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:
- I am guessing that the 2D smoothing applies only to the surface and is smoothing on the surface space. Is this correct?
Yes
- I'm also guessing that the 3D smoothing applies only to the subcortical regions. Is all this also correct?
Yes
- 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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