Hi Jon,
Thanks!

I have a question about when selfreqavg.  When do I use selfreqavg?  Is it called when I run fieldsign-sess or do I have to run it in addition to the below?

I've been doing the following:

mkanalysis-sess -a rtopy.self.lh -surface self lh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force
mkanalysis-sess -a rtopy.self.rh -surface self rh -TR 2 -retinotopy 48 -paradigm rtopy.par -nskip 4 -fwhm 0 -force

preproc-sess -surface self lhrh -fwhm 5 -per-run -s sj09 -force

selxavg3-sess -a rtopy.self.lh -s sj09
selxavg3-sess -a rtopy.self.rh -s sj09
fieldsign-sess -a rtopy.self.lh -occip -s sj09
fieldsign-sess -a rtopy.self.rh -occip -s sj09

Thanks for your help.
Michelle


On Mon, Oct 10, 2011 at 5:30 PM, Jonathan Polimeni <jonp@nmr.mgh.harvard.edu> wrote:

 
hi michelle,

the Sereno et al. 1995 Science paper has details about the phase encoded
retinotopic data analysis, especially in the endnotes of the article. also
for more details you can look at the MATLAB code embedded in the command
'selfreqavg', which is used for the basic retinotopy analysis and is quite
readable.

hope this helps,


-jon



On Wed, 21 Sep 2011, Michelle Umali wrote:

> Hi Freesurfers.
> Is there text describing the retinotopy analysis in Freesurfer
> mathematically?
>
> Thanks.
> Michelle
>


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