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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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 > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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