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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 713-363-9003tel:713-363-9003
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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
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