In general, it is better not so smooth in the volume. However, we often
smooth some (< 5mm) as the epi-anatomical registration is sometimes
inaccurate due to epi distortion.
doug
[EMAIL PROTECTED] wrote:
Hi Christine,
I'm not certain you'd want to smooth on the volume at all.
See this paper for illustrations
Desai R, Liebenthal E, Possing ET, Waldron E, Binder JR. (2005)
Volumetric vs. surface-based alignment for localization of auditory
cortex activation. Neuroimage 26:4 1019–1029.[CrossRef]
<http://cercor.oxfordjournals.org/cgi/external_ref?access_num=10.1016/j.neuroimage.2005.03.024&link_type=DOI>
[ISI]
<http://cercor.oxfordjournals.org/cgi/external_ref?access_num=000230071300005&link_type=ISI>[Medline]
<http://cercor.oxfordjournals.org/cgi/external_ref?access_num=15893476&link_type=MED>
Also, when smoothing on the surface (and clustering) in FreeSurfer,
consider that Freesurfer currently defines vertexes as part of the
same cluster only when those vertexes are strictly adjacent (share an
edge; there is no adjacency parameter that can be dynamically set), so
when smoothing on the surface, you might want to use a decent
smoothing kernel (If you use permutations methods to cluster, this
would be controlled for as permutations control for smoothing).
U.
On 5/9/07, [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>
<[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]>> wrote:
Thank you very much!
I assume that when doing the first-level analysis with Feat and
then project onto the surface, one shouldn't smooth so much in 3D
volume space, right? How much smoothing should be used?
Thanks a lot,
Christine
Bruce Fischl < [EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Hi Christine,
we have a set of tools we use mainly written by Doug called
FS-FAST, but we
have also worked hard with FMRIB to make it easy to do
surface-based
analysis using FSL. I think there are some tutorials on this
on our wiki,
and perhaps on one of the Oxford sites as well (Steve and
Doug: can you
chime in?).
Surface-based as a lot of advantages, mainly in terms of the
accuracy of
cross-subject registration and the power gained in smoothing
on the surface
as opposed to the volume. The disadvantages mainly come from the
possibility of misregistration and thus missing data, as you
note. And of
course it doesn't represent activation in deep structures
(e.g. caudate).
cheers,
Bruce
On Tue, 8 May 2007,
[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> wrote:
Hi Doug & Ohers,
I see that there are nice interfaces between Feat and
Freesurfer for rendering Feat output onto the surface. Now for
group fMRI stats it would obviously be advantageous to do all
the stats directly on the surface, avoiding volume space
altogether. Especially clsuter thresholding might be an issue
here. Am I correct there?
What approach would you suggest in terms of what software to
use for the fMRI analysis. In our lab we have used mainly FSL
tools to do volumetric fMRI analysis, and are hence most
familiar with these, but are considering to moving to doing
all this on the surface. What are people's views on that? Is
that an entirely good thing or are there advantages to volume
space analysis? What if spatial distortions are present in the
BOLD images and haven't been corrected for? Any comments and
suggestions on these issues would be greatly appreciated.
Thanks a lot,
Christine
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