Re: [Freesurfer] Spatial smoothing during preprocessing

[Douglas Greve]

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 



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[Freesurfer] Spatial smoothing during preprocessing

[Ben Smith]

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?
   2. I'm also guessing that the 3D smoothing applies only to the
   subcortical regions. Is all this also correct?
   3. 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?

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
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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.