External Email - Use Caution        

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.

Houston Methodist is ranked by U.S. News & World Report as the No. 1 hospital in Texas for patient care. Houston Methodist is nationally ranked in 8 specialties and is designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and facebook.com/HoustonMethodist.

***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.