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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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, oxro03@yahoo.com 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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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 fischl@nmr.mgh.harvard.edu 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, oxro03@yahoo.com 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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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, oxro03@yahoo.com oxro03@yahoo.com 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 fischl@nmr.mgh.harvard.edu* 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, oxro03@yahoo.com 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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Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
zvalim@gmail.com 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, oxro03@yahoo.com mailto:oxro03@yahoo.com <oxro03@yahoo.com mailto:oxro03@yahoo.com> 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 < fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> 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, oxro03@yahoo.com <mailto:oxro03@yahoo.com> 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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