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Sorry for another message,

I have the aparc + aseg file, is that the file I should use?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.uk>
Sent: Sunday, May 16, 2021 10:37:04 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

Thanks a lot for your help!

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

Do I put the labels 7,8,46,47 where it says labels in the code above?

Can I use the ROI files for co-registration into the diffusion space and then tractography?

Thanks!

Regards,

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDU>
Date: Sunday, 16 May 2021 at 22:25
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation

The labels that you are looking for are: 7,8, 46, 47

You can use the below command

isolate_labels.csh --vol aseg.mgz --outprefix aseg_labels --L $label

in order to get these from the aseg volume.

That will result in 4 ROI files that you can use in your further analysis.

Lilla

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.uk>
Sent: Sunday, May 16, 2021 4:34 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation

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Hi Lilla,

That would be ideal!

Thanks

Akila

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@mgh.harvard.edu>
Sent: Sunday, May 16, 2021 5:22:08 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation

Is your question then how to isolate the cerebellar WM/GM labels from aseg?

Lila

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.uk>
Sent: Friday, May 14, 2021 12:13 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation

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Hey,

Thanks for your message. Yes I have!

Akila

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Zollei, Lilla,Ph.D. <LZOLLEI@MGH.HARVARD.EDU>
Date: Friday, 14 May 2021 at 16:44
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Cerebellum Segementation

Hi Akila,

Have you run recon_all on your structural data?

Lilla

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of A.R. Sekar <ars66@cam.ac.uk>
Sent: Friday, May 14, 2021 10:35 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Cerebellum Segementation

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Hello Experts!

This is the first time I am doing tractography and my aim is to do it specifically for the cerebellum. I saw online that FreeSurfurer can segment the cerebellum, to create the ROI but I’m not entirely sure how to go about this. So far I have done the pre-processing, co-registration onto diffusion space and created FOD. It would be great if you could give me advice and any feedback about the pipeline.

Thanks for your help!

Regards,

Akila