Hi!

Just pinging. Is there a way to get the surface+overlay file as mentioned above using freesurfer? Thank you!

Best regards,

Sam

---------- Forwarded message ---------
From: Sam W <samfmri@gmail.com>
Date: Fri, Jul 10, 2020 at 9:05 PM
Subject: Re: [Freesurfer] label to surface
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>

Hi Doug and Tim,
I'm running probtrackx with freesurfer surfaces as seeds. However probtrackx requires a file that contains both the whole surface file (eg, lh.pial) as well as the overlay (the scalar values associated with the vertices of the roi).
I can create such a file with FSL's label2surf command which creates a gifti file that encodes both the surface and the overlay.
My question is whether I can do the same with freesurfer? Running probtrackx with the overlay from mri_label2label --outmask does not work. It also needs the associated pial or white surface.

Best regards,

Sam

On Fri, Jul 10, 2020 at 4:29 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:

what do you mean merge with the pial?

On 7/9/2020 8:07 PM, Sam W wrote:
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It works great Doug, thanks a lot!
Can I ask you a follow up question please? I created the overlay with mri_label2label using --outmask as you suggested, but now I'd like to merge that overlay with the pial surface (lh.pial). Is there a tool I can use to achieve that result?

Best regards,

Sam
On Thu, Jul 9, 2020 at 7:31 PM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Use mri_label2label with the --outmask option

On 7/8/2020 10:14 PM, Sam W wrote:
External Email - Use Caution

Hi,

Is there a way to convert a label file into a surface/overlay? Thank you!

Best regards,

Sam
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