On 1/31/18 8:33 PM, Ben Smith wrote:
Hi all,
I read from the freesurfer discussion archives that when combining FSL
FEAT with freesurfer, one should definitely NOT do spatial smoothing
in the preprocessing when preparing to examine cortical data.
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg11536.html
However I can see that in the FSFast pipeline, 2D and 3D smoothing
*/is*/ included in the FSFast preprocessing.
So:
1. I am guessing that the 2D smoothing applies only to the surface
and is smoothing on the surface space. Is this correct?
Yes
1. I'm also guessing that the 3D smoothing applies only to the
subcortical regions. Is all this also correct?
Yes
1. The freesurfer.feat.ppt guide does NOT contain any instructions
for doing any smoothing on data derived from FSL. But I assume
that, if smoothing is done during FSFast preprocessing but is not
done when preprocessing in FSL, then smoothing will still need to
be done at a subsequent point with the FSL data. But I don't see
instructions on that in the Freesurfer FEAT documentation on
freesurfer.feat.ppt. If I do FSL preprocessing+1st-level analysis
with no spatial smoothing, and then proceed with the analysis, at
which point do I apply preprocessing? Is there a guide
specifically describing how to apply smoothing to data originating
from FSL?
You can apply it after concatenate the surface overlays together. Use
mri_surf2surf or mris_fwhm
Thank you very much to anyone willing to help!
Best regards
Ben
_______________________
Ben Smith, MSc.
Ph.D. Candidate
University of Southern California
https://bjsmith.github.io/
w | +1 213-740 7851
m | +1 323-385 9349
skype | ben.smith.nz <http://ben.smith.nz/>
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