Freesurfer Experts,

thanks for the response! There was no command for projabs, but looking through the help I think projdist was about what I needed?

I was also curious though if there were a way to get it into an annotation--like the one available for the Yeo parcellations on the freesurfer webpage. Is there any way to convert a lookup nifti to an annotation, or one of these surface overlays into one? I can't seem to figure it out from the documentation, but it's almost surely user error...

Quentin Funk, PhD
Houston Methodist Research Institute
713-363-9003

Message: 13
Date: Fri, 25 May 2018 11:06:15 -0400
From: Douglas Greve <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Lookup table to surface overlay
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <5cb3e6da-99cb-8365-c4f5-4f1cb17f7150@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

You might be sampling outside of the brain. Try adding

--projabs -2

To sample 2mm below the pial surface

On 5/25/18 10:32 AM, Funk, Quentin wrote:
>
>
> Freesurfer experts,
>
>
> I have some lookup table volume files in MNI space that I'd like to
> overlay on a surface (say, fsaverage's lh.pial). Currently I'm using
> this command:
>
>
> mri_vol2surf --mov look_up_table.nii --regheader fsaverage --interp
> nearest --hemi lh --surf pial --o lh_lookup_overlay.mgh
>
>
> Then I choose "color wheel" as the overlay option in freeview. This
> works OK, but it's a bit imperfect. There are voxels that somehow
> don't get a value (and show up in the configuration window as 0's
> (even though the entire MNI brain is covered by the LUT), and it's a
> bit 'edgy' and not smooth.
>
>
> Are there any better ways to do this?
>
>
> Thanks for any help!
>
>
>
> Quentin Funk, PhD
> Houston Methodist Research Institute
> 713-363-9003 <tel:713-363-9003>
>
> Houston Methodist. Leading Medicine.

Houston Methodist. Leading Medicine.

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