Hi Doug,

All maps were smoothed before starting the analyses. But I think that because of running some of the analyses in R (incl bootstrapping), they do look a bit patchy when zooming in.

This resulted in a huge amount of clusters. But I managed to solve it, I found an option in tksurfer to smooth the stats map just a little bit 😊 (only used to get clusters, not for the p-value).

Heidi

 

Hi Heidi, I'm not sure I understand what you are trying to do. Can you elaborate? What do you mean that you do not have statistical info any more? It is unusual to smooth p-values. Probably you should apply smoothing before your analysis

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Hi all,

 

I created an overlay surface map of my analyses (with pvalues in log10) using R.

Now I would like to smooth this map to extract clusters and I tried to use:

mri_surf2surf --prune --s fsaverage --hemi lh --fwhm 3 --sval lh_analyses.mgh --tval lh_analyses_smoothed.mgh --cortex 

 

This seems to work, but is there a way to also map the original values in the output surface overlay? I now have clusters that are colored yellow with no statistical information anymore.

 

I also tried to use: mri_surfcluster --in lh_analyses.mgh --thmin 1.3 --thmax 6 --no-adjust --subject fsaverage --fwhm 3 --sum lh_analyses_smoothed_summary --hemi lh --sign pos

 

But whether or not I add in the smoothing, the output is the same.

 

Any help would be greatly appreciated.

 

Thanks!

Heidi

 

 

 

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