try registering your subjects to MNI, propagating the thalamic segmentations, and analyzing the data in that coordinate frame.

Cheers,

/Eugenio

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of 邹广源zouguangyuan@pku.edu.cn *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Wednesday, July 8, 2020 at 20:46 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] The thalamic atlas in MNI space

*        External Email - Use Caution *

Dear experts

I am performing a fMRI analysis about the thalamus. I would like to see the overlap of my thalamic ROI with the atlas derived in /'A probabilistic atlas of the human thalamic nuclei combining ex vivo MRI and histology' (Iglesias, NeuroImage, 2018)/. Is there a version of this atlas in the MNI space? I found the 'ThalamicNuclei' folder in FreeSurfer but it seems not an atlas in the MNI space. I am new in FreeSurfer. Could you please give me some suggestions?

Thanks for your time.

Best,

Guangyuan Zou

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