Hi Freesurfers, I'm troubleshooting my retinotopy data and am still having issues with wonky fieldsign data. The registration looked ok, so now I am trying to look at the retinotopy results using rtview. I got an error message saying it can't find the register.dof6.dat file. So, now I am stepping back to the beginning. Below are the commands I used for the analysis.

-Does one need to specify starting position of wedge/size of wedge?

Any help would be greatly appreciated. Michelle _____________ Here are the commands I used:

recon-all -all ld09

tksurfer sj09 lh inflated and then for rh. Then I cut occipital patches.

Then I registered the eccen and polar f.nii files: bbregister --s ld09 --mov f.nii --init-fsl --reg register.dat tkregister2 --mov f.nii --reg register.dat --surf mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat 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

So when viewing with tksurfer I am assuming that -map angle shows the polar data. It looks ok. There's a lot of yellow and red, which I am assuming is the overall significance and not significance by position yes?

tksurfer-sess -a rtopy.self.lh -s sj09 -map angle

To view eccen data, is it -map eccen?

thanks. michelle

Quoting Douglas N Greve greve@nmr.mgh.harvard.edu:

How do the eccen and polar look by themselves? You can look at them with tksurfer-sess doug

Michelle Umali wrote:

...

Hi Freesurfers, I'm troubleshooting my retinotopy data and am still having issues with wonky fieldsign data. The registration looked ok, so now I am trying to look at the retinotopy results using rtview. I got an error message saying it can't find the register.dof6.dat file. So, now I am stepping back to the beginning. Below are the commands I used for the analysis.

-Does one need to specify starting position of wedge/size of wedge?

Any help would be greatly appreciated. Michelle _____________ Here are the commands I used:

recon-all -all ld09

tksurfer sj09 lh inflated and then for rh. Then I cut occipital patches.

Then I registered the eccen and polar f.nii files: bbregister --s ld09 --mov f.nii --init-fsl --reg register.dat tkregister2 --mov f.nii --reg register.dat --surf mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat 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

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