Re: [Freesurfer] selfreqavg

selfreqavg has been incorporated into selxavg3.m (called by selxavg3-sess). But the ideas are still the same, just setting up a sine and cosine at the fundamental and estimating the amplitude using a GLM. doug

Michelle Umali wrote:

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 mailto: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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